2024-04-23 02:04
ftp://ftp.de.debian.org/debian/pool/main/v/vt/vt_0.57721+ds.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j1
platform: Linux-5.15.0-105-generic-x86_64-with-glibc2.35
python: 3.10.12
client-version: 1.3.56
compiler: g++ (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
cppcheck: head 2.14.0
head-info: bd7136d (2024-04-22 21:34:48 +0200)
count: 4296 4296
elapsed-time: 129.2 131.2
head-timing-info:

old-timing-info:

head results:
vt-0.57721/ahmm.cpp:129:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:168:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:196:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:432:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:478:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:596:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:687:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:737:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:1019:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:1134:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:1153:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:1171:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:1202:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:1224:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:1272:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::rlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::plen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::lflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::lflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::motif_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::motif_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::rflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::rflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::exact_motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::motif_m' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::motif_xid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::last_motif_pos' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::frac_no_repeats' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::motif_concordance' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::trf_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::max_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::max_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::optimal_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::optimal_state' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::optimal_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::optimal_probe_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::optimal_path_ptr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.cpp:74:7: warning: Member variable 'AHMM::optimal_path_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ahmm.h:212:13: style:inconclusive: Technically the member function 'AHMM::get_lflank_model_spos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:300:15: note: Technically the member function 'AHMM::get_lflank_model_spos1' can be const.
vt-0.57721/ahmm.h:212:13: note: Technically the member function 'AHMM::get_lflank_model_spos1' can be const.
vt-0.57721/ahmm.h:217:13: style:inconclusive: Technically the member function 'AHMM::get_lflank_model_epos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:308:15: note: Technically the member function 'AHMM::get_lflank_model_epos1' can be const.
vt-0.57721/ahmm.h:217:13: note: Technically the member function 'AHMM::get_lflank_model_epos1' can be const.
vt-0.57721/ahmm.h:222:13: style:inconclusive: Technically the member function 'AHMM::get_motif_model_spos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:316:15: note: Technically the member function 'AHMM::get_motif_model_spos1' can be const.
vt-0.57721/ahmm.h:222:13: note: Technically the member function 'AHMM::get_motif_model_spos1' can be const.
vt-0.57721/ahmm.h:227:13: style:inconclusive: Technically the member function 'AHMM::get_motif_model_epos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:324:15: note: Technically the member function 'AHMM::get_motif_model_epos1' can be const.
vt-0.57721/ahmm.h:227:13: note: Technically the member function 'AHMM::get_motif_model_epos1' can be const.
vt-0.57721/ahmm.h:232:13: style:inconclusive: Technically the member function 'AHMM::get_rflank_model_spos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:332:15: note: Technically the member function 'AHMM::get_rflank_model_spos1' can be const.
vt-0.57721/ahmm.h:232:13: note: Technically the member function 'AHMM::get_rflank_model_spos1' can be const.
vt-0.57721/ahmm.h:237:13: style:inconclusive: Technically the member function 'AHMM::get_rflank_model_epos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:340:15: note: Technically the member function 'AHMM::get_rflank_model_epos1' can be const.
vt-0.57721/ahmm.h:237:13: note: Technically the member function 'AHMM::get_rflank_model_epos1' can be const.
vt-0.57721/ahmm.h:242:13: style:inconclusive: Technically the member function 'AHMM::get_lflank_read_spos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:348:15: note: Technically the member function 'AHMM::get_lflank_read_spos1' can be const.
vt-0.57721/ahmm.h:242:13: note: Technically the member function 'AHMM::get_lflank_read_spos1' can be const.
vt-0.57721/ahmm.h:247:13: style:inconclusive: Technically the member function 'AHMM::get_lflank_read_epos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:356:15: note: Technically the member function 'AHMM::get_lflank_read_epos1' can be const.
vt-0.57721/ahmm.h:247:13: note: Technically the member function 'AHMM::get_lflank_read_epos1' can be const.
vt-0.57721/ahmm.h:252:13: style:inconclusive: Technically the member function 'AHMM::get_motif_read_spos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:364:15: note: Technically the member function 'AHMM::get_motif_read_spos1' can be const.
vt-0.57721/ahmm.h:252:13: note: Technically the member function 'AHMM::get_motif_read_spos1' can be const.
vt-0.57721/ahmm.h:257:13: style:inconclusive: Technically the member function 'AHMM::get_motif_read_epos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:372:15: note: Technically the member function 'AHMM::get_motif_read_epos1' can be const.
vt-0.57721/ahmm.h:257:13: note: Technically the member function 'AHMM::get_motif_read_epos1' can be const.
vt-0.57721/ahmm.h:262:13: style:inconclusive: Technically the member function 'AHMM::get_rflank_read_spos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:380:15: note: Technically the member function 'AHMM::get_rflank_read_spos1' can be const.
vt-0.57721/ahmm.h:262:13: note: Technically the member function 'AHMM::get_rflank_read_spos1' can be const.
vt-0.57721/ahmm.h:267:13: style:inconclusive: Technically the member function 'AHMM::get_rflank_read_epos1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:388:15: note: Technically the member function 'AHMM::get_rflank_read_epos1' can be const.
vt-0.57721/ahmm.h:267:13: note: Technically the member function 'AHMM::get_rflank_read_epos1' can be const.
vt-0.57721/ahmm.h:272:11: style:inconclusive: Technically the member function 'AHMM::get_motif_concordance' can be const. [functionConst]
vt-0.57721/ahmm.cpp:396:13: note: Technically the member function 'AHMM::get_motif_concordance' can be const.
vt-0.57721/ahmm.h:272:11: note: Technically the member function 'AHMM::get_motif_concordance' can be const.
vt-0.57721/ahmm.h:277:14: style:inconclusive: Technically the member function 'AHMM::get_exact_motif_count' can be const. [functionConst]
vt-0.57721/ahmm.cpp:404:16: note: Technically the member function 'AHMM::get_exact_motif_count' can be const.
vt-0.57721/ahmm.h:277:14: note: Technically the member function 'AHMM::get_exact_motif_count' can be const.
vt-0.57721/ahmm.h:282:14: style:inconclusive: Technically the member function 'AHMM::get_motif_count' can be const. [functionConst]
vt-0.57721/ahmm.cpp:412:16: note: Technically the member function 'AHMM::get_motif_count' can be const.
vt-0.57721/ahmm.h:282:14: note: Technically the member function 'AHMM::get_motif_count' can be const.
vt-0.57721/ahmm.h:309:11: performance:inconclusive: Technically the member function 'AHMM::log10_emission_odds' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/ahmm.cpp:776:13: note: Technically the member function 'AHMM::log10_emission_odds' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:309:11: note: Technically the member function 'AHMM::log10_emission_odds' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:314:11: style:inconclusive: Technically the member function 'AHMM::log10_emission_odds' can be const. [functionConst]
vt-0.57721/ahmm.cpp:796:13: note: Technically the member function 'AHMM::log10_emission_odds' can be const.
vt-0.57721/ahmm.h:314:11: note: Technically the member function 'AHMM::log10_emission_odds' can be const.
vt-0.57721/ahmm.h:319:17: performance:inconclusive: Technically the member function 'AHMM::state2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/ahmm.cpp:816:19: note: Technically the member function 'AHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:319:17: note: Technically the member function 'AHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:324:17: performance:inconclusive: Technically the member function 'AHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/ahmm.cpp:855:19: note: Technically the member function 'AHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:324:17: note: Technically the member function 'AHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:329:17: style:inconclusive: Technically the member function 'AHMM::track2cigarstring1' can be const. [functionConst]
vt-0.57721/ahmm.cpp:894:19: note: Technically the member function 'AHMM::track2cigarstring1' can be const.
vt-0.57721/ahmm.h:329:17: note: Technically the member function 'AHMM::track2cigarstring1' can be const.
vt-0.57721/ahmm.h:334:17: performance:inconclusive: Technically the member function 'AHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/ahmm.cpp:946:19: note: Technically the member function 'AHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:334:17: note: Technically the member function 'AHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:339:17: performance:inconclusive: Technically the member function 'AHMM::component2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/ahmm.cpp:971:19: note: Technically the member function 'AHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:339:17: note: Technically the member function 'AHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/ahmm.h:354:10: style:inconclusive: Technically the member function 'AHMM::print' can be const. [functionConst]
vt-0.57721/ahmm.cpp:1131:12: note: Technically the member function 'AHMM::print' can be const.
vt-0.57721/ahmm.h:354:10: note: Technically the member function 'AHMM::print' can be const.
vt-0.57721/ahmm.h:359:10: style:inconclusive: Technically the member function 'AHMM::print' can be const. [functionConst]
vt-0.57721/ahmm.cpp:1150:12: note: Technically the member function 'AHMM::print' can be const.
vt-0.57721/ahmm.h:359:10: note: Technically the member function 'AHMM::print' can be const.
vt-0.57721/ahmm.h:394:10: style:inconclusive: Technically the member function 'AHMM::flanks_are_mapped' can be const. [functionConst]
vt-0.57721/ahmm.cpp:767:12: note: Technically the member function 'AHMM::flanks_are_mapped' can be const.
vt-0.57721/ahmm.h:394:10: note: Technically the member function 'AHMM::flanks_are_mapped' can be const.
vt-0.57721/ahmm.h:418:13: performance:inconclusive: Technically the member function 'AHMM::move_S_M' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/ahmm.h:428:13: style:inconclusive: Technically the member function 'AHMM::move_M_M' can be const. [functionConst]
vt-0.57721/ahmm.h:446:13: style:inconclusive: Technically the member function 'AHMM::move_D_M' can be const. [functionConst]
vt-0.57721/ahmm.h:464:13: style:inconclusive: Technically the member function 'AHMM::move_I_M' can be const. [functionConst]
vt-0.57721/ahmm.h:482:13: performance:inconclusive: Technically the member function 'AHMM::move_S_D' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/ahmm.h:492:13: style:inconclusive: Technically the member function 'AHMM::move_M_D' can be const. [functionConst]
vt-0.57721/ahmm.h:510:13: style:inconclusive: Technically the member function 'AHMM::move_D_D' can be const. [functionConst]
vt-0.57721/ahmm.h:528:13: performance:inconclusive: Technically the member function 'AHMM::move_S_I' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/ahmm.h:538:13: style:inconclusive: Technically the member function 'AHMM::move_M_I' can be const. [functionConst]
vt-0.57721/ahmm.h:548:13: style:inconclusive: Technically the member function 'AHMM::move_I_I' can be const. [functionConst]
vt-0.57721/ahmm.h:147:5: style: Class 'AHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/ahmm.cpp:595:12: style: The scope of the variable 'c' can be reduced. [variableScope]
vt-0.57721/ahmm.cpp:635:13: style: The scope of the variable 'u' can be reduced. [variableScope]
vt-0.57721/ahmm.cpp:636:13: style: The scope of the variable 'des_t' can be reduced. [variableScope]
vt-0.57721/ahmm.cpp:427:52: style:inconclusive: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'. [funcArgNamesDifferent]
vt-0.57721/ahmm.h:294:50: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/ahmm.cpp:427:52: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/ahmm.cpp:468:30: style:inconclusive: Function 'align' argument 1 names different: declaration 'y' definition 'read'. [funcArgNamesDifferent]
vt-0.57721/ahmm.h:299:28: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/ahmm.cpp:468:30: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/ahmm.cpp:676:39: style:inconclusive: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'. [funcArgNamesDifferent]
vt-0.57721/ahmm.h:379:37: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/ahmm.cpp:676:39: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/ahmm.cpp:676:54: style:inconclusive: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'. [funcArgNamesDifferent]
vt-0.57721/ahmm.h:379:49: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/ahmm.cpp:676:54: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/ahmm.cpp:776:38: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty' [funcArgOrderDifferent]
vt-0.57721/ahmm.h:309:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty'
vt-0.57721/ahmm.cpp:776:38: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty'
vt-0.57721/ahmm.cpp:796:38: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl' [funcArgOrderDifferent]
vt-0.57721/ahmm.h:314:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/ahmm.cpp:796:38: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/ahmm.cpp:1015:41: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/ahmm.cpp:1131:25: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/ahmm.cpp:1150:27: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/ahmm.cpp:1200:29: style: Parameter 'U' can be declared as pointer to const [constParameterPointer]
vt-0.57721/ahmm.cpp:1225:14: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
vt-0.57721/ahmm.cpp:1226:12: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
vt-0.57721/ahmm.cpp:483:15: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
vt-0.57721/ahmm.cpp:484:18: style: Variable 'maxPath' is assigned a value that is never used. [unreadVariable]
vt-0.57721/ahmm.cpp:1066:15: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_synced_reader.h:108:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.h:104:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.h:104:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/align.cpp:33:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/align.cpp:135:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/align.cpp:143:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/align.cpp:400:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/align.cpp:419:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/genome_interval.h:39:5: warning:inconclusive: Member variable 'GenomeInterval::start1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genome_interval.h:39:5: warning:inconclusive: Member variable 'GenomeInterval::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/bcf_synced_reader.h:48:5: warning: Member variable 'bcfptr::h' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/interval.h:38:5: warning:inconclusive: Member variable 'Interval::beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/interval.h:38:5: warning:inconclusive: Member variable 'Interval::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/bcf_synced_reader.h:54:9: performance: Variable 'alleles' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/bcf_synced_reader.h:64:9: performance: Variable 'alleles' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/bcf_synced_reader.h:89:10: style:inconclusive: Technically the member function 'CompareBCFPtr::operator()' can be const. [functionConst]
vt-0.57721/program.h:124:10: performance:inconclusive: Technically the member function 'Program::initialize' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.h:129:10: performance:inconclusive: Technically the member function 'Program::print_options' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.h:134:10: performance:inconclusive: Technically the member function 'Program::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.h:336:13: performance:inconclusive: Technically the member function 'CHMM::move_S_X' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.h:341:13: style:inconclusive: Technically the member function 'CHMM::move_X_X' can be const. [functionConst]
vt-0.57721/chmm.h:352:13: performance:inconclusive: Technically the member function 'CHMM::move_S_Y' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.h:357:13: style:inconclusive: Technically the member function 'CHMM::move_X_Y' can be const. [functionConst]
vt-0.57721/chmm.h:367:13: style:inconclusive: Technically the member function 'CHMM::move_Y_Y' can be const. [functionConst]
vt-0.57721/chmm.h:380:13: performance:inconclusive: Technically the member function 'CHMM::move_S_ML' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.h:390:13: style:inconclusive: Technically the member function 'CHMM::move_X_ML' can be const. [functionConst]
vt-0.57721/chmm.h:401:13: style:inconclusive: Technically the member function 'CHMM::move_Y_ML' can be const. [functionConst]
vt-0.57721/chmm.h:412:13: style:inconclusive: Technically the member function 'CHMM::move_ML_ML' can be const. [functionConst]
vt-0.57721/chmm.h:423:13: style:inconclusive: Technically the member function 'CHMM::move_DL_ML' can be const. [functionConst]
vt-0.57721/chmm.h:434:13: style:inconclusive: Technically the member function 'CHMM::move_IL_ML' can be const. [functionConst]
vt-0.57721/chmm.h:445:13: style:inconclusive: Technically the member function 'CHMM::move_ML_DL' can be const. [functionConst]
vt-0.57721/chmm.h:456:13: style:inconclusive: Technically the member function 'CHMM::move_DL_DL' can be const. [functionConst]
vt-0.57721/chmm.h:467:13: style:inconclusive: Technically the member function 'CHMM::move_ML_IL' can be const. [functionConst]
vt-0.57721/chmm.h:478:13: style:inconclusive: Technically the member function 'CHMM::move_IL_IL' can be const. [functionConst]
vt-0.57721/chmm.h:493:13: performance:inconclusive: Technically the member function 'CHMM::move_S_M' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.h:503:13: style:inconclusive: Technically the member function 'CHMM::move_X_M' can be const. [functionConst]
vt-0.57721/chmm.h:514:13: style:inconclusive: Technically the member function 'CHMM::move_Y_M' can be const. [functionConst]
vt-0.57721/chmm.h:525:13: style:inconclusive: Technically the member function 'CHMM::move_ML_M' can be const. [functionConst]
vt-0.57721/chmm.h:536:13: style:inconclusive: Technically the member function 'CHMM::move_M_M' can be const. [functionConst]
vt-0.57721/chmm.h:554:13: style:inconclusive: Technically the member function 'CHMM::move_D_M' can be const. [functionConst]
vt-0.57721/chmm.h:572:13: style:inconclusive: Technically the member function 'CHMM::move_I_M' can be const. [functionConst]
vt-0.57721/chmm.h:590:13: style:inconclusive: Technically the member function 'CHMM::move_ML_D' can be const. [functionConst]
vt-0.57721/chmm.h:602:13: style:inconclusive: Technically the member function 'CHMM::move_M_D' can be const. [functionConst]
vt-0.57721/chmm.h:620:13: style:inconclusive: Technically the member function 'CHMM::move_D_D' can be const. [functionConst]
vt-0.57721/chmm.h:638:13: style:inconclusive: Technically the member function 'CHMM::move_ML_I' can be const. [functionConst]
vt-0.57721/chmm.h:648:13: style:inconclusive: Technically the member function 'CHMM::move_M_I' can be const. [functionConst]
vt-0.57721/chmm.h:658:13: style:inconclusive: Technically the member function 'CHMM::move_I_I' can be const. [functionConst]
vt-0.57721/chmm.h:672:13: performance:inconclusive: Technically the member function 'CHMM::move_S_MR' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.h:677:13: style:inconclusive: Technically the member function 'CHMM::move_X_MR' can be const. [functionConst]
vt-0.57721/chmm.h:687:13: style:inconclusive: Technically the member function 'CHMM::move_Y_MR' can be const. [functionConst]
vt-0.57721/chmm.h:705:13: style:inconclusive: Technically the member function 'CHMM::move_ML_MR' can be const. [functionConst]
vt-0.57721/chmm.h:716:13: style:inconclusive: Technically the member function 'CHMM::move_M_MR' can be const. [functionConst]
vt-0.57721/chmm.h:726:13: style:inconclusive: Technically the member function 'CHMM::move_D_MR' can be const. [functionConst]
vt-0.57721/chmm.h:737:13: style:inconclusive: Technically the member function 'CHMM::move_I_MR' can be const. [functionConst]
vt-0.57721/chmm.h:748:13: style:inconclusive: Technically the member function 'CHMM::move_MR_MR' can be const. [functionConst]
vt-0.57721/chmm.h:759:13: style:inconclusive: Technically the member function 'CHMM::move_DR_MR' can be const. [functionConst]
vt-0.57721/chmm.h:770:13: style:inconclusive: Technically the member function 'CHMM::move_IR_MR' can be const. [functionConst]
vt-0.57721/chmm.h:781:13: style:inconclusive: Technically the member function 'CHMM::move_MR_DR' can be const. [functionConst]
vt-0.57721/chmm.h:792:13: style:inconclusive: Technically the member function 'CHMM::move_DR_DR' can be const. [functionConst]
vt-0.57721/chmm.h:803:13: style:inconclusive: Technically the member function 'CHMM::move_MR_IR' can be const. [functionConst]
vt-0.57721/chmm.h:813:13: style:inconclusive: Technically the member function 'CHMM::move_IR_IR' can be const. [functionConst]
vt-0.57721/chmm.h:827:13: style:inconclusive: Technically the member function 'CHMM::move_X_W' can be const. [functionConst]
vt-0.57721/chmm.h:837:13: style:inconclusive: Technically the member function 'CHMM::move_Y_W' can be const. [functionConst]
vt-0.57721/chmm.h:847:13: style:inconclusive: Technically the member function 'CHMM::move_ML_W' can be const. [functionConst]
vt-0.57721/chmm.h:857:13: style:inconclusive: Technically the member function 'CHMM::move_M_W' can be const. [functionConst]
vt-0.57721/chmm.h:867:13: style:inconclusive: Technically the member function 'CHMM::move_D_W' can be const. [functionConst]
vt-0.57721/chmm.h:877:13: style:inconclusive: Technically the member function 'CHMM::move_I_W' can be const. [functionConst]
vt-0.57721/chmm.h:887:13: style:inconclusive: Technically the member function 'CHMM::move_MR_W' can be const. [functionConst]
vt-0.57721/chmm.h:898:13: style:inconclusive: Technically the member function 'CHMM::move_W_W' can be const. [functionConst]
vt-0.57721/chmm.h:912:13: style:inconclusive: Technically the member function 'CHMM::move_MR_Z' can be const. [functionConst]
vt-0.57721/chmm.h:922:13: style:inconclusive: Technically the member function 'CHMM::move_W_Z' can be const. [functionConst]
vt-0.57721/chmm.h:933:13: style:inconclusive: Technically the member function 'CHMM::move_Z_Z' can be const. [functionConst]
vt-0.57721/lfhmm.h:413:13: performance:inconclusive: Technically the member function 'LFHMM::move_S_ML' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lfhmm.h:423:13: style:inconclusive: Technically the member function 'LFHMM::move_ML_ML' can be const. [functionConst]
vt-0.57721/lfhmm.h:437:13: performance:inconclusive: Technically the member function 'LFHMM::move_S_M' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lfhmm.h:447:13: style:inconclusive: Technically the member function 'LFHMM::move_ML_M' can be const. [functionConst]
vt-0.57721/lfhmm.h:458:13: style:inconclusive: Technically the member function 'LFHMM::move_M_M' can be const. [functionConst]
vt-0.57721/lfhmm.h:476:13: style:inconclusive: Technically the member function 'LFHMM::move_D_M' can be const. [functionConst]
vt-0.57721/lfhmm.h:494:13: style:inconclusive: Technically the member function 'LFHMM::move_I_M' can be const. [functionConst]
vt-0.57721/lfhmm.h:512:13: style:inconclusive: Technically the member function 'LFHMM::move_ML_D' can be const. [functionConst]
vt-0.57721/lfhmm.h:522:13: style:inconclusive: Technically the member function 'LFHMM::move_M_D' can be const. [functionConst]
vt-0.57721/lfhmm.h:540:13: style:inconclusive: Technically the member function 'LFHMM::move_D_D' can be const. [functionConst]
vt-0.57721/lfhmm.h:558:13: style:inconclusive: Technically the member function 'LFHMM::move_ML_I' can be const. [functionConst]
vt-0.57721/lfhmm.h:568:13: style:inconclusive: Technically the member function 'LFHMM::move_M_I' can be const. [functionConst]
vt-0.57721/lfhmm.h:578:13: style:inconclusive: Technically the member function 'LFHMM::move_I_I' can be const. [functionConst]
vt-0.57721/lfhmm.h:591:13: style:inconclusive: Technically the member function 'LFHMM::move_M_Z' can be const. [functionConst]
vt-0.57721/lfhmm.h:606:13: style:inconclusive: Technically the member function 'LFHMM::move_D_Z' can be const. [functionConst]
vt-0.57721/lfhmm.h:617:13: style:inconclusive: Technically the member function 'LFHMM::move_I_Z' can be const. [functionConst]
vt-0.57721/lfhmm.h:628:13: style:inconclusive: Technically the member function 'LFHMM::move_Z_Z' can be const. [functionConst]
vt-0.57721/rfhmm.h:102:10: style:inconclusive: Technically the member function 'RFHMMParameters::print' can be const. [functionConst]
vt-0.57721/rfhmm.h:407:13: performance:inconclusive: Technically the member function 'RFHMM::move_S_Y' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.h:412:13: style:inconclusive: Technically the member function 'RFHMM::move_Y_Y' can be const. [functionConst]
vt-0.57721/rfhmm.h:426:13: performance:inconclusive: Technically the member function 'RFHMM::move_S_M' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.h:436:13: style:inconclusive: Technically the member function 'RFHMM::move_Y_M' can be const. [functionConst]
vt-0.57721/rfhmm.h:447:13: style:inconclusive: Technically the member function 'RFHMM::move_M_M' can be const. [functionConst]
vt-0.57721/rfhmm.h:465:13: style:inconclusive: Technically the member function 'RFHMM::move_D_M' can be const. [functionConst]
vt-0.57721/rfhmm.h:483:13: style:inconclusive: Technically the member function 'RFHMM::move_I_M' can be const. [functionConst]
vt-0.57721/rfhmm.h:501:13: performance:inconclusive: Technically the member function 'RFHMM::move_S_D' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.h:511:13: style:inconclusive: Technically the member function 'RFHMM::move_Y_D' can be const. [functionConst]
vt-0.57721/rfhmm.h:521:13: style:inconclusive: Technically the member function 'RFHMM::move_M_D' can be const. [functionConst]
vt-0.57721/rfhmm.h:539:13: style:inconclusive: Technically the member function 'RFHMM::move_D_D' can be const. [functionConst]
vt-0.57721/rfhmm.h:557:13: performance:inconclusive: Technically the member function 'RFHMM::move_S_I' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.h:567:13: style:inconclusive: Technically the member function 'RFHMM::move_Y_I' can be const. [functionConst]
vt-0.57721/rfhmm.h:579:13: style:inconclusive: Technically the member function 'RFHMM::move_M_I' can be const. [functionConst]
vt-0.57721/rfhmm.h:589:13: style:inconclusive: Technically the member function 'RFHMM::move_I_I' can be const. [functionConst]
vt-0.57721/rfhmm.h:602:13: performance:inconclusive: Technically the member function 'RFHMM::move_S_MR' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.h:612:13: style:inconclusive: Technically the member function 'RFHMM::move_Y_MR' can be const. [functionConst]
vt-0.57721/rfhmm.h:634:13: style:inconclusive: Technically the member function 'RFHMM::move_M_MR' can be const. [functionConst]
vt-0.57721/rfhmm.h:649:13: style:inconclusive: Technically the member function 'RFHMM::move_D_MR' can be const. [functionConst]
vt-0.57721/rfhmm.h:664:13: style:inconclusive: Technically the member function 'RFHMM::move_I_MR' can be const. [functionConst]
vt-0.57721/rfhmm.h:679:13: style:inconclusive: Technically the member function 'RFHMM::move_MR_MR' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:102:10: style:inconclusive: Technically the member function 'RFHMM_XParameters::print' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:407:13: performance:inconclusive: Technically the member function 'RFHMM_X::move_S_Y' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.h:412:13: style:inconclusive: Technically the member function 'RFHMM_X::move_Y_Y' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:426:13: performance:inconclusive: Technically the member function 'RFHMM_X::move_S_M' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.h:436:13: style:inconclusive: Technically the member function 'RFHMM_X::move_Y_M' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:447:13: style:inconclusive: Technically the member function 'RFHMM_X::move_M_M' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:465:13: style:inconclusive: Technically the member function 'RFHMM_X::move_D_M' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:483:13: style:inconclusive: Technically the member function 'RFHMM_X::move_I_M' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:501:13: performance:inconclusive: Technically the member function 'RFHMM_X::move_S_D' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.h:511:13: style:inconclusive: Technically the member function 'RFHMM_X::move_Y_D' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:521:13: style:inconclusive: Technically the member function 'RFHMM_X::move_M_D' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:539:13: style:inconclusive: Technically the member function 'RFHMM_X::move_D_D' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:557:13: performance:inconclusive: Technically the member function 'RFHMM_X::move_S_I' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.h:567:13: style:inconclusive: Technically the member function 'RFHMM_X::move_Y_I' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:579:13: style:inconclusive: Technically the member function 'RFHMM_X::move_M_I' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:589:13: style:inconclusive: Technically the member function 'RFHMM_X::move_I_I' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:602:13: performance:inconclusive: Technically the member function 'RFHMM_X::move_S_MR' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.h:612:13: style:inconclusive: Technically the member function 'RFHMM_X::move_Y_MR' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:634:13: style:inconclusive: Technically the member function 'RFHMM_X::move_M_MR' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:649:13: style:inconclusive: Technically the member function 'RFHMM_X::move_D_MR' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:664:13: style:inconclusive: Technically the member function 'RFHMM_X::move_I_MR' can be const. [functionConst]
vt-0.57721/rfhmm_x.h:679:13: style:inconclusive: Technically the member function 'RFHMM_X::move_MR_MR' can be const. [functionConst]
vt-0.57721/align.cpp:398:10: style:inconclusive: Technically the member function '::Igor::print_options' can be const. [functionConst]
vt-0.57721/align.cpp:417:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/align.cpp:398:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/align.cpp:398:10: note: Derived function 'Igor::print_options'
vt-0.57721/align.cpp:417:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/align.cpp:417:10: note: Derived function 'Igor::print_stats'
vt-0.57721/genome_interval.h:54:5: style: Class 'GenomeInterval' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/bcf_ordered_writer.h:63:5: style: Class 'BCFOrderedWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/allele.h:68:5: style: Class 'Allele' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/filter.h:139:5: style: Class 'Node' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/filter.h:175:5: style: Class 'Filter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/tbx_ordered_reader.h:84:5: style: Class 'TBXOrderedReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/bed.h:40:5: style: Class 'BEDRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/bed.h:45:5: style: Class 'BEDRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/bed.h:50:5: style: Class 'BEDRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/ordered_region_overlap_matcher.h:62:5: style: Class 'OrderedRegionOverlapMatcher' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/variant_manip.h:46:5: style: Class 'VariantManip' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/reference_sequence.h:85:5: style: Class 'ReferenceSequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/lhmm.h:102:5: style: Class 'LHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/chmm.h:154:5: style: Class 'CHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/lfhmm.h:157:5: style: Class 'LFHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/rfhmm.h:160:5: style: Class 'RFHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/rfhmm_x.h:160:5: style: Class 'RFHMM_X' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/wdp_ahmm.h:108:5: style: Class 'WDP_AHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/wdp_ahmm.h:113:5: style: Class 'WDP_AHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/candidate_region_extractor.h:58:5: style: Class 'CandidateRegionExtractor' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/align.cpp:210:19: style: Local variable 'delta' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:65:11: note: Shadowed declaration
vt-0.57721/align.cpp:210:19: note: Shadow variable
vt-0.57721/align.cpp:211:19: style: Local variable 'epsilon' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:66:11: note: Shadowed declaration
vt-0.57721/align.cpp:211:19: note: Shadow variable
vt-0.57721/align.cpp:212:19: style: Local variable 'tau' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:67:11: note: Shadowed declaration
vt-0.57721/align.cpp:212:19: note: Shadow variable
vt-0.57721/align.cpp:213:19: style: Local variable 'eta' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:68:11: note: Shadowed declaration
vt-0.57721/align.cpp:213:19: note: Shadow variable
vt-0.57721/align.cpp:214:19: style: Local variable 'mismatch_penalty' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:69:11: note: Shadowed declaration
vt-0.57721/align.cpp:214:19: note: Shadow variable
vt-0.57721/align.cpp:248:19: style: Local variable 'delta' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:65:11: note: Shadowed declaration
vt-0.57721/align.cpp:248:19: note: Shadow variable
vt-0.57721/align.cpp:249:19: style: Local variable 'epsilon' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:66:11: note: Shadowed declaration
vt-0.57721/align.cpp:249:19: note: Shadow variable
vt-0.57721/align.cpp:250:19: style: Local variable 'tau' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:67:11: note: Shadowed declaration
vt-0.57721/align.cpp:250:19: note: Shadow variable
vt-0.57721/align.cpp:251:19: style: Local variable 'eta' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:68:11: note: Shadowed declaration
vt-0.57721/align.cpp:251:19: note: Shadow variable
vt-0.57721/align.cpp:252:19: style: Local variable 'mismatch_penalty' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:69:11: note: Shadowed declaration
vt-0.57721/align.cpp:252:19: note: Shadow variable
vt-0.57721/align.cpp:285:19: style: Local variable 'delta' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:65:11: note: Shadowed declaration
vt-0.57721/align.cpp:285:19: note: Shadow variable
vt-0.57721/align.cpp:286:19: style: Local variable 'epsilon' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:66:11: note: Shadowed declaration
vt-0.57721/align.cpp:286:19: note: Shadow variable
vt-0.57721/align.cpp:287:19: style: Local variable 'tau' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:67:11: note: Shadowed declaration
vt-0.57721/align.cpp:287:19: note: Shadow variable
vt-0.57721/align.cpp:288:19: style: Local variable 'eta' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:68:11: note: Shadowed declaration
vt-0.57721/align.cpp:288:19: note: Shadow variable
vt-0.57721/align.cpp:289:19: style: Local variable 'mismatch_penalty' shadows outer variable [shadowVariable]
vt-0.57721/align.cpp:69:11: note: Shadowed declaration
vt-0.57721/align.cpp:289:19: note: Shadow variable
vt-0.57721/bcf_synced_reader.h:89:29: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
vt-0.57721/bcf_synced_reader.h:89:40: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
vt-0.57721/chmm.h:480:17: style: Unused variable: p [unusedVariable]
vt-0.57721/chmm.h:506:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
vt-0.57721/chmm.h:517:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
vt-0.57721/chmm.h:528:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
vt-0.57721/chmm.h:708:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
vt-0.57721/chmm.h:729:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
vt-0.57721/chmm.h:739:17: style: Unused variable: p [unusedVariable]
vt-0.57721/chmm.h:924:17: style: Unused variable: p [unusedVariable]
vt-0.57721/chmm.h:935:17: style: Unused variable: p [unusedVariable]
vt-0.57721/lfhmm.h:450:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lfhmm.h:608:17: style: Unused variable: p [unusedVariable]
vt-0.57721/lfhmm.h:619:17: style: Unused variable: p [unusedVariable]
vt-0.57721/lfhmm.h:630:17: style: Unused variable: p [unusedVariable]
vt-0.57721/rfhmm.h:438:17: style: Unused variable: p [unusedVariable]
vt-0.57721/rfhmm_x.h:438:17: style: Unused variable: p [unusedVariable]
vt-0.57721/align.cpp:178:20: style: Unused variable: llk [unusedVariable]
vt-0.57721/align.cpp:217:20: style: Unused variable: llk [unusedVariable]
vt-0.57721/allele.cpp:140:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/allele.h:94:10: style:inconclusive: Technically the member function 'Allele::print' can be const. [functionConst]
vt-0.57721/allele.cpp:138:14: note: Technically the member function 'Allele::print' can be const.
vt-0.57721/allele.h:94:10: note: Technically the member function 'Allele::print' can be const.
vt-0.57721/allele.cpp:85:49: style: Parameter 'sv_type' can be declared as reference to const [constParameterReference]
vt-0.57721/annotate_1000g.cpp:98:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_1000g.cpp:195:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_1000g.cpp:207:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_1000g.cpp:69:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_1000g.cpp:69:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_1000g.cpp:69:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_1000g.cpp:69:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_1000g.cpp:69:5: warning: Member variable 'Igor::no_annotated_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_1000g.cpp:69:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_1000g.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/annotate_1000g.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/annotate_1000g.cpp:103:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/annotate_1000g.cpp:103:10: note: Derived function 'Igor::initialize'
vt-0.57721/annotate_1000g.cpp:193:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/annotate_1000g.cpp:193:10: note: Derived function 'Igor::print_options'
vt-0.57721/annotate_1000g.cpp:205:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/annotate_1000g.cpp:205:10: note: Derived function 'Igor::print_stats'
vt-0.57721/annotate_1000g.cpp:143:21: style: Variable 'dv' can be declared as pointer to const [constVariablePointer]
vt-0.57721/annotate_1000g.cpp:43:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/annotate_dbsnp_rsid.cpp:98:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:194:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:206:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:69:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:69:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:69:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:69:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:69:5: warning: Member variable 'Igor::no_annotated_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:69:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_dbsnp_rsid.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/annotate_dbsnp_rsid.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/annotate_dbsnp_rsid.cpp:103:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/annotate_dbsnp_rsid.cpp:103:10: note: Derived function 'Igor::initialize'
vt-0.57721/annotate_dbsnp_rsid.cpp:192:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/annotate_dbsnp_rsid.cpp:192:10: note: Derived function 'Igor::print_options'
vt-0.57721/annotate_dbsnp_rsid.cpp:204:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/annotate_dbsnp_rsid.cpp:204:10: note: Derived function 'Igor::print_stats'
vt-0.57721/annotate_dbsnp_rsid.cpp:43:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/annotate_indels.cpp:146:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_indels.cpp:243:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_indels.cpp:256:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::override_tag' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::add_flank_annotation' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::no_indels_annotated' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::va' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:113:5: warning: Member variable 'Igor::rs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels.cpp:115:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/motif_tree.h:89:10: style:inconclusive: Technically the member function 'CompareCandidateMotif::operator()' can be const. [functionConst]
vt-0.57721/annotate_indels.cpp:254:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/annotate_indels.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/annotate_indels.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/annotate_indels.cpp:155:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/annotate_indels.cpp:155:10: note: Derived function 'Igor::initialize'
vt-0.57721/annotate_indels.cpp:241:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/annotate_indels.cpp:241:10: note: Derived function 'Igor::print_options'
vt-0.57721/annotate_indels.cpp:254:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/annotate_indels.cpp:254:10: note: Derived function 'Igor::print_stats'
vt-0.57721/motif_map.h:52:5: style: Class 'MotifMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/motif_tree.h:126:5: style: Class 'MotifTree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/candidate_motif_picker.h:61:5: style: Class 'CandidateMotifPicker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/flank_detector.h:101:5: style: Class 'FlankDetector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/vntr_annotator.h:69:5: style: Class 'VNTRAnnotator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/motif_tree.h:74:32: performance: Function parameter 'motif' should be passed by const reference. [passedByValue]
vt-0.57721/motif_tree.h:89:37: style: Parameter 'a' can be declared as reference to const [constParameterReference]
vt-0.57721/motif_tree.h:89:56: style: Parameter 'b' can be declared as reference to const [constParameterReference]
vt-0.57721/annotate_indels.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/annotate_indels.cpp:44:10: style: class member 'Igor::override_tag' is never used. [unusedStructMember]
vt-0.57721/annotate_indels.cpp:290:17: style: Variable 'no_exact' is assigned a value that is never used. [unreadVariable]
vt-0.57721/annotate_indels.cpp:291:17: style: Variable 'no_inexact' is assigned a value that is never used. [unreadVariable]
vt-0.57721/annotate_indels2.cpp:146:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_indels2.cpp:243:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_indels2.cpp:256:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::override_tag' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::add_flank_annotation' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::no_indels_annotated' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::ia' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:113:5: warning: Member variable 'Igor::rs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_indels2.cpp:115:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/annotate_indels2.cpp:254:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/annotate_indels2.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/annotate_indels2.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/annotate_indels2.cpp:155:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/annotate_indels2.cpp:155:10: note: Derived function 'Igor::initialize'
vt-0.57721/annotate_indels2.cpp:241:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/annotate_indels2.cpp:241:10: note: Derived function 'Igor::print_options'
vt-0.57721/annotate_indels2.cpp:254:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/annotate_indels2.cpp:254:10: note: Derived function 'Igor::print_stats'
vt-0.57721/indel_annotator.h:124:5: style: Class 'IndelAnnotator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/annotate_indels2.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/annotate_indels2.cpp:44:10: style: class member 'Igor::override_tag' is never used. [unusedStructMember]
vt-0.57721/annotate_indels2.cpp:290:17: style: Variable 'no_exact' is assigned a value that is never used. [unreadVariable]
vt-0.57721/annotate_indels2.cpp:291:17: style: Variable 'no_inexact' is assigned a value that is never used. [unreadVariable]
vt-0.57721/annotate_regions.cpp:123:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_regions.cpp:173:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_regions.cpp:186:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_regions.cpp:204:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_regions.cpp:220:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::use_bed' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::no_variants_annotated' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::orom_regions' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:81:5: warning: Member variable 'Igor::obom_regions' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_regions.cpp:83:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/annotate_regions.cpp:202:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/annotate_regions.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/annotate_regions.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/annotate_regions.cpp:130:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/annotate_regions.cpp:130:10: note: Derived function 'Igor::initialize'
vt-0.57721/annotate_regions.cpp:184:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/annotate_regions.cpp:184:10: note: Derived function 'Igor::print_options'
vt-0.57721/annotate_regions.cpp:202:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/annotate_regions.cpp:202:10: note: Derived function 'Igor::print_stats'
vt-0.57721/annotate_regions.cpp:143:25: style: Local variable 'hrec' shadows outer variable [shadowVariable]
vt-0.57721/annotate_regions.cpp:139:21: note: Shadowed declaration
vt-0.57721/annotate_regions.cpp:143:25: note: Shadow variable
vt-0.57721/annotate_regions.cpp:148:25: style: Local variable 'hrec' shadows outer variable [shadowVariable]
vt-0.57721/annotate_regions.cpp:139:21: note: Shadowed declaration
vt-0.57721/annotate_regions.cpp:148:25: note: Shadow variable
vt-0.57721/annotate_regions.cpp:236:22: style: Local variable 'overlaps' shadows outer variable [shadowVariable]
vt-0.57721/annotate_regions.cpp:215:32: note: Shadowed declaration
vt-0.57721/annotate_regions.cpp:236:22: note: Shadow variable
vt-0.57721/annotate_regions.cpp:267:22: style: Local variable 'overlaps' shadows outer variable [shadowVariable]
vt-0.57721/annotate_regions.cpp:215:32: note: Shadowed declaration
vt-0.57721/annotate_regions.cpp:267:22: note: Shadow variable
vt-0.57721/annotate_regions.cpp:242:48: style: Variable 'regs' can be declared as reference to const [constVariableReference]
vt-0.57721/annotate_regions.cpp:39:17: style: class member 'Igor::ref_fasta_file' is never used. [unusedStructMember]
vt-0.57721/annotate_regions.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/annotate_regions.cpp:47:17: style: class member 'Igor::REGIONS_LEFT_TAG_DESC' is never used. [unusedStructMember]
vt-0.57721/annotate_regions.cpp:49:17: style: class member 'Igor::REGIONS_RIGHT_TAG_DESC' is never used. [unusedStructMember]
vt-0.57721/annotate_regions.cpp:215:32: style: Unused variable: overlaps [unusedVariable]
vt-0.57721/annotate_variants.cpp:110:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_variants.cpp:161:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_variants.cpp:174:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_variants.cpp:189:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_variants.cpp:73:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_variants.cpp:73:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_variants.cpp:73:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_variants.cpp:73:5: warning: Member variable 'Igor::no_variants_annotated' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_variants.cpp:73:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_variants.cpp:73:5: warning: Member variable 'Igor::orom_lc' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_variants.cpp:73:5: warning: Member variable 'Igor::orom_cds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_variants.cpp:75:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/annotate_variants.cpp:172:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/annotate_variants.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/annotate_variants.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/annotate_variants.cpp:117:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/annotate_variants.cpp:117:10: note: Derived function 'Igor::initialize'
vt-0.57721/annotate_variants.cpp:159:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/annotate_variants.cpp:159:10: note: Derived function 'Igor::print_options'
vt-0.57721/annotate_variants.cpp:172:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/annotate_variants.cpp:172:10: note: Derived function 'Igor::print_stats'
vt-0.57721/annotate_variants.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/annotate_variants.cpp:228:34: style: Variable 'overlap' is assigned a value that is never used. [unreadVariable]
vt-0.57721/annotate_variants.cpp:184:32: style: Unused variable: overlaps [unusedVariable]
vt-0.57721/annotate_vntrs.cpp:129:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_vntrs.cpp:193:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_vntrs.cpp:208:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_vntrs.cpp:256:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::vntr_classification' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::override_tag' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::add_vntr_record' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::add_flank_annotation' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::no_vntrs_annotated' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::va' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:96:5: warning: Member variable 'Igor::rs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/annotate_vntrs.cpp:98:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/annotate_vntrs.cpp:206:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/annotate_vntrs.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/annotate_vntrs.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/annotate_vntrs.cpp:138:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/annotate_vntrs.cpp:138:10: note: Derived function 'Igor::initialize'
vt-0.57721/annotate_vntrs.cpp:191:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/annotate_vntrs.cpp:191:10: note: Derived function 'Igor::print_options'
vt-0.57721/annotate_vntrs.cpp:206:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/annotate_vntrs.cpp:206:10: note: Derived function 'Igor::print_stats'
vt-0.57721/annotate_vntrs.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/annotate_vntrs.cpp:44:17: style: class member 'Igor::method' is never used. [unusedStructMember]
vt-0.57721/annotate_vntrs.cpp:45:17: style: class member 'Igor::vntr_annotation_mode' is never used. [unusedStructMember]
vt-0.57721/annotate_vntrs.cpp:46:13: style: class member 'Igor::vntr_classification' is never used. [unusedStructMember]
vt-0.57721/augmented_bam_record.cpp:84:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/augmented_bam_record.cpp:400:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/augmented_bam_record.cpp:29:21: warning: Member variable 'AugmentedBAMRecord::h' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/augmented_bam_record.cpp:29:21: warning: Member variable 'AugmentedBAMRecord::beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/augmented_bam_record.cpp:29:21: warning: Member variable 'AugmentedBAMRecord::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/augmented_bam_record.h:100:10: performance:inconclusive: Technically the member function 'AugmentedBAMRecord::left_align' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/augmented_bam_record.cpp:326:26: note: Technically the member function 'AugmentedBAMRecord::left_align' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/augmented_bam_record.h:100:10: note: Technically the member function 'AugmentedBAMRecord::left_align' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/augmented_bam_record.h:110:10: performance:inconclusive: Technically the member function 'AugmentedBAMRecord::right_align' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/augmented_bam_record.cpp:337:26: note: Technically the member function 'AugmentedBAMRecord::right_align' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/augmented_bam_record.h:110:10: note: Technically the member function 'AugmentedBAMRecord::right_align' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/augmented_bam_record.cpp:360:5: style: Statements following 'return' will never be executed. [unreachableCode]
vt-0.57721/augmented_bam_record.cpp:60:10: style: The scope of the variable 'opchr' can be reduced. [variableScope]
vt-0.57721/augmented_bam_record.cpp:61:13: style: The scope of the variable 'oplen' can be reduced. [variableScope]
vt-0.57721/augmented_bam_record.cpp:360:10: style: The scope of the variable 'has_indels' can be reduced. [variableScope]
vt-0.57721/augmented_bam_record.cpp:256:29: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/augmented_bam_record.cpp:76:18: note: Shadowed declaration
vt-0.57721/augmented_bam_record.cpp:256:29: note: Shadow variable
vt-0.57721/augmented_bam_record.cpp:281:18: style: Local variable 'oplen' shadows outer variable [shadowVariable]
vt-0.57721/augmented_bam_record.cpp:61:13: note: Shadowed declaration
vt-0.57721/augmented_bam_record.cpp:281:18: note: Shadow variable
vt-0.57721/augmented_bam_record.cpp:282:14: style: Local variable 'opchr' shadows outer variable [shadowVariable]
vt-0.57721/augmented_bam_record.cpp:60:10: note: Shadowed declaration
vt-0.57721/augmented_bam_record.cpp:282:14: note: Shadow variable
vt-0.57721/augmented_bam_record.cpp:277:14: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
vt-0.57721/augmented_bam_record.cpp:467:14: style: Variable 'qual' can be declared as pointer to const [constVariablePointer]
vt-0.57721/augmented_bam_record.cpp:175:34: style: Variable 'mlen' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:203:25: style: Variable 'is_del' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:360:21: style: Variable 'has_indels' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:375:23: style: Variable 'flag' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:384:24: style: Variable 'has_indels' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:389:27: style: Variable 'oplen' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:394:28: style: Variable 'has_indels' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:427:24: style: Variable 'has_indels' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:432:27: style: Variable 'oplen' is assigned a value that is never used. [unreadVariable]
vt-0.57721/augmented_bam_record.cpp:437:28: style: Variable 'has_indels' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bam_ordered_reader.cpp:34:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/bam_ordered_reader.cpp:67:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/bam_ordered_reader.cpp:30:15: style: C-style pointer casting [cstyleCast]
vt-0.57721/bam_ordered_reader.cpp:52:48: performance: Function parameter 'file_name' should be passed by const reference. [passedByValue]
vt-0.57721/bam_ordered_reader.cpp:52:111: performance: Function parameter 'ref_fasta_file' should be passed by const reference. [passedByValue]
vt-0.57721/bam_ordered_reader.cpp:52:88: style: Parameter 'intervals' can be declared as reference to const [constParameterReference]
vt-0.57721/bam_ordered_reader.cpp:118:18: error: Out of bounds access in 'intervals[interval_index++]', if 'intervals' size is 1 and 'interval_index++' is 1 [containerOutOfBounds]
vt-0.57721/bam_ordered_reader.cpp:116:26: note: Assignment 'interval_index=0', assigned value is 0
vt-0.57721/bam_ordered_reader.cpp:118:19: note: interval_index is incremented', new value is 1
vt-0.57721/bam_ordered_reader.cpp:118:18: note: Access out of bounds
vt-0.57721/bcf_genotyping_buffered_reader.cpp:55:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:693:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2318:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::h' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::rid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::pos1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::vtype' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::dlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::no_nonref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::depth' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::depth_fwd' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::depth_rev' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::base_qualities_sum' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::n_filter' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::bqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::bqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::mqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::mqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::cyr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::cyr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::str_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::str_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::nmr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::nmr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::ior_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::ior_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::nm0_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::nm0_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::nm1_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::nm1_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::abe_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::abe_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::abz_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::abz_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::ns_nref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::dp_sum' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::max_gq' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_dp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_dp_ra' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_bq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_bq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_mq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_mq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_cy_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_cy_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_st_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_st_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_al_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_bq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_mq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_cy_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_st_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_nm_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_nm_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_nm_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_oth_exp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_oth_obs_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:139:5: warning:inconclusive: Member variable 'GenotypingRecord::tmp_ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::h' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::rid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::pos1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::vtype' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::dlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::no_nonref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::depth' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::depth_fwd' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::depth_rev' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::base_qualities_sum' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::n_filter' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::bqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::bqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::mqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::mqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::cyr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::cyr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::str_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::str_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::nmr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::nmr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::ior_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::ior_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::nm0_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::nm0_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::nm1_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::nm1_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::abe_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::abe_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::abz_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::abz_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::ns_nref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::dp_sum' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::max_gq' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_dp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_dp_ra' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_bq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_bq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_mq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_mq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_cy_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_cy_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_st_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_st_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_al_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_bq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_mq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_cy_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_st_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_nm_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_nm_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_nm_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_oth_exp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_oth_obs_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotyping_record.h:151:5: warning: Member variable 'GenotypingRecord::tmp_ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::dlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::n_filter' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::bqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::bqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::mqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::mqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::cyr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::cyr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::str_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::str_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::nmr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::nmr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::ior_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::ior_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::nm0_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::nm0_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::nm1_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::nm1_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::abe_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::abe_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::abz_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::abz_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::ns_nref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::dp_sum' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::max_gq' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_dp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_dp_ra' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_bq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_bq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_mq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_mq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_cy_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_cy_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_st_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_st_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_al_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_bq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_mq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_cy_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_st_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_nm_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_nm_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_nm_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_oth_exp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_oth_obs_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_genotyping_record.h:94:5: warning:inconclusive: Member variable 'IndelGenotypingRecord::tmp_ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:34:5: warning: Class 'BCFGenotypingBufferedReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:34:5: warning: Class 'BCFGenotypingBufferedReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/indel_genotyping_record.h:48:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'dlen' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:68:13: note: Parent variable 'GenotypingRecord::dlen'
vt-0.57721/indel_genotyping_record.h:48:13: note: Derived variable 'IndelGenotypingRecord::dlen'
vt-0.57721/indel_genotyping_record.h:49:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'len' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:69:13: note: Parent variable 'GenotypingRecord::len'
vt-0.57721/indel_genotyping_record.h:49:13: note: Derived variable 'IndelGenotypingRecord::len'
vt-0.57721/indel_genotyping_record.h:50:17: warning: The class 'IndelGenotypingRecord' defines member variable with name 'indel' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:70:17: note: Parent variable 'GenotypingRecord::indel'
vt-0.57721/indel_genotyping_record.h:50:17: note: Derived variable 'IndelGenotypingRecord::indel'
vt-0.57721/indel_genotyping_record.h:53:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'nsamples' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:100:13: note: Parent variable 'GenotypingRecord::nsamples'
vt-0.57721/indel_genotyping_record.h:53:13: note: Derived variable 'IndelGenotypingRecord::nsamples'
vt-0.57721/indel_genotyping_record.h:54:15: warning: The class 'IndelGenotypingRecord' defines member variable with name 'alleles' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:101:15: note: Parent variable 'GenotypingRecord::alleles'
vt-0.57721/indel_genotyping_record.h:54:15: note: Derived variable 'IndelGenotypingRecord::alleles'
vt-0.57721/indel_genotyping_record.h:55:30: warning: The class 'IndelGenotypingRecord' defines member variable with name 'v_alleles' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:102:30: note: Parent variable 'GenotypingRecord::v_alleles'
vt-0.57721/indel_genotyping_record.h:55:30: note: Derived variable 'IndelGenotypingRecord::v_alleles'
vt-0.57721/indel_genotyping_record.h:56:14: warning: The class 'IndelGenotypingRecord' defines member variable with name 'n_filter' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:103:14: note: Parent variable 'GenotypingRecord::n_filter'
vt-0.57721/indel_genotyping_record.h:56:14: note: Derived variable 'IndelGenotypingRecord::n_filter'
vt-0.57721/indel_genotyping_record.h:58:14: warning: The class 'IndelGenotypingRecord' defines member variable with name 'pls' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:105:14: note: Parent variable 'GenotypingRecord::pls'
vt-0.57721/indel_genotyping_record.h:58:14: note: Derived variable 'IndelGenotypingRecord::pls'
vt-0.57721/indel_genotyping_record.h:59:14: warning: The class 'IndelGenotypingRecord' defines member variable with name 'ads' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:106:14: note: Parent variable 'GenotypingRecord::ads'
vt-0.57721/indel_genotyping_record.h:59:14: note: Derived variable 'IndelGenotypingRecord::ads'
vt-0.57721/indel_genotyping_record.h:62:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'bqr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:109:11: note: Parent variable 'GenotypingRecord::bqr_num'
vt-0.57721/indel_genotyping_record.h:62:11: note: Derived variable 'IndelGenotypingRecord::bqr_num'
vt-0.57721/indel_genotyping_record.h:62:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'bqr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:109:20: note: Parent variable 'GenotypingRecord::bqr_den'
vt-0.57721/indel_genotyping_record.h:62:20: note: Derived variable 'IndelGenotypingRecord::bqr_den'
vt-0.57721/indel_genotyping_record.h:63:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'mqr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:110:11: note: Parent variable 'GenotypingRecord::mqr_num'
vt-0.57721/indel_genotyping_record.h:63:11: note: Derived variable 'IndelGenotypingRecord::mqr_num'
vt-0.57721/indel_genotyping_record.h:63:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'mqr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:110:20: note: Parent variable 'GenotypingRecord::mqr_den'
vt-0.57721/indel_genotyping_record.h:63:20: note: Derived variable 'IndelGenotypingRecord::mqr_den'
vt-0.57721/indel_genotyping_record.h:64:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'cyr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:111:11: note: Parent variable 'GenotypingRecord::cyr_num'
vt-0.57721/indel_genotyping_record.h:64:11: note: Derived variable 'IndelGenotypingRecord::cyr_num'
vt-0.57721/indel_genotyping_record.h:64:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'cyr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:111:20: note: Parent variable 'GenotypingRecord::cyr_den'
vt-0.57721/indel_genotyping_record.h:64:20: note: Derived variable 'IndelGenotypingRecord::cyr_den'
vt-0.57721/indel_genotyping_record.h:65:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'str_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:112:11: note: Parent variable 'GenotypingRecord::str_num'
vt-0.57721/indel_genotyping_record.h:65:11: note: Derived variable 'IndelGenotypingRecord::str_num'
vt-0.57721/indel_genotyping_record.h:65:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'str_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:112:20: note: Parent variable 'GenotypingRecord::str_den'
vt-0.57721/indel_genotyping_record.h:65:20: note: Derived variable 'IndelGenotypingRecord::str_den'
vt-0.57721/indel_genotyping_record.h:66:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'nmr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:113:11: note: Parent variable 'GenotypingRecord::nmr_num'
vt-0.57721/indel_genotyping_record.h:66:11: note: Derived variable 'IndelGenotypingRecord::nmr_num'
vt-0.57721/indel_genotyping_record.h:66:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'nmr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:113:20: note: Parent variable 'GenotypingRecord::nmr_den'
vt-0.57721/indel_genotyping_record.h:66:20: note: Derived variable 'IndelGenotypingRecord::nmr_den'
vt-0.57721/indel_genotyping_record.h:67:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'ior_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:114:11: note: Parent variable 'GenotypingRecord::ior_num'
vt-0.57721/indel_genotyping_record.h:67:11: note: Derived variable 'IndelGenotypingRecord::ior_num'
vt-0.57721/indel_genotyping_record.h:67:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'ior_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:114:20: note: Parent variable 'GenotypingRecord::ior_den'
vt-0.57721/indel_genotyping_record.h:67:20: note: Derived variable 'IndelGenotypingRecord::ior_den'
vt-0.57721/indel_genotyping_record.h:68:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'nm0_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:115:11: note: Parent variable 'GenotypingRecord::nm0_num'
vt-0.57721/indel_genotyping_record.h:68:11: note: Derived variable 'IndelGenotypingRecord::nm0_num'
vt-0.57721/indel_genotyping_record.h:68:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'nm0_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:115:20: note: Parent variable 'GenotypingRecord::nm0_den'
vt-0.57721/indel_genotyping_record.h:68:20: note: Derived variable 'IndelGenotypingRecord::nm0_den'
vt-0.57721/indel_genotyping_record.h:69:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'nm1_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:116:11: note: Parent variable 'GenotypingRecord::nm1_num'
vt-0.57721/indel_genotyping_record.h:69:11: note: Derived variable 'IndelGenotypingRecord::nm1_num'
vt-0.57721/indel_genotyping_record.h:69:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'nm1_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:116:20: note: Parent variable 'GenotypingRecord::nm1_den'
vt-0.57721/indel_genotyping_record.h:69:20: note: Derived variable 'IndelGenotypingRecord::nm1_den'
vt-0.57721/indel_genotyping_record.h:70:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'abe_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:117:11: note: Parent variable 'GenotypingRecord::abe_num'
vt-0.57721/indel_genotyping_record.h:70:11: note: Derived variable 'IndelGenotypingRecord::abe_num'
vt-0.57721/indel_genotyping_record.h:70:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'abe_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:117:20: note: Parent variable 'GenotypingRecord::abe_den'
vt-0.57721/indel_genotyping_record.h:70:20: note: Derived variable 'IndelGenotypingRecord::abe_den'
vt-0.57721/indel_genotyping_record.h:71:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'abz_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:118:11: note: Parent variable 'GenotypingRecord::abz_num'
vt-0.57721/indel_genotyping_record.h:71:11: note: Derived variable 'IndelGenotypingRecord::abz_num'
vt-0.57721/indel_genotyping_record.h:71:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'abz_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:118:20: note: Parent variable 'GenotypingRecord::abz_den'
vt-0.57721/indel_genotyping_record.h:71:20: note: Derived variable 'IndelGenotypingRecord::abz_den'
vt-0.57721/indel_genotyping_record.h:72:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'ns_nref' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:11: note: Parent variable 'GenotypingRecord::ns_nref'
vt-0.57721/indel_genotyping_record.h:72:11: note: Derived variable 'IndelGenotypingRecord::ns_nref'
vt-0.57721/indel_genotyping_record.h:72:20: warning: The class 'IndelGenotypingRecord' defines member variable with name 'dp_sum' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:20: note: Parent variable 'GenotypingRecord::dp_sum'
vt-0.57721/indel_genotyping_record.h:72:20: note: Derived variable 'IndelGenotypingRecord::dp_sum'
vt-0.57721/indel_genotyping_record.h:72:28: warning: The class 'IndelGenotypingRecord' defines member variable with name 'max_gq' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:28: note: Parent variable 'GenotypingRecord::max_gq'
vt-0.57721/indel_genotyping_record.h:72:28: note: Derived variable 'IndelGenotypingRecord::max_gq'
vt-0.57721/indel_genotyping_record.h:74:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_dp_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:122:13: note: Parent variable 'GenotypingRecord::tmp_dp_q20'
vt-0.57721/indel_genotyping_record.h:74:13: note: Derived variable 'IndelGenotypingRecord::tmp_dp_q20'
vt-0.57721/indel_genotyping_record.h:75:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_dp_ra' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:123:13: note: Parent variable 'GenotypingRecord::tmp_dp_ra'
vt-0.57721/indel_genotyping_record.h:75:13: note: Derived variable 'IndelGenotypingRecord::tmp_dp_ra'
vt-0.57721/indel_genotyping_record.h:76:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_bq_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:124:13: note: Parent variable 'GenotypingRecord::tmp_bq_s1'
vt-0.57721/indel_genotyping_record.h:76:13: note: Derived variable 'IndelGenotypingRecord::tmp_bq_s1'
vt-0.57721/indel_genotyping_record.h:76:24: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_bq_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:124:24: note: Parent variable 'GenotypingRecord::tmp_bq_s2'
vt-0.57721/indel_genotyping_record.h:76:24: note: Derived variable 'IndelGenotypingRecord::tmp_bq_s2'
vt-0.57721/indel_genotyping_record.h:77:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_mq_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:125:13: note: Parent variable 'GenotypingRecord::tmp_mq_s1'
vt-0.57721/indel_genotyping_record.h:77:13: note: Derived variable 'IndelGenotypingRecord::tmp_mq_s1'
vt-0.57721/indel_genotyping_record.h:77:24: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_mq_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:125:24: note: Parent variable 'GenotypingRecord::tmp_mq_s2'
vt-0.57721/indel_genotyping_record.h:77:24: note: Derived variable 'IndelGenotypingRecord::tmp_mq_s2'
vt-0.57721/indel_genotyping_record.h:78:11: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_cy_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:126:11: note: Parent variable 'GenotypingRecord::tmp_cy_s1'
vt-0.57721/indel_genotyping_record.h:78:11: note: Derived variable 'IndelGenotypingRecord::tmp_cy_s1'
vt-0.57721/indel_genotyping_record.h:78:22: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_cy_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:126:22: note: Parent variable 'GenotypingRecord::tmp_cy_s2'
vt-0.57721/indel_genotyping_record.h:78:22: note: Derived variable 'IndelGenotypingRecord::tmp_cy_s2'
vt-0.57721/indel_genotyping_record.h:79:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_st_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:127:13: note: Parent variable 'GenotypingRecord::tmp_st_s1'
vt-0.57721/indel_genotyping_record.h:79:13: note: Derived variable 'IndelGenotypingRecord::tmp_st_s1'
vt-0.57721/indel_genotyping_record.h:79:24: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_st_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:127:24: note: Parent variable 'GenotypingRecord::tmp_st_s2'
vt-0.57721/indel_genotyping_record.h:79:24: note: Derived variable 'IndelGenotypingRecord::tmp_st_s2'
vt-0.57721/indel_genotyping_record.h:80:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_al_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:13: note: Parent variable 'GenotypingRecord::tmp_al_s1'
vt-0.57721/indel_genotyping_record.h:80:13: note: Derived variable 'IndelGenotypingRecord::tmp_al_s1'
vt-0.57721/indel_genotyping_record.h:80:24: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_bq_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:24: note: Parent variable 'GenotypingRecord::tmp_bq_al'
vt-0.57721/indel_genotyping_record.h:80:24: note: Derived variable 'IndelGenotypingRecord::tmp_bq_al'
vt-0.57721/indel_genotyping_record.h:80:35: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_mq_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:35: note: Parent variable 'GenotypingRecord::tmp_mq_al'
vt-0.57721/indel_genotyping_record.h:80:35: note: Derived variable 'IndelGenotypingRecord::tmp_mq_al'
vt-0.57721/indel_genotyping_record.h:81:12: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_cy_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:129:12: note: Parent variable 'GenotypingRecord::tmp_cy_al'
vt-0.57721/indel_genotyping_record.h:81:12: note: Derived variable 'IndelGenotypingRecord::tmp_cy_al'
vt-0.57721/indel_genotyping_record.h:82:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_st_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:130:13: note: Parent variable 'GenotypingRecord::tmp_st_al'
vt-0.57721/indel_genotyping_record.h:82:13: note: Derived variable 'IndelGenotypingRecord::tmp_st_al'
vt-0.57721/indel_genotyping_record.h:82:24: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_nm_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:130:24: note: Parent variable 'GenotypingRecord::tmp_nm_al'
vt-0.57721/indel_genotyping_record.h:82:24: note: Derived variable 'IndelGenotypingRecord::tmp_nm_al'
vt-0.57721/indel_genotyping_record.h:83:13: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_nm_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:131:13: note: Parent variable 'GenotypingRecord::tmp_nm_s1'
vt-0.57721/indel_genotyping_record.h:83:13: note: Derived variable 'IndelGenotypingRecord::tmp_nm_s1'
vt-0.57721/indel_genotyping_record.h:83:24: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_nm_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:131:24: note: Parent variable 'GenotypingRecord::tmp_nm_s2'
vt-0.57721/indel_genotyping_record.h:83:24: note: Derived variable 'IndelGenotypingRecord::tmp_nm_s2'
vt-0.57721/indel_genotyping_record.h:84:12: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_oth_exp_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:132:12: note: Parent variable 'GenotypingRecord::tmp_oth_exp_q20'
vt-0.57721/indel_genotyping_record.h:84:12: note: Derived variable 'IndelGenotypingRecord::tmp_oth_exp_q20'
vt-0.57721/indel_genotyping_record.h:84:29: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_oth_obs_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:132:29: note: Parent variable 'GenotypingRecord::tmp_oth_obs_q20'
vt-0.57721/indel_genotyping_record.h:84:29: note: Derived variable 'IndelGenotypingRecord::tmp_oth_obs_q20'
vt-0.57721/indel_genotyping_record.h:85:12: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_pls' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:133:12: note: Parent variable 'GenotypingRecord::tmp_pls'
vt-0.57721/indel_genotyping_record.h:85:12: note: Derived variable 'IndelGenotypingRecord::tmp_pls'
vt-0.57721/indel_genotyping_record.h:86:12: warning: The class 'IndelGenotypingRecord' defines member variable with name 'tmp_ads' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:134:12: note: Parent variable 'GenotypingRecord::tmp_ads'
vt-0.57721/indel_genotyping_record.h:86:12: note: Derived variable 'IndelGenotypingRecord::tmp_ads'
vt-0.57721/estimator.h:50:5: style: Class 'Estimator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/indel_genotyping_record.h:105:10: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:161:18: note: Virtual function in base class
vt-0.57721/indel_genotyping_record.h:105:10: note: Function in derived class
vt-0.57721/indel_genotyping_record.h:110:10: style: The function 'clearTemp' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:166:18: note: Virtual function in base class
vt-0.57721/indel_genotyping_record.h:110:10: note: Function in derived class
vt-0.57721/indel_genotyping_record.h:115:13: style: The function 'flush_variant' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:172:21: note: Virtual function in base class
vt-0.57721/indel_genotyping_record.h:115:13: note: Function in derived class
vt-0.57721/indel_genotyping_record.h:120:10: style: The function 'flush_sample' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:177:18: note: Virtual function in base class
vt-0.57721/indel_genotyping_record.h:120:10: note: Function in derived class
vt-0.57721/indel_genotyping_record.h:125:10: style: The function 'add_allele' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:182:18: note: Virtual function in base class
vt-0.57721/indel_genotyping_record.h:125:10: note: Function in derived class
vt-0.57721/indel_genotyping_record.h:130:10: style: The function 'process_read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:187:18: note: Virtual function in base class
vt-0.57721/indel_genotyping_record.h:130:10: note: Function in derived class
vt-0.57721/indel_genotyping_record.h:135:6: style: The destructor '~IndelGenotypingRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:156:14: note: Virtual destructor in base class
vt-0.57721/indel_genotyping_record.h:135:6: note: Destructor in derived class
vt-0.57721/bcf_genotyping_buffered_reader.cpp:114:21: style: Condition 'tid>g->rid' is always true [knownConditionTrueFalse]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:83:16: note: Assuming that condition 'tid==g->rid' is not redundant
vt-0.57721/bcf_genotyping_buffered_reader.cpp:114:21: note: Condition 'tid>g->rid' is always true
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1872:27: style: The scope of the variable 'g' can be reduced. [variableScope]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1886:27: style: The scope of the variable 'g' can be reduced. [variableScope]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2117:15: style: The scope of the variable 'p' can be reduced. [variableScope]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:972:43: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:933:31: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:972:43: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1048:43: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:933:31: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1048:43: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1257:43: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1218:31: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1257:43: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1333:43: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1218:31: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1333:43: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1649:43: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1610:31: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1649:43: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1725:43: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1610:31: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1725:43: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2240:17: style: Local variable 'len' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2233:14: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2240:17: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2395:21: style: Local variable 'gts' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2353:17: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2395:21: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2548:21: style: Local variable 'gts' shadows outer variable [shadowVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2504:17: note: Shadowed declaration
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2548:21: note: Shadow variable
vt-0.57721/bcf_genotyping_buffered_reader.cpp:29:70: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:29:132: performance: Function parameter 'ref_fasta_file' should be passed by const reference. [passedByValue]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1994:72: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1994:104: style: Parameter 'quals' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1994:184: style: Parameter 'pl_offset' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2146:74: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2146:106: style: Parameter 'quals' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2187:49: style: Parameter 'alleles' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2188:36: style: Parameter 'obs_indel' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2190:45: style: Parameter 'als' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2185:57: style: Parameter 'lflank_state' can be declared as const array [constParameter]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2185:82: style: Parameter 'lflank_qual' can be declared as const array [constParameter]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2186:28: style: Parameter 'rflank_state' can be declared as const array [constParameter]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2186:53: style: Parameter 'rflank_qual' can be declared as const array [constParameter]
vt-0.57721/genotyping_record.h:151:33: style: Parameter 'h' can be declared as pointer to const [constParameterPointer]
vt-0.57721/genotyping_record.h:151:44: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.h:50:24: style: Parameter 'lt' can be declared as pointer to const [constParameterPointer]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1867:30: warning: Uninitialized variables: g.h, g.v, g.rid, g.pos1, g.beg1, g.end1, g.vtype, g.dlen, g.len, g.no_nonref, g.depth, g.depth_fwd, g.depth_rev, g.base_qualities_sum, g.nsamples, g.n_filter, g.pls, g.ads, g.bqr_num, g.bqr_den, g.mqr_num, g.mqr_den, g.cyr_num, g.cyr_den, g.str_num, g.str_den, g.nmr_num, g.nmr_den, g.ior_num, g.ior_den, g.nm0_num, g.nm0_den, g.nm1_num, g.nm1_den, g.abe_num, g.abe_den, g.abz_num, g.abz_den, g.ns_nref, g.dp_sum, g.max_gq, g.tmp_dp_q20, g.tmp_dp_ra, g.tmp_bq_s1, g.tmp_bq_s2, g.tmp_mq_s1, g.tmp_mq_s2, g.tmp_cy_s1, g.tmp_cy_s2, g.tmp_st_s1, g.tmp_st_s2, g.tmp_al_s1, g.tmp_bq_al, g.tmp_mq_al, g.tmp_cy_al, g.tmp_st_al, g.tmp_nm_al, g.tmp_nm_s1, g.tmp_nm_s2, g.tmp_oth_exp_q20, g.tmp_oth_obs_q20 [uninitvar]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1863:22: note: Assuming condition is false
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1867:30: note: Uninitialized variables: g.h, g.v, g.rid, g.pos1, g.beg1, g.end1, g.vtype, g.dlen, g.len, g.no_nonref, g.depth, g.depth_fwd, g.depth_rev, g.base_qualities_sum, g.nsamples, g.n_filter, g.pls, g.ads, g.bqr_num, g.bqr_den, g.mqr_num, g.mqr_den, g.cyr_num, g.cyr_den, g.str_num, g.str_den, g.nmr_num, g.nmr_den, g.ior_num, g.ior_den, g.nm0_num, g.nm0_den, g.nm1_num, g.nm1_den, g.abe_num, g.abe_den, g.abz_num, g.abz_den, g.ns_nref, g.dp_sum, g.max_gq, g.tmp_dp_q20, g.tmp_dp_ra, g.tmp_bq_s1, g.tmp_bq_s2, g.tmp_mq_s1, g.tmp_mq_s2, g.tmp_cy_s1, g.tmp_cy_s2, g.tmp_st_s1, g.tmp_st_s2, g.tmp_al_s1, g.tmp_bq_al, g.tmp_mq_al, g.tmp_cy_al, g.tmp_st_al, g.tmp_nm_al, g.tmp_nm_s1, g.tmp_nm_s2, g.tmp_oth_exp_q20, g.tmp_oth_obs_q20
vt-0.57721/bcf_genotyping_buffered_reader.cpp:625:27: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:626:26: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:755:27: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:756:26: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:890:31: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:894:30: style: Variable 'mapq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:897:30: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:913:44: style: Variable 'fuzzy_lflank_state' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:914:44: style: Variable 'fuzzy_rflank_state' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:915:47: style: Variable 'fuzzy_lflank_qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:916:47: style: Variable 'fuzzy_rflank_qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:919:31: style: Variable 'cend1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1175:31: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1179:30: style: Variable 'mapq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1182:30: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1198:44: style: Variable 'fuzzy_lflank_state' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1199:44: style: Variable 'fuzzy_rflank_state' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1200:47: style: Variable 'fuzzy_lflank_qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1201:47: style: Variable 'fuzzy_rflank_qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1204:31: style: Variable 'cend1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1458:24: style: Variable 'allele' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1459:23: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1460:22: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1461:23: style: Variable 'qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1462:23: style: Variable 'rlen' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1463:22: style: Variable 'mapq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1567:31: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1571:30: style: Variable 'mapq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1574:30: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1590:44: style: Variable 'fuzzy_lflank_state' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1591:44: style: Variable 'fuzzy_rflank_state' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1592:47: style: Variable 'fuzzy_lflank_qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1593:47: style: Variable 'fuzzy_rflank_qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:1596:31: style: Variable 'cend1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2119:22: style: Variable 'offset' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2124:15: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2130:23: style: Variable 'pG[i]' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2225:15: style: Variable 'tau' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2233:18: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_genotyping_buffered_reader.cpp:2259:31: style: Variable 'allele_likelihoods[i]' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_ordered_reader.cpp:64:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_ordered_reader.cpp:149:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_ordered_reader.cpp:208:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_ordered_reader.cpp:242:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_ordered_reader.cpp:307:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_ordered_reader.h:128:10: style:inconclusive: Technically the member function 'BCFOrderedReader::is_index_loaded' can be const. [functionConst]
vt-0.57721/bcf_ordered_reader.cpp:187:24: note: Technically the member function 'BCFOrderedReader::is_index_loaded' can be const.
vt-0.57721/bcf_ordered_reader.h:128:10: note: Technically the member function 'BCFOrderedReader::is_index_loaded' can be const.
vt-0.57721/bcf_ordered_reader.cpp:45:48: style:inconclusive: Function 'BCFOrderedReader' argument 1 names different: declaration 'input_vcf_file_name' definition 'file_name'. [funcArgNamesDifferent]
vt-0.57721/bcf_ordered_reader.h:95:34: note: Function 'BCFOrderedReader' argument 1 names different: declaration 'input_vcf_file_name' definition 'file_name'.
vt-0.57721/bcf_ordered_reader.cpp:45:48: note: Function 'BCFOrderedReader' argument 1 names different: declaration 'input_vcf_file_name' definition 'file_name'.
vt-0.57721/bcf_ordered_reader.cpp:45:48: performance: Function parameter 'file_name' should be passed by const reference. [passedByValue]
vt-0.57721/bcf_ordered_reader.cpp:45:88: style: Parameter 'intervals' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_ordered_reader.cpp:151:22: error: Out of bounds access in 'intervals[interval_index++]', if 'intervals' size is 1 and 'interval_index++' is 1 [containerOutOfBounds]
vt-0.57721/bcf_ordered_reader.cpp:148:26: note: Assignment 'interval_index=0', assigned value is 0
vt-0.57721/bcf_ordered_reader.cpp:151:23: note: interval_index is incremented', new value is 1
vt-0.57721/bcf_ordered_reader.cpp:151:22: note: Access out of bounds
vt-0.57721/bcf_ordered_reader.cpp:162:22: error: Out of bounds access in 'intervals[interval_index++]', if 'intervals' size is 1 and 'interval_index++' is 1 [containerOutOfBounds]
vt-0.57721/bcf_ordered_reader.cpp:148:26: note: Assignment 'interval_index=0', assigned value is 0
vt-0.57721/bcf_ordered_reader.cpp:162:23: note: interval_index is incremented', new value is 1
vt-0.57721/bcf_ordered_reader.cpp:162:22: note: Access out of bounds
vt-0.57721/bcf_ordered_writer.cpp:80:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_ordered_writer.cpp:161:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_ordered_writer.cpp:213:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
vt-0.57721/bcf_ordered_writer.cpp:145:23: style: Redundant initialization for 'i'. The initialized value is overwritten before it is read. [redundantInitialization]
vt-0.57721/bcf_ordered_writer.cpp:143:48: note: i is initialized
vt-0.57721/bcf_ordered_writer.cpp:145:23: note: i is overwritten
vt-0.57721/bcf_ordered_writer.cpp:26:48: performance: Function parameter 'output_vcf_file_name' should be passed by const reference. [passedByValue]
vt-0.57721/bcf_ordered_writer.cpp:149:21: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::n_filter' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::est' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::bqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::bqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::mqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::mqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::cyr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::cyr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::str_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::str_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::nmr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::nmr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::ior_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::ior_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::nm0_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::nm0_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::nm1_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::nm1_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::abe_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::abe_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::abz_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::abz_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::ns_nref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::dp_sum' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::max_gq' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_dp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_dp_ra' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_bq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_bq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_mq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_mq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_cy_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_cy_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_st_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_st_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_al_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_bq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_mq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_cy_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_st_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_nm_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_nm_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_nm_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_oth_exp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_oth_obs_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_genotyping_record.h:100:5: warning:inconclusive: Member variable 'VNTRGenotypingRecord::tmp_ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:29:36: warning: Member variable 'BCFSingleGenotypingBufferedReader::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:29:36: warning: Member variable 'BCFSingleGenotypingBufferedReader::fai' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:34:5: warning: Class 'BCFSingleGenotypingBufferedReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:34:5: warning: Class 'BCFSingleGenotypingBufferedReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/snp_genotyping_record.h:46:16: warning: The class 'SNPGenotypingRecord' defines member variable with name 'h' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:49:16: note: Parent variable 'GenotypingRecord::h'
vt-0.57721/snp_genotyping_record.h:46:16: note: Derived variable 'SNPGenotypingRecord::h'
vt-0.57721/snp_genotyping_record.h:47:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'v' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:50:13: note: Parent variable 'GenotypingRecord::v'
vt-0.57721/snp_genotyping_record.h:47:13: note: Derived variable 'SNPGenotypingRecord::v'
vt-0.57721/snp_genotyping_record.h:48:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'rid' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:51:13: note: Parent variable 'GenotypingRecord::rid'
vt-0.57721/snp_genotyping_record.h:48:13: note: Derived variable 'SNPGenotypingRecord::rid'
vt-0.57721/snp_genotyping_record.h:49:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'pos1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:52:13: note: Parent variable 'GenotypingRecord::pos1'
vt-0.57721/snp_genotyping_record.h:49:13: note: Derived variable 'SNPGenotypingRecord::pos1'
vt-0.57721/snp_genotyping_record.h:60:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'beg1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:63:13: note: Parent variable 'GenotypingRecord::beg1'
vt-0.57721/snp_genotyping_record.h:60:13: note: Derived variable 'SNPGenotypingRecord::beg1'
vt-0.57721/snp_genotyping_record.h:61:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'end1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:64:13: note: Parent variable 'GenotypingRecord::end1'
vt-0.57721/snp_genotyping_record.h:61:13: note: Derived variable 'SNPGenotypingRecord::end1'
vt-0.57721/snp_genotyping_record.h:64:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'dlen' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:68:13: note: Parent variable 'GenotypingRecord::dlen'
vt-0.57721/snp_genotyping_record.h:64:13: note: Derived variable 'SNPGenotypingRecord::dlen'
vt-0.57721/snp_genotyping_record.h:65:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'len' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:69:13: note: Parent variable 'GenotypingRecord::len'
vt-0.57721/snp_genotyping_record.h:65:13: note: Derived variable 'SNPGenotypingRecord::len'
vt-0.57721/snp_genotyping_record.h:66:17: warning: The class 'SNPGenotypingRecord' defines member variable with name 'indel' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:70:17: note: Parent variable 'GenotypingRecord::indel'
vt-0.57721/snp_genotyping_record.h:66:17: note: Derived variable 'SNPGenotypingRecord::indel'
vt-0.57721/snp_genotyping_record.h:69:17: warning: The class 'SNPGenotypingRecord' defines member variable with name 'motif' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:73:17: note: Parent variable 'GenotypingRecord::motif'
vt-0.57721/snp_genotyping_record.h:69:17: note: Derived variable 'SNPGenotypingRecord::motif'
vt-0.57721/snp_genotyping_record.h:75:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'nsamples' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:100:13: note: Parent variable 'GenotypingRecord::nsamples'
vt-0.57721/snp_genotyping_record.h:75:13: note: Derived variable 'SNPGenotypingRecord::nsamples'
vt-0.57721/snp_genotyping_record.h:76:15: warning: The class 'SNPGenotypingRecord' defines member variable with name 'alleles' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:101:15: note: Parent variable 'GenotypingRecord::alleles'
vt-0.57721/snp_genotyping_record.h:76:15: note: Derived variable 'SNPGenotypingRecord::alleles'
vt-0.57721/snp_genotyping_record.h:77:30: warning: The class 'SNPGenotypingRecord' defines member variable with name 'v_alleles' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:102:30: note: Parent variable 'GenotypingRecord::v_alleles'
vt-0.57721/snp_genotyping_record.h:77:30: note: Derived variable 'SNPGenotypingRecord::v_alleles'
vt-0.57721/snp_genotyping_record.h:78:14: warning: The class 'SNPGenotypingRecord' defines member variable with name 'n_filter' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:103:14: note: Parent variable 'GenotypingRecord::n_filter'
vt-0.57721/snp_genotyping_record.h:78:14: note: Derived variable 'SNPGenotypingRecord::n_filter'
vt-0.57721/snp_genotyping_record.h:80:14: warning: The class 'SNPGenotypingRecord' defines member variable with name 'pls' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:105:14: note: Parent variable 'GenotypingRecord::pls'
vt-0.57721/snp_genotyping_record.h:80:14: note: Derived variable 'SNPGenotypingRecord::pls'
vt-0.57721/snp_genotyping_record.h:81:14: warning: The class 'SNPGenotypingRecord' defines member variable with name 'ads' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:106:14: note: Parent variable 'GenotypingRecord::ads'
vt-0.57721/snp_genotyping_record.h:81:14: note: Derived variable 'SNPGenotypingRecord::ads'
vt-0.57721/snp_genotyping_record.h:84:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'bqr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:109:11: note: Parent variable 'GenotypingRecord::bqr_num'
vt-0.57721/snp_genotyping_record.h:84:11: note: Derived variable 'SNPGenotypingRecord::bqr_num'
vt-0.57721/snp_genotyping_record.h:84:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'bqr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:109:20: note: Parent variable 'GenotypingRecord::bqr_den'
vt-0.57721/snp_genotyping_record.h:84:20: note: Derived variable 'SNPGenotypingRecord::bqr_den'
vt-0.57721/snp_genotyping_record.h:85:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'mqr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:110:11: note: Parent variable 'GenotypingRecord::mqr_num'
vt-0.57721/snp_genotyping_record.h:85:11: note: Derived variable 'SNPGenotypingRecord::mqr_num'
vt-0.57721/snp_genotyping_record.h:85:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'mqr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:110:20: note: Parent variable 'GenotypingRecord::mqr_den'
vt-0.57721/snp_genotyping_record.h:85:20: note: Derived variable 'SNPGenotypingRecord::mqr_den'
vt-0.57721/snp_genotyping_record.h:86:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'cyr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:111:11: note: Parent variable 'GenotypingRecord::cyr_num'
vt-0.57721/snp_genotyping_record.h:86:11: note: Derived variable 'SNPGenotypingRecord::cyr_num'
vt-0.57721/snp_genotyping_record.h:86:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'cyr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:111:20: note: Parent variable 'GenotypingRecord::cyr_den'
vt-0.57721/snp_genotyping_record.h:86:20: note: Derived variable 'SNPGenotypingRecord::cyr_den'
vt-0.57721/snp_genotyping_record.h:87:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'str_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:112:11: note: Parent variable 'GenotypingRecord::str_num'
vt-0.57721/snp_genotyping_record.h:87:11: note: Derived variable 'SNPGenotypingRecord::str_num'
vt-0.57721/snp_genotyping_record.h:87:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'str_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:112:20: note: Parent variable 'GenotypingRecord::str_den'
vt-0.57721/snp_genotyping_record.h:87:20: note: Derived variable 'SNPGenotypingRecord::str_den'
vt-0.57721/snp_genotyping_record.h:88:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'nmr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:113:11: note: Parent variable 'GenotypingRecord::nmr_num'
vt-0.57721/snp_genotyping_record.h:88:11: note: Derived variable 'SNPGenotypingRecord::nmr_num'
vt-0.57721/snp_genotyping_record.h:88:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'nmr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:113:20: note: Parent variable 'GenotypingRecord::nmr_den'
vt-0.57721/snp_genotyping_record.h:88:20: note: Derived variable 'SNPGenotypingRecord::nmr_den'
vt-0.57721/snp_genotyping_record.h:89:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'ior_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:114:11: note: Parent variable 'GenotypingRecord::ior_num'
vt-0.57721/snp_genotyping_record.h:89:11: note: Derived variable 'SNPGenotypingRecord::ior_num'
vt-0.57721/snp_genotyping_record.h:89:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'ior_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:114:20: note: Parent variable 'GenotypingRecord::ior_den'
vt-0.57721/snp_genotyping_record.h:89:20: note: Derived variable 'SNPGenotypingRecord::ior_den'
vt-0.57721/snp_genotyping_record.h:90:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'nm0_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:115:11: note: Parent variable 'GenotypingRecord::nm0_num'
vt-0.57721/snp_genotyping_record.h:90:11: note: Derived variable 'SNPGenotypingRecord::nm0_num'
vt-0.57721/snp_genotyping_record.h:90:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'nm0_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:115:20: note: Parent variable 'GenotypingRecord::nm0_den'
vt-0.57721/snp_genotyping_record.h:90:20: note: Derived variable 'SNPGenotypingRecord::nm0_den'
vt-0.57721/snp_genotyping_record.h:91:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'nm1_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:116:11: note: Parent variable 'GenotypingRecord::nm1_num'
vt-0.57721/snp_genotyping_record.h:91:11: note: Derived variable 'SNPGenotypingRecord::nm1_num'
vt-0.57721/snp_genotyping_record.h:91:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'nm1_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:116:20: note: Parent variable 'GenotypingRecord::nm1_den'
vt-0.57721/snp_genotyping_record.h:91:20: note: Derived variable 'SNPGenotypingRecord::nm1_den'
vt-0.57721/snp_genotyping_record.h:92:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'abe_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:117:11: note: Parent variable 'GenotypingRecord::abe_num'
vt-0.57721/snp_genotyping_record.h:92:11: note: Derived variable 'SNPGenotypingRecord::abe_num'
vt-0.57721/snp_genotyping_record.h:92:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'abe_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:117:20: note: Parent variable 'GenotypingRecord::abe_den'
vt-0.57721/snp_genotyping_record.h:92:20: note: Derived variable 'SNPGenotypingRecord::abe_den'
vt-0.57721/snp_genotyping_record.h:93:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'abz_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:118:11: note: Parent variable 'GenotypingRecord::abz_num'
vt-0.57721/snp_genotyping_record.h:93:11: note: Derived variable 'SNPGenotypingRecord::abz_num'
vt-0.57721/snp_genotyping_record.h:93:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'abz_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:118:20: note: Parent variable 'GenotypingRecord::abz_den'
vt-0.57721/snp_genotyping_record.h:93:20: note: Derived variable 'SNPGenotypingRecord::abz_den'
vt-0.57721/snp_genotyping_record.h:94:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'ns_nref' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:11: note: Parent variable 'GenotypingRecord::ns_nref'
vt-0.57721/snp_genotyping_record.h:94:11: note: Derived variable 'SNPGenotypingRecord::ns_nref'
vt-0.57721/snp_genotyping_record.h:94:20: warning: The class 'SNPGenotypingRecord' defines member variable with name 'dp_sum' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:20: note: Parent variable 'GenotypingRecord::dp_sum'
vt-0.57721/snp_genotyping_record.h:94:20: note: Derived variable 'SNPGenotypingRecord::dp_sum'
vt-0.57721/snp_genotyping_record.h:94:28: warning: The class 'SNPGenotypingRecord' defines member variable with name 'max_gq' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:28: note: Parent variable 'GenotypingRecord::max_gq'
vt-0.57721/snp_genotyping_record.h:94:28: note: Derived variable 'SNPGenotypingRecord::max_gq'
vt-0.57721/snp_genotyping_record.h:97:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_dp_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:122:13: note: Parent variable 'GenotypingRecord::tmp_dp_q20'
vt-0.57721/snp_genotyping_record.h:97:13: note: Derived variable 'SNPGenotypingRecord::tmp_dp_q20'
vt-0.57721/snp_genotyping_record.h:98:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_dp_ra' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:123:13: note: Parent variable 'GenotypingRecord::tmp_dp_ra'
vt-0.57721/snp_genotyping_record.h:98:13: note: Derived variable 'SNPGenotypingRecord::tmp_dp_ra'
vt-0.57721/snp_genotyping_record.h:99:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_bq_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:124:13: note: Parent variable 'GenotypingRecord::tmp_bq_s1'
vt-0.57721/snp_genotyping_record.h:99:13: note: Derived variable 'SNPGenotypingRecord::tmp_bq_s1'
vt-0.57721/snp_genotyping_record.h:99:24: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_bq_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:124:24: note: Parent variable 'GenotypingRecord::tmp_bq_s2'
vt-0.57721/snp_genotyping_record.h:99:24: note: Derived variable 'SNPGenotypingRecord::tmp_bq_s2'
vt-0.57721/snp_genotyping_record.h:100:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_mq_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:125:13: note: Parent variable 'GenotypingRecord::tmp_mq_s1'
vt-0.57721/snp_genotyping_record.h:100:13: note: Derived variable 'SNPGenotypingRecord::tmp_mq_s1'
vt-0.57721/snp_genotyping_record.h:100:24: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_mq_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:125:24: note: Parent variable 'GenotypingRecord::tmp_mq_s2'
vt-0.57721/snp_genotyping_record.h:100:24: note: Derived variable 'SNPGenotypingRecord::tmp_mq_s2'
vt-0.57721/snp_genotyping_record.h:101:11: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_cy_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:126:11: note: Parent variable 'GenotypingRecord::tmp_cy_s1'
vt-0.57721/snp_genotyping_record.h:101:11: note: Derived variable 'SNPGenotypingRecord::tmp_cy_s1'
vt-0.57721/snp_genotyping_record.h:101:22: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_cy_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:126:22: note: Parent variable 'GenotypingRecord::tmp_cy_s2'
vt-0.57721/snp_genotyping_record.h:101:22: note: Derived variable 'SNPGenotypingRecord::tmp_cy_s2'
vt-0.57721/snp_genotyping_record.h:102:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_st_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:127:13: note: Parent variable 'GenotypingRecord::tmp_st_s1'
vt-0.57721/snp_genotyping_record.h:102:13: note: Derived variable 'SNPGenotypingRecord::tmp_st_s1'
vt-0.57721/snp_genotyping_record.h:102:24: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_st_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:127:24: note: Parent variable 'GenotypingRecord::tmp_st_s2'
vt-0.57721/snp_genotyping_record.h:102:24: note: Derived variable 'SNPGenotypingRecord::tmp_st_s2'
vt-0.57721/snp_genotyping_record.h:103:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_al_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:13: note: Parent variable 'GenotypingRecord::tmp_al_s1'
vt-0.57721/snp_genotyping_record.h:103:13: note: Derived variable 'SNPGenotypingRecord::tmp_al_s1'
vt-0.57721/snp_genotyping_record.h:103:24: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_bq_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:24: note: Parent variable 'GenotypingRecord::tmp_bq_al'
vt-0.57721/snp_genotyping_record.h:103:24: note: Derived variable 'SNPGenotypingRecord::tmp_bq_al'
vt-0.57721/snp_genotyping_record.h:103:35: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_mq_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:35: note: Parent variable 'GenotypingRecord::tmp_mq_al'
vt-0.57721/snp_genotyping_record.h:103:35: note: Derived variable 'SNPGenotypingRecord::tmp_mq_al'
vt-0.57721/snp_genotyping_record.h:104:12: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_cy_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:129:12: note: Parent variable 'GenotypingRecord::tmp_cy_al'
vt-0.57721/snp_genotyping_record.h:104:12: note: Derived variable 'SNPGenotypingRecord::tmp_cy_al'
vt-0.57721/snp_genotyping_record.h:105:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_st_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:130:13: note: Parent variable 'GenotypingRecord::tmp_st_al'
vt-0.57721/snp_genotyping_record.h:105:13: note: Derived variable 'SNPGenotypingRecord::tmp_st_al'
vt-0.57721/snp_genotyping_record.h:105:24: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_nm_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:130:24: note: Parent variable 'GenotypingRecord::tmp_nm_al'
vt-0.57721/snp_genotyping_record.h:105:24: note: Derived variable 'SNPGenotypingRecord::tmp_nm_al'
vt-0.57721/snp_genotyping_record.h:106:13: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_nm_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:131:13: note: Parent variable 'GenotypingRecord::tmp_nm_s1'
vt-0.57721/snp_genotyping_record.h:106:13: note: Derived variable 'SNPGenotypingRecord::tmp_nm_s1'
vt-0.57721/snp_genotyping_record.h:106:24: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_nm_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:131:24: note: Parent variable 'GenotypingRecord::tmp_nm_s2'
vt-0.57721/snp_genotyping_record.h:106:24: note: Derived variable 'SNPGenotypingRecord::tmp_nm_s2'
vt-0.57721/snp_genotyping_record.h:107:12: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_oth_exp_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:132:12: note: Parent variable 'GenotypingRecord::tmp_oth_exp_q20'
vt-0.57721/snp_genotyping_record.h:107:12: note: Derived variable 'SNPGenotypingRecord::tmp_oth_exp_q20'
vt-0.57721/snp_genotyping_record.h:107:29: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_oth_obs_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:132:29: note: Parent variable 'GenotypingRecord::tmp_oth_obs_q20'
vt-0.57721/snp_genotyping_record.h:107:29: note: Derived variable 'SNPGenotypingRecord::tmp_oth_obs_q20'
vt-0.57721/snp_genotyping_record.h:108:12: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_pls' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:133:12: note: Parent variable 'GenotypingRecord::tmp_pls'
vt-0.57721/snp_genotyping_record.h:108:12: note: Derived variable 'SNPGenotypingRecord::tmp_pls'
vt-0.57721/snp_genotyping_record.h:109:12: warning: The class 'SNPGenotypingRecord' defines member variable with name 'tmp_ads' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:134:12: note: Parent variable 'GenotypingRecord::tmp_ads'
vt-0.57721/snp_genotyping_record.h:109:12: note: Derived variable 'SNPGenotypingRecord::tmp_ads'
vt-0.57721/vntr_genotyping_record.h:52:17: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'motif' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:73:17: note: Parent variable 'GenotypingRecord::motif'
vt-0.57721/vntr_genotyping_record.h:52:17: note: Derived variable 'VNTRGenotypingRecord::motif'
vt-0.57721/vntr_genotyping_record.h:58:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'nsamples' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:100:13: note: Parent variable 'GenotypingRecord::nsamples'
vt-0.57721/vntr_genotyping_record.h:58:13: note: Derived variable 'VNTRGenotypingRecord::nsamples'
vt-0.57721/vntr_genotyping_record.h:59:15: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'alleles' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:101:15: note: Parent variable 'GenotypingRecord::alleles'
vt-0.57721/vntr_genotyping_record.h:59:15: note: Derived variable 'VNTRGenotypingRecord::alleles'
vt-0.57721/vntr_genotyping_record.h:60:30: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'v_alleles' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:102:30: note: Parent variable 'GenotypingRecord::v_alleles'
vt-0.57721/vntr_genotyping_record.h:60:30: note: Derived variable 'VNTRGenotypingRecord::v_alleles'
vt-0.57721/vntr_genotyping_record.h:61:14: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'n_filter' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:103:14: note: Parent variable 'GenotypingRecord::n_filter'
vt-0.57721/vntr_genotyping_record.h:61:14: note: Derived variable 'VNTRGenotypingRecord::n_filter'
vt-0.57721/vntr_genotyping_record.h:63:14: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'pls' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:105:14: note: Parent variable 'GenotypingRecord::pls'
vt-0.57721/vntr_genotyping_record.h:63:14: note: Derived variable 'VNTRGenotypingRecord::pls'
vt-0.57721/vntr_genotyping_record.h:64:14: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'ads' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:106:14: note: Parent variable 'GenotypingRecord::ads'
vt-0.57721/vntr_genotyping_record.h:64:14: note: Derived variable 'VNTRGenotypingRecord::ads'
vt-0.57721/vntr_genotyping_record.h:68:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'bqr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:109:11: note: Parent variable 'GenotypingRecord::bqr_num'
vt-0.57721/vntr_genotyping_record.h:68:11: note: Derived variable 'VNTRGenotypingRecord::bqr_num'
vt-0.57721/vntr_genotyping_record.h:68:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'bqr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:109:20: note: Parent variable 'GenotypingRecord::bqr_den'
vt-0.57721/vntr_genotyping_record.h:68:20: note: Derived variable 'VNTRGenotypingRecord::bqr_den'
vt-0.57721/vntr_genotyping_record.h:69:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'mqr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:110:11: note: Parent variable 'GenotypingRecord::mqr_num'
vt-0.57721/vntr_genotyping_record.h:69:11: note: Derived variable 'VNTRGenotypingRecord::mqr_num'
vt-0.57721/vntr_genotyping_record.h:69:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'mqr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:110:20: note: Parent variable 'GenotypingRecord::mqr_den'
vt-0.57721/vntr_genotyping_record.h:69:20: note: Derived variable 'VNTRGenotypingRecord::mqr_den'
vt-0.57721/vntr_genotyping_record.h:70:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'cyr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:111:11: note: Parent variable 'GenotypingRecord::cyr_num'
vt-0.57721/vntr_genotyping_record.h:70:11: note: Derived variable 'VNTRGenotypingRecord::cyr_num'
vt-0.57721/vntr_genotyping_record.h:70:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'cyr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:111:20: note: Parent variable 'GenotypingRecord::cyr_den'
vt-0.57721/vntr_genotyping_record.h:70:20: note: Derived variable 'VNTRGenotypingRecord::cyr_den'
vt-0.57721/vntr_genotyping_record.h:71:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'str_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:112:11: note: Parent variable 'GenotypingRecord::str_num'
vt-0.57721/vntr_genotyping_record.h:71:11: note: Derived variable 'VNTRGenotypingRecord::str_num'
vt-0.57721/vntr_genotyping_record.h:71:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'str_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:112:20: note: Parent variable 'GenotypingRecord::str_den'
vt-0.57721/vntr_genotyping_record.h:71:20: note: Derived variable 'VNTRGenotypingRecord::str_den'
vt-0.57721/vntr_genotyping_record.h:72:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'nmr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:113:11: note: Parent variable 'GenotypingRecord::nmr_num'
vt-0.57721/vntr_genotyping_record.h:72:11: note: Derived variable 'VNTRGenotypingRecord::nmr_num'
vt-0.57721/vntr_genotyping_record.h:72:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'nmr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:113:20: note: Parent variable 'GenotypingRecord::nmr_den'
vt-0.57721/vntr_genotyping_record.h:72:20: note: Derived variable 'VNTRGenotypingRecord::nmr_den'
vt-0.57721/vntr_genotyping_record.h:73:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'ior_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:114:11: note: Parent variable 'GenotypingRecord::ior_num'
vt-0.57721/vntr_genotyping_record.h:73:11: note: Derived variable 'VNTRGenotypingRecord::ior_num'
vt-0.57721/vntr_genotyping_record.h:73:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'ior_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:114:20: note: Parent variable 'GenotypingRecord::ior_den'
vt-0.57721/vntr_genotyping_record.h:73:20: note: Derived variable 'VNTRGenotypingRecord::ior_den'
vt-0.57721/vntr_genotyping_record.h:74:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'nm0_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:115:11: note: Parent variable 'GenotypingRecord::nm0_num'
vt-0.57721/vntr_genotyping_record.h:74:11: note: Derived variable 'VNTRGenotypingRecord::nm0_num'
vt-0.57721/vntr_genotyping_record.h:74:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'nm0_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:115:20: note: Parent variable 'GenotypingRecord::nm0_den'
vt-0.57721/vntr_genotyping_record.h:74:20: note: Derived variable 'VNTRGenotypingRecord::nm0_den'
vt-0.57721/vntr_genotyping_record.h:75:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'nm1_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:116:11: note: Parent variable 'GenotypingRecord::nm1_num'
vt-0.57721/vntr_genotyping_record.h:75:11: note: Derived variable 'VNTRGenotypingRecord::nm1_num'
vt-0.57721/vntr_genotyping_record.h:75:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'nm1_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:116:20: note: Parent variable 'GenotypingRecord::nm1_den'
vt-0.57721/vntr_genotyping_record.h:75:20: note: Derived variable 'VNTRGenotypingRecord::nm1_den'
vt-0.57721/vntr_genotyping_record.h:76:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'abe_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:117:11: note: Parent variable 'GenotypingRecord::abe_num'
vt-0.57721/vntr_genotyping_record.h:76:11: note: Derived variable 'VNTRGenotypingRecord::abe_num'
vt-0.57721/vntr_genotyping_record.h:76:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'abe_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:117:20: note: Parent variable 'GenotypingRecord::abe_den'
vt-0.57721/vntr_genotyping_record.h:76:20: note: Derived variable 'VNTRGenotypingRecord::abe_den'
vt-0.57721/vntr_genotyping_record.h:77:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'abz_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:118:11: note: Parent variable 'GenotypingRecord::abz_num'
vt-0.57721/vntr_genotyping_record.h:77:11: note: Derived variable 'VNTRGenotypingRecord::abz_num'
vt-0.57721/vntr_genotyping_record.h:77:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'abz_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:118:20: note: Parent variable 'GenotypingRecord::abz_den'
vt-0.57721/vntr_genotyping_record.h:77:20: note: Derived variable 'VNTRGenotypingRecord::abz_den'
vt-0.57721/vntr_genotyping_record.h:78:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'ns_nref' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:11: note: Parent variable 'GenotypingRecord::ns_nref'
vt-0.57721/vntr_genotyping_record.h:78:11: note: Derived variable 'VNTRGenotypingRecord::ns_nref'
vt-0.57721/vntr_genotyping_record.h:78:20: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'dp_sum' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:20: note: Parent variable 'GenotypingRecord::dp_sum'
vt-0.57721/vntr_genotyping_record.h:78:20: note: Derived variable 'VNTRGenotypingRecord::dp_sum'
vt-0.57721/vntr_genotyping_record.h:78:28: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'max_gq' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:28: note: Parent variable 'GenotypingRecord::max_gq'
vt-0.57721/vntr_genotyping_record.h:78:28: note: Derived variable 'VNTRGenotypingRecord::max_gq'
vt-0.57721/vntr_genotyping_record.h:80:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_dp_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:122:13: note: Parent variable 'GenotypingRecord::tmp_dp_q20'
vt-0.57721/vntr_genotyping_record.h:80:13: note: Derived variable 'VNTRGenotypingRecord::tmp_dp_q20'
vt-0.57721/vntr_genotyping_record.h:81:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_dp_ra' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:123:13: note: Parent variable 'GenotypingRecord::tmp_dp_ra'
vt-0.57721/vntr_genotyping_record.h:81:13: note: Derived variable 'VNTRGenotypingRecord::tmp_dp_ra'
vt-0.57721/vntr_genotyping_record.h:82:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_bq_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:124:13: note: Parent variable 'GenotypingRecord::tmp_bq_s1'
vt-0.57721/vntr_genotyping_record.h:82:13: note: Derived variable 'VNTRGenotypingRecord::tmp_bq_s1'
vt-0.57721/vntr_genotyping_record.h:82:24: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_bq_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:124:24: note: Parent variable 'GenotypingRecord::tmp_bq_s2'
vt-0.57721/vntr_genotyping_record.h:82:24: note: Derived variable 'VNTRGenotypingRecord::tmp_bq_s2'
vt-0.57721/vntr_genotyping_record.h:83:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_mq_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:125:13: note: Parent variable 'GenotypingRecord::tmp_mq_s1'
vt-0.57721/vntr_genotyping_record.h:83:13: note: Derived variable 'VNTRGenotypingRecord::tmp_mq_s1'
vt-0.57721/vntr_genotyping_record.h:83:24: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_mq_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:125:24: note: Parent variable 'GenotypingRecord::tmp_mq_s2'
vt-0.57721/vntr_genotyping_record.h:83:24: note: Derived variable 'VNTRGenotypingRecord::tmp_mq_s2'
vt-0.57721/vntr_genotyping_record.h:84:11: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_cy_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:126:11: note: Parent variable 'GenotypingRecord::tmp_cy_s1'
vt-0.57721/vntr_genotyping_record.h:84:11: note: Derived variable 'VNTRGenotypingRecord::tmp_cy_s1'
vt-0.57721/vntr_genotyping_record.h:84:22: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_cy_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:126:22: note: Parent variable 'GenotypingRecord::tmp_cy_s2'
vt-0.57721/vntr_genotyping_record.h:84:22: note: Derived variable 'VNTRGenotypingRecord::tmp_cy_s2'
vt-0.57721/vntr_genotyping_record.h:85:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_st_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:127:13: note: Parent variable 'GenotypingRecord::tmp_st_s1'
vt-0.57721/vntr_genotyping_record.h:85:13: note: Derived variable 'VNTRGenotypingRecord::tmp_st_s1'
vt-0.57721/vntr_genotyping_record.h:85:24: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_st_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:127:24: note: Parent variable 'GenotypingRecord::tmp_st_s2'
vt-0.57721/vntr_genotyping_record.h:85:24: note: Derived variable 'VNTRGenotypingRecord::tmp_st_s2'
vt-0.57721/vntr_genotyping_record.h:86:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_al_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:13: note: Parent variable 'GenotypingRecord::tmp_al_s1'
vt-0.57721/vntr_genotyping_record.h:86:13: note: Derived variable 'VNTRGenotypingRecord::tmp_al_s1'
vt-0.57721/vntr_genotyping_record.h:86:24: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_bq_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:24: note: Parent variable 'GenotypingRecord::tmp_bq_al'
vt-0.57721/vntr_genotyping_record.h:86:24: note: Derived variable 'VNTRGenotypingRecord::tmp_bq_al'
vt-0.57721/vntr_genotyping_record.h:86:35: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_mq_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:35: note: Parent variable 'GenotypingRecord::tmp_mq_al'
vt-0.57721/vntr_genotyping_record.h:86:35: note: Derived variable 'VNTRGenotypingRecord::tmp_mq_al'
vt-0.57721/vntr_genotyping_record.h:87:12: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_cy_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:129:12: note: Parent variable 'GenotypingRecord::tmp_cy_al'
vt-0.57721/vntr_genotyping_record.h:87:12: note: Derived variable 'VNTRGenotypingRecord::tmp_cy_al'
vt-0.57721/vntr_genotyping_record.h:88:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_st_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:130:13: note: Parent variable 'GenotypingRecord::tmp_st_al'
vt-0.57721/vntr_genotyping_record.h:88:13: note: Derived variable 'VNTRGenotypingRecord::tmp_st_al'
vt-0.57721/vntr_genotyping_record.h:88:24: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_nm_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:130:24: note: Parent variable 'GenotypingRecord::tmp_nm_al'
vt-0.57721/vntr_genotyping_record.h:88:24: note: Derived variable 'VNTRGenotypingRecord::tmp_nm_al'
vt-0.57721/vntr_genotyping_record.h:89:13: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_nm_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:131:13: note: Parent variable 'GenotypingRecord::tmp_nm_s1'
vt-0.57721/vntr_genotyping_record.h:89:13: note: Derived variable 'VNTRGenotypingRecord::tmp_nm_s1'
vt-0.57721/vntr_genotyping_record.h:89:24: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_nm_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:131:24: note: Parent variable 'GenotypingRecord::tmp_nm_s2'
vt-0.57721/vntr_genotyping_record.h:89:24: note: Derived variable 'VNTRGenotypingRecord::tmp_nm_s2'
vt-0.57721/vntr_genotyping_record.h:90:12: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_oth_exp_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:132:12: note: Parent variable 'GenotypingRecord::tmp_oth_exp_q20'
vt-0.57721/vntr_genotyping_record.h:90:12: note: Derived variable 'VNTRGenotypingRecord::tmp_oth_exp_q20'
vt-0.57721/vntr_genotyping_record.h:90:29: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_oth_obs_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:132:29: note: Parent variable 'GenotypingRecord::tmp_oth_obs_q20'
vt-0.57721/vntr_genotyping_record.h:90:29: note: Derived variable 'VNTRGenotypingRecord::tmp_oth_obs_q20'
vt-0.57721/vntr_genotyping_record.h:91:12: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_pls' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:133:12: note: Parent variable 'GenotypingRecord::tmp_pls'
vt-0.57721/vntr_genotyping_record.h:91:12: note: Derived variable 'VNTRGenotypingRecord::tmp_pls'
vt-0.57721/vntr_genotyping_record.h:92:12: warning: The class 'VNTRGenotypingRecord' defines member variable with name 'tmp_ads' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:134:12: note: Parent variable 'GenotypingRecord::tmp_ads'
vt-0.57721/vntr_genotyping_record.h:92:12: note: Derived variable 'VNTRGenotypingRecord::tmp_ads'
vt-0.57721/snp_genotyping_record.h:126:6: style: The destructor '~SNPGenotypingRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:156:14: note: Virtual destructor in base class
vt-0.57721/snp_genotyping_record.h:126:6: note: Destructor in derived class
vt-0.57721/snp_genotyping_record.h:131:10: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:161:18: note: Virtual function in base class
vt-0.57721/snp_genotyping_record.h:131:10: note: Function in derived class
vt-0.57721/snp_genotyping_record.h:136:10: style: The function 'clearTemp' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:166:18: note: Virtual function in base class
vt-0.57721/snp_genotyping_record.h:136:10: note: Function in derived class
vt-0.57721/snp_genotyping_record.h:141:13: style: The function 'flush_variant' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:172:21: note: Virtual function in base class
vt-0.57721/snp_genotyping_record.h:141:13: note: Function in derived class
vt-0.57721/snp_genotyping_record.h:146:10: style: The function 'flush_sample' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:177:18: note: Virtual function in base class
vt-0.57721/snp_genotyping_record.h:146:10: note: Function in derived class
vt-0.57721/snp_genotyping_record.h:151:10: style: The function 'add_allele' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:182:18: note: Virtual function in base class
vt-0.57721/snp_genotyping_record.h:151:10: note: Function in derived class
vt-0.57721/snp_genotyping_record.h:156:10: style: The function 'process_read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:187:18: note: Virtual function in base class
vt-0.57721/snp_genotyping_record.h:156:10: note: Function in derived class
vt-0.57721/vntr_genotyping_record.h:111:10: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:161:18: note: Virtual function in base class
vt-0.57721/vntr_genotyping_record.h:111:10: note: Function in derived class
vt-0.57721/vntr_genotyping_record.h:116:10: style: The function 'clearTemp' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:166:18: note: Virtual function in base class
vt-0.57721/vntr_genotyping_record.h:116:10: note: Function in derived class
vt-0.57721/vntr_genotyping_record.h:121:13: style: The function 'flush_variant' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:172:21: note: Virtual function in base class
vt-0.57721/vntr_genotyping_record.h:121:13: note: Function in derived class
vt-0.57721/vntr_genotyping_record.h:126:10: style: The function 'flush_sample' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:177:18: note: Virtual function in base class
vt-0.57721/vntr_genotyping_record.h:126:10: note: Function in derived class
vt-0.57721/vntr_genotyping_record.h:131:10: style: The function 'add_allele' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:182:18: note: Virtual function in base class
vt-0.57721/vntr_genotyping_record.h:131:10: note: Function in derived class
vt-0.57721/vntr_genotyping_record.h:136:10: style: The function 'process_read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:187:18: note: Virtual function in base class
vt-0.57721/vntr_genotyping_record.h:136:10: note: Function in derived class
vt-0.57721/vntr_genotyping_record.h:141:6: style: The destructor '~VNTRGenotypingRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:156:14: note: Virtual destructor in base class
vt-0.57721/vntr_genotyping_record.h:141:6: note: Destructor in derived class
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:114:21: style: Condition 'tid>g->rid' is always true [knownConditionTrueFalse]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:83:16: note: Assuming that condition 'tid==g->rid' is not redundant
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:114:21: note: Condition 'tid>g->rid' is always true
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:172:27: style: The scope of the variable 'g' can be reduced. [variableScope]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:186:27: style: The scope of the variable 'g' can be reduced. [variableScope]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:29:82: performance: Function parameter 'input_vcf_file' should be passed by const reference. [passedByValue]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:29:150: performance: Function parameter 'output_vcf_file' should be passed by const reference. [passedByValue]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:222:130: style: Parameter 'variant' can be declared as reference to const [constParameterReference]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:126:23: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_single_genotyping_buffered_reader.cpp:165:27: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bcf_synced_reader.cpp:73:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_synced_reader.cpp:202:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable format [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_synced_reader.cpp:268:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_synced_reader.cpp:454:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable format [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_synced_reader.cpp:507:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable format [valueFlowBailoutIncompleteVar]
vt-0.57721/bcf_synced_reader.cpp:333:5: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
vt-0.57721/bcf_synced_reader.cpp:31:18: warning: Member variable 'BCFSyncedReader::neofs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/bcf_synced_reader.cpp:31:18: warning: Member variable 'BCFSyncedReader::current_rid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/bcf_synced_reader.h:198:13: style:inconclusive: Technically the member function 'BCFSyncedReader::bcfptr_cmp' can be const. [functionConst]
vt-0.57721/bcf_synced_reader.cpp:339:26: note: Technically the member function 'BCFSyncedReader::bcfptr_cmp' can be const.
vt-0.57721/bcf_synced_reader.h:198:13: note: Technically the member function 'BCFSyncedReader::bcfptr_cmp' can be const.
vt-0.57721/bcf_synced_reader.h:229:13: style:inconclusive: Technically the member function 'BCFSyncedReader::get_nfiles' can be const. [functionConst]
vt-0.57721/bcf_synced_reader.cpp:231:26: note: Technically the member function 'BCFSyncedReader::get_nfiles' can be const.
vt-0.57721/bcf_synced_reader.h:229:13: note: Technically the member function 'BCFSyncedReader::get_nfiles' can be const.
vt-0.57721/bcf_synced_reader.h:239:13: style:inconclusive: Technically the member function 'BCFSyncedReader::get_current_pos1' can be const. [functionConst]
vt-0.57721/bcf_synced_reader.cpp:256:26: note: Technically the member function 'BCFSyncedReader::get_current_pos1' can be const.
vt-0.57721/bcf_synced_reader.h:239:13: note: Technically the member function 'BCFSyncedReader::get_current_pos1' can be const.
vt-0.57721/bcf_synced_reader.cpp:31:60: style:inconclusive: Function 'BCFSyncedReader' argument 1 names different: declaration '_vcf_files' definition 'file_names'. [funcArgNamesDifferent]
vt-0.57721/bcf_synced_reader.h:193:47: note: Function 'BCFSyncedReader' argument 1 names different: declaration '_vcf_files' definition 'file_names'.
vt-0.57721/bcf_synced_reader.cpp:31:60: note: Function 'BCFSyncedReader' argument 1 names different: declaration '_vcf_files' definition 'file_names'.
vt-0.57721/bcf_synced_reader.cpp:31:101: style:inconclusive: Function 'BCFSyncedReader' argument 2 names different: declaration '_intervals' definition 'intervals'. [funcArgNamesDifferent]
vt-0.57721/bcf_synced_reader.h:193:88: note: Function 'BCFSyncedReader' argument 2 names different: declaration '_intervals' definition 'intervals'.
vt-0.57721/bcf_synced_reader.cpp:31:101: note: Function 'BCFSyncedReader' argument 2 names different: declaration '_intervals' definition 'intervals'.
vt-0.57721/bcf_synced_reader.cpp:241:30: style: Local variable 's' shadows outer variable [shadowVariable]
vt-0.57721/bcf_synced_reader.h:179:15: note: Shadowed declaration
vt-0.57721/bcf_synced_reader.cpp:241:30: note: Shadow variable
vt-0.57721/bcf_synced_reader.cpp:339:45: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
vt-0.57721/bcf_synced_reader.cpp:339:56: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
vt-0.57721/bcf_synced_reader.cpp:162:56: performance: Searching before insertion is not necessary. Instead of 'intervals_map[seq]=intervals_map.size()' consider using 'intervals_map.try_emplace(seq, intervals_map.size());'. [stlFindInsert]
vt-0.57721/bcf_synced_reader.cpp:177:56: performance: Searching before insertion is not necessary. Instead of 'intervals_map[seq]=intervals_map.size()' consider using 'intervals_map.try_emplace(seq, intervals_map.size());'. [stlFindInsert]
vt-0.57721/bcf_synced_reader.cpp:192:53: performance: Searching before insertion is not necessary. Instead of 'intervals_map[interval]=intervals_map.size()' consider using 'intervals_map.try_emplace(interval, intervals_map.size());'. [stlFindInsert]
vt-0.57721/bcf_synced_reader.cpp:333:7: style: Variable 'v' is assigned a value that is never used. [unreadVariable]
vt-0.57721/bed.cpp:82:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/bed.h:60:10: style:inconclusive: Technically the member function 'BEDRecord::print' can be const. [functionConst]
vt-0.57721/bed.cpp:80:17: note: Technically the member function 'BEDRecord::print' can be const.
vt-0.57721/bed.h:60:10: note: Technically the member function 'BEDRecord::print' can be const.
vt-0.57721/bed.cpp:56:35: style: Parameter 's' can be declared as reference to const [constParameterReference]
vt-0.57721/bed.cpp:70:35: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/bed.cpp:42:28: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
vt-0.57721/candidate_motif_picker.cpp:58:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/candidate_motif_picker.cpp:220:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/candidate_motif_picker.cpp:246:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/candidate_motif_picker.cpp:376:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/candidate_motif_picker.cpp:29:23: warning: Member variable 'CandidateMotifPicker::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/candidate_motif_picker.cpp:29:23: warning: Member variable 'CandidateMotifPicker::max_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/candidate_motif_picker.h:85:10: performance:inconclusive: Technically the member function 'CandidateMotifPicker::set_motif_from_info_field' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/candidate_motif_picker.cpp:157:28: note: Technically the member function 'CandidateMotifPicker::set_motif_from_info_field' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_motif_picker.h:85:10: note: Technically the member function 'CandidateMotifPicker::set_motif_from_info_field' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_motif_picker.h:103:10: performance:inconclusive: Technically the member function 'CandidateMotifPicker::get_indel' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/candidate_motif_picker.cpp:181:28: note: Technically the member function 'CandidateMotifPicker::get_indel' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_motif_picker.h:103:10: note: Technically the member function 'CandidateMotifPicker::get_indel' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_motif_picker.h:108:10: style:inconclusive: Technically the member function 'CandidateMotifPicker::is_in_indel_fragment' can be const. [functionConst]
vt-0.57721/candidate_motif_picker.cpp:452:28: note: Technically the member function 'CandidateMotifPicker::is_in_indel_fragment' can be const.
vt-0.57721/candidate_motif_picker.h:108:10: note: Technically the member function 'CandidateMotifPicker::is_in_indel_fragment' can be const.
vt-0.57721/candidate_motif_picker.cpp:32:5: warning: Class 'CandidateMotifPicker' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/candidate_motif_picker.cpp:32:5: warning: Class 'CandidateMotifPicker' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/candidate_motif_picker.cpp:66:14: style: The scope of the variable 'pos1' can be reduced. [variableScope]
vt-0.57721/candidate_motif_picker.cpp:116:25: style: Local variable 'spiked_seq' shadows outer variable [shadowVariable]
vt-0.57721/candidate_motif_picker.cpp:109:21: note: Shadowed declaration
vt-0.57721/candidate_motif_picker.cpp:116:25: note: Shadow variable
vt-0.57721/candidate_motif_picker.cpp:236:13: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/candidate_motif_picker.h:47:13: note: Shadowed declaration
vt-0.57721/candidate_motif_picker.cpp:236:13: note: Shadow variable
vt-0.57721/candidate_motif_picker.cpp:309:25: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/candidate_motif_picker.cpp:290:22: note: Shadowed declaration
vt-0.57721/candidate_motif_picker.cpp:309:25: note: Shadow variable
vt-0.57721/candidate_motif_picker.cpp:460:23: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/candidate_motif_picker.cpp:454:19: note: Shadowed declaration
vt-0.57721/candidate_motif_picker.cpp:460:23: note: Shadow variable
vt-0.57721/candidate_motif_picker.cpp:452:61: performance: Function parameter 'motif' should be passed by const reference. [passedByValue]
vt-0.57721/candidate_motif_picker.cpp:475:67: style: Parameter 'ref' can be declared as reference to const [constParameterReference]
vt-0.57721/candidate_motif_picker.cpp:64:32: style: Variable 'alt_is_longest_allele' is assigned a value that is never used. [unreadVariable]
vt-0.57721/candidate_motif_picker.cpp:116:36: style: Variable 'spiked_seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/candidate_region_extractor.cpp:98:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/candidate_region_extractor.cpp:166:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/candidate_region_extractor.cpp:276:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/candidate_region_extractor.h:83:17: performance:inconclusive: Technically the member function 'CandidateRegionExtractor::choose_repeat_unit' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/candidate_region_extractor.cpp:119:39: note: Technically the member function 'CandidateRegionExtractor::choose_repeat_unit' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_region_extractor.h:83:17: note: Technically the member function 'CandidateRegionExtractor::choose_repeat_unit' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_region_extractor.h:88:10: performance:inconclusive: Technically the member function 'CandidateRegionExtractor::trim' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/candidate_region_extractor.cpp:472:32: note: Technically the member function 'CandidateRegionExtractor::trim' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_region_extractor.h:88:10: note: Technically the member function 'CandidateRegionExtractor::trim' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_region_extractor.h:93:10: performance:inconclusive: Technically the member function 'CandidateRegionExtractor::is_homopolymer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/candidate_region_extractor.cpp:136:32: note: Technically the member function 'CandidateRegionExtractor::is_homopolymer' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_region_extractor.h:93:10: note: Technically the member function 'CandidateRegionExtractor::is_homopolymer' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/candidate_region_extractor.cpp:31:5: warning: Class 'CandidateRegionExtractor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/candidate_region_extractor.cpp:31:5: warning: Class 'CandidateRegionExtractor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/candidate_region_extractor.cpp:166:13: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
vt-0.57721/candidate_region_extractor.cpp:164:9: note: outer condition: debug
vt-0.57721/candidate_region_extractor.cpp:166:13: note: identical inner condition: debug
vt-0.57721/candidate_region_extractor.cpp:276:13: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
vt-0.57721/candidate_region_extractor.cpp:274:9: note: outer condition: debug
vt-0.57721/candidate_region_extractor.cpp:276:13: note: identical inner condition: debug
vt-0.57721/candidate_region_extractor.cpp:374:18: style: Redundant initialization for 'pos1_sub'. The initialized value is overwritten before it is read. [redundantInitialization]
vt-0.57721/candidate_region_extractor.cpp:361:27: note: pos1_sub is initialized
vt-0.57721/candidate_region_extractor.cpp:374:18: note: pos1_sub is overwritten
vt-0.57721/candidate_region_extractor.cpp:443:18: style: Redundant initialization for 'pos1_sub'. The initialized value is overwritten before it is read. [redundantInitialization]
vt-0.57721/candidate_region_extractor.cpp:430:27: note: pos1_sub is initialized
vt-0.57721/candidate_region_extractor.cpp:443:18: note: pos1_sub is overwritten
vt-0.57721/candidate_region_extractor.cpp:379:25: style: Local variable 'new_ref' shadows outer variable [shadowVariable]
vt-0.57721/candidate_region_extractor.cpp:367:21: note: Shadowed declaration
vt-0.57721/candidate_region_extractor.cpp:379:25: note: Shadow variable
vt-0.57721/candidate_region_extractor.cpp:388:25: style: Local variable 'new_alt' shadows outer variable [shadowVariable]
vt-0.57721/candidate_region_extractor.cpp:368:21: note: Shadowed declaration
vt-0.57721/candidate_region_extractor.cpp:388:25: note: Shadow variable
vt-0.57721/candidate_region_extractor.cpp:448:25: style: Local variable 'new_ref' shadows outer variable [shadowVariable]
vt-0.57721/candidate_region_extractor.cpp:436:21: note: Shadowed declaration
vt-0.57721/candidate_region_extractor.cpp:448:25: note: Shadow variable
vt-0.57721/candidate_region_extractor.cpp:457:25: style: Local variable 'new_alt' shadows outer variable [shadowVariable]
vt-0.57721/candidate_region_extractor.cpp:437:21: note: Shadowed declaration
vt-0.57721/candidate_region_extractor.cpp:457:25: note: Shadow variable
vt-0.57721/candidate_region_extractor.cpp:119:71: style: Parameter 'ref' can be declared as reference to const [constParameterReference]
vt-0.57721/candidate_region_extractor.cpp:136:69: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/candidate_region_extractor.cpp:31:14: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam]
vt-0.57721/candidate_region_extractor.cpp:55:18: style: Variable 'h' is assigned a value that is never used. [unreadVariable]
vt-0.57721/candidate_region_extractor.cpp:139:22: style: Variable 'ref_len' is assigned a value that is never used. [unreadVariable]
vt-0.57721/candidate_region_extractor.cpp:142:24: style: Variable 'ref' is assigned a value that is never used. [unreadVariable]
vt-0.57721/candidate_region_extractor.cpp:143:24: style: Variable 'alt' is assigned a value that is never used. [unreadVariable]
vt-0.57721/candidate_region_extractor.cpp:144:22: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/candidate_region_extractor.cpp:208:17: style: Unused variable: seq_len [unusedVariable]
vt-0.57721/candidate_region_extractor.cpp:241:13: style: Unused variable: seq_len [unusedVariable]
vt-0.57721/candidate_region_extractor.cpp:280:18: style: Variable 'h' is assigned a value that is never used. [unreadVariable]
vt-0.57721/cat.cpp:110:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/cat.cpp:122:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/cat.cpp:292:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/cat.cpp:306:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/cat.cpp:73:5: warning: Member variable 'Igor::naive' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/cat.cpp:73:5: warning: Member variable 'Igor::print_sites_only' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/cat.cpp:73:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/cat.cpp:73:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/cat.cpp:73:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/cat.cpp:73:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/cat.cpp:73:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/cat.cpp:302:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/cat.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/cat.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/cat.cpp:115:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/cat.cpp:115:10: note: Derived function 'Igor::initialize'
vt-0.57721/cat.cpp:288:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/cat.cpp:288:10: note: Derived function 'Igor::print_options'
vt-0.57721/cat.cpp:302:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/cat.cpp:302:10: note: Derived function 'Igor::print_stats'
vt-0.57721/cat.cpp:39:17: style: class member 'Igor::input_vcf_file_list' is never used. [unusedStructMember]
vt-0.57721/cat.cpp:43:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/cat.cpp:47:10: style: class member 'Igor::print_sites_only' is never used. [unusedStructMember]
vt-0.57721/chmm.cpp:139:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:225:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:318:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:590:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:636:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:932:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1106:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1151:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1471:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1595:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1614:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1634:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1660:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1682:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:1730:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::rlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::plen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::lflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::lflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::motif_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::motif_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::rflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::rflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::exact_motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::motif_m' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::motif_xid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::motif_concordance' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::max_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::max_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::optimal_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::optimal_state' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::optimal_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::optimal_probe_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::optimal_path_ptr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.cpp:83:7: warning: Member variable 'CHMM::optimal_path_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/chmm.h:236:11: style:inconclusive: Technically the member function 'CHMM::log10_emission_odds' can be const. [functionConst]
vt-0.57721/chmm.cpp:1145:13: note: Technically the member function 'CHMM::log10_emission_odds' can be const.
vt-0.57721/chmm.h:236:11: note: Technically the member function 'CHMM::log10_emission_odds' can be const.
vt-0.57721/chmm.h:241:17: performance:inconclusive: Technically the member function 'CHMM::state2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.cpp:1167:19: note: Technically the member function 'CHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/chmm.h:241:17: note: Technically the member function 'CHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/chmm.h:246:17: performance:inconclusive: Technically the member function 'CHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.cpp:1246:19: note: Technically the member function 'CHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/chmm.h:246:17: note: Technically the member function 'CHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/chmm.h:251:17: style:inconclusive: Technically the member function 'CHMM::track2cigarstring1' can be const. [functionConst]
vt-0.57721/chmm.cpp:1325:19: note: Technically the member function 'CHMM::track2cigarstring1' can be const.
vt-0.57721/chmm.h:251:17: note: Technically the member function 'CHMM::track2cigarstring1' can be const.
vt-0.57721/chmm.h:256:17: performance:inconclusive: Technically the member function 'CHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.cpp:1389:19: note: Technically the member function 'CHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/chmm.h:256:17: note: Technically the member function 'CHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/chmm.h:261:17: performance:inconclusive: Technically the member function 'CHMM::component2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/chmm.cpp:1421:19: note: Technically the member function 'CHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/chmm.h:261:17: note: Technically the member function 'CHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/chmm.h:276:10: style:inconclusive: Technically the member function 'CHMM::print' can be const. [functionConst]
vt-0.57721/chmm.cpp:1592:12: note: Technically the member function 'CHMM::print' can be const.
vt-0.57721/chmm.h:276:10: note: Technically the member function 'CHMM::print' can be const.
vt-0.57721/chmm.h:281:10: style:inconclusive: Technically the member function 'CHMM::print' can be const. [functionConst]
vt-0.57721/chmm.cpp:1611:12: note: Technically the member function 'CHMM::print' can be const.
vt-0.57721/chmm.h:281:10: note: Technically the member function 'CHMM::print' can be const.
vt-0.57721/chmm.h:316:10: style:inconclusive: Technically the member function 'CHMM::flanks_are_mapped' can be const. [functionConst]
vt-0.57721/chmm.cpp:1137:12: note: Technically the member function 'CHMM::flanks_are_mapped' can be const.
vt-0.57721/chmm.h:316:10: note: Technically the member function 'CHMM::flanks_are_mapped' can be const.
vt-0.57721/chmm.cpp:931:12: style: The scope of the variable 'c' can be reduced. [variableScope]
vt-0.57721/chmm.cpp:970:13: style: The scope of the variable 'u' can be reduced. [variableScope]
vt-0.57721/chmm.cpp:971:13: style: The scope of the variable 'des_t' can be reduced. [variableScope]
vt-0.57721/chmm.cpp:520:54: style:inconclusive: Function 'set_model' argument 2 names different: declaration 'ru' definition 'motif'. [funcArgNamesDifferent]
vt-0.57721/chmm.h:184:52: note: Function 'set_model' argument 2 names different: declaration 'ru' definition 'motif'.
vt-0.57721/chmm.cpp:520:54: note: Function 'set_model' argument 2 names different: declaration 'ru' definition 'motif'.
vt-0.57721/chmm.cpp:585:52: style:inconclusive: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'. [funcArgNamesDifferent]
vt-0.57721/chmm.h:221:50: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/chmm.cpp:585:52: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/chmm.cpp:626:30: style:inconclusive: Function 'align' argument 1 names different: declaration 'y' definition 'read'. [funcArgNamesDifferent]
vt-0.57721/chmm.h:226:28: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/chmm.cpp:626:30: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/chmm.cpp:1011:39: style:inconclusive: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'. [funcArgNamesDifferent]
vt-0.57721/chmm.h:301:37: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/chmm.cpp:1011:39: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/chmm.cpp:1011:54: style:inconclusive: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'. [funcArgNamesDifferent]
vt-0.57721/chmm.h:301:49: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/chmm.cpp:1011:54: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/chmm.cpp:1145:38: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl' [funcArgOrderDifferent]
vt-0.57721/chmm.h:236:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/chmm.cpp:1145:38: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/chmm.cpp:1465:41: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/chmm.cpp:1592:25: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/chmm.cpp:1611:27: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/chmm.cpp:1658:29: style: Parameter 'U' can be declared as pointer to const [constParameterPointer]
vt-0.57721/chmm.cpp:1683:14: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
vt-0.57721/chmm.cpp:1684:12: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
vt-0.57721/chmm.cpp:311:14: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/chmm.cpp:640:15: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
vt-0.57721/chmm.cpp:641:18: style: Variable 'maxPath' is assigned a value that is never used. [unreadVariable]
vt-0.57721/chmm.cpp:1528:15: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/circular_buffer.cpp:90:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/circular_buffer.cpp:125:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
vt-0.57721/circular_buffer.cpp:133:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
vt-0.57721/circular_buffer.cpp:159:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/circular_buffer.cpp:278:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/circular_buffer.cpp:308:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/circular_buffer.cpp:326:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/circular_buffer.cpp:31:17: warning: Member variable 'CircularBuffer::fai' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/circular_buffer.h:83:10: style:inconclusive: Technically the member function 'CircularBuffer::fetch_base' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:272:22: note: Technically the member function 'CircularBuffer::fetch_base' can be const.
vt-0.57721/circular_buffer.h:83:10: note: Technically the member function 'CircularBuffer::fetch_base' can be const.
vt-0.57721/circular_buffer.h:107:14: style:inconclusive: Technically the member function 'CircularBuffer::max_size' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:59:26: note: Technically the member function 'CircularBuffer::max_size' can be const.
vt-0.57721/circular_buffer.h:107:14: note: Technically the member function 'CircularBuffer::max_size' can be const.
vt-0.57721/circular_buffer.h:112:14: style:inconclusive: Technically the member function 'CircularBuffer::size' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:67:26: note: Technically the member function 'CircularBuffer::size' can be const.
vt-0.57721/circular_buffer.h:112:14: note: Technically the member function 'CircularBuffer::size' can be const.
vt-0.57721/circular_buffer.h:117:10: style:inconclusive: Technically the member function 'CircularBuffer::is_empty' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:75:22: note: Technically the member function 'CircularBuffer::is_empty' can be const.
vt-0.57721/circular_buffer.h:117:10: note: Technically the member function 'CircularBuffer::is_empty' can be const.
vt-0.57721/circular_buffer.h:137:14: style:inconclusive: Technically the member function 'CircularBuffer::get_tid' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:115:26: note: Technically the member function 'CircularBuffer::get_tid' can be const.
vt-0.57721/circular_buffer.h:137:14: note: Technically the member function 'CircularBuffer::get_tid' can be const.
vt-0.57721/circular_buffer.h:147:17: performance:inconclusive: Technically the member function 'CircularBuffer::get_chrom' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/circular_buffer.cpp:131:29: note: Technically the member function 'CircularBuffer::get_chrom' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/circular_buffer.h:147:17: note: Technically the member function 'CircularBuffer::get_chrom' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/circular_buffer.h:152:14: style:inconclusive: Technically the member function 'CircularBuffer::get_window_size' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:139:26: note: Technically the member function 'CircularBuffer::get_window_size' can be const.
vt-0.57721/circular_buffer.h:152:14: note: Technically the member function 'CircularBuffer::get_window_size' can be const.
vt-0.57721/circular_buffer.h:162:14: style:inconclusive: Technically the member function 'CircularBuffer::get_gbeg1' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:185:26: note: Technically the member function 'CircularBuffer::get_gbeg1' can be const.
vt-0.57721/circular_buffer.h:162:14: note: Technically the member function 'CircularBuffer::get_gbeg1' can be const.
vt-0.57721/circular_buffer.h:182:14: style:inconclusive: Technically the member function 'CircularBuffer::begin' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:224:26: note: Technically the member function 'CircularBuffer::begin' can be const.
vt-0.57721/circular_buffer.h:182:14: note: Technically the member function 'CircularBuffer::begin' can be const.
vt-0.57721/circular_buffer.h:187:14: style:inconclusive: Technically the member function 'CircularBuffer::end' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:232:26: note: Technically the member function 'CircularBuffer::end' can be const.
vt-0.57721/circular_buffer.h:187:14: note: Technically the member function 'CircularBuffer::end' can be const.
vt-0.57721/circular_buffer.h:192:14: style:inconclusive: Technically the member function 'CircularBuffer::inc' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:169:26: note: Technically the member function 'CircularBuffer::inc' can be const.
vt-0.57721/circular_buffer.h:192:14: note: Technically the member function 'CircularBuffer::inc' can be const.
vt-0.57721/circular_buffer.h:207:14: style:inconclusive: Technically the member function 'CircularBuffer::inc' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:264:26: note: Technically the member function 'CircularBuffer::inc' can be const.
vt-0.57721/circular_buffer.h:207:14: note: Technically the member function 'CircularBuffer::inc' can be const.
vt-0.57721/circular_buffer.h:217:14: style:inconclusive: Technically the member function 'CircularBuffer::diff' can be const. [functionConst]
vt-0.57721/circular_buffer.cpp:240:26: note: Technically the member function 'CircularBuffer::diff' can be const.
vt-0.57721/circular_buffer.h:217:14: note: Technically the member function 'CircularBuffer::diff' can be const.
vt-0.57721/circular_buffer.h:97:5: style: Class 'CircularBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/circular_buffer.cpp:159:13: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/circular_buffer.cpp:159:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/circular_buffer.cpp:278:9: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/circular_buffer.cpp:83:49: style: Parameter 'ref_fasta_file' can be declared as reference to const [constParameterReference]
vt-0.57721/circular_buffer.cpp:123:45: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/circular_buffer.cpp:272:46: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/circular_buffer.cpp:272:63: style: Parameter 'pos1' can be declared as reference to const [constParameterReference]
vt-0.57721/complex_genotyping_record.cpp:339:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/complex_genotyping_record.cpp:624:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/complex_genotyping_record.cpp:390:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/complex_genotyping_record.cpp:391:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/complex_genotyping_record.cpp:392:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/complex_genotyping_record.cpp:393:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::h' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::rid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::pos1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::vtype' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::dlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::n_filter' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::bqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::bqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::mqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::mqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::cyr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::cyr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::str_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::str_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::nmr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::nmr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::ior_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::ior_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::nm0_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::nm0_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::nm1_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::nm1_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::abe_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::abe_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::abz_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::abz_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::ns_nref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::dp_sum' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::max_gq' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_dp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_dp_ra' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_bq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_bq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_mq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_mq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_cy_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_cy_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_st_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_st_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_al_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_bq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_mq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_cy_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_st_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_nm_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_nm_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_nm_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_oth_exp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_oth_obs_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:117:5: warning:inconclusive: Member variable 'ComplexGenotypingRecord::tmp_ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/complex_genotyping_record.h:46:16: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'h' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:49:16: note: Parent variable 'GenotypingRecord::h'
vt-0.57721/complex_genotyping_record.h:46:16: note: Derived variable 'ComplexGenotypingRecord::h'
vt-0.57721/complex_genotyping_record.h:48:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'rid' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:51:13: note: Parent variable 'GenotypingRecord::rid'
vt-0.57721/complex_genotyping_record.h:48:13: note: Derived variable 'ComplexGenotypingRecord::rid'
vt-0.57721/complex_genotyping_record.h:49:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'pos1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:52:13: note: Parent variable 'GenotypingRecord::pos1'
vt-0.57721/complex_genotyping_record.h:49:13: note: Derived variable 'ComplexGenotypingRecord::pos1'
vt-0.57721/complex_genotyping_record.h:60:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'beg1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:63:13: note: Parent variable 'GenotypingRecord::beg1'
vt-0.57721/complex_genotyping_record.h:60:13: note: Derived variable 'ComplexGenotypingRecord::beg1'
vt-0.57721/complex_genotyping_record.h:61:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'end1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:64:13: note: Parent variable 'GenotypingRecord::end1'
vt-0.57721/complex_genotyping_record.h:61:13: note: Derived variable 'ComplexGenotypingRecord::end1'
vt-0.57721/complex_genotyping_record.h:62:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'vtype' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:65:13: note: Parent variable 'GenotypingRecord::vtype'
vt-0.57721/complex_genotyping_record.h:62:13: note: Derived variable 'ComplexGenotypingRecord::vtype'
vt-0.57721/complex_genotyping_record.h:65:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'dlen' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:68:13: note: Parent variable 'GenotypingRecord::dlen'
vt-0.57721/complex_genotyping_record.h:65:13: note: Derived variable 'ComplexGenotypingRecord::dlen'
vt-0.57721/complex_genotyping_record.h:66:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'len' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:69:13: note: Parent variable 'GenotypingRecord::len'
vt-0.57721/complex_genotyping_record.h:66:13: note: Derived variable 'ComplexGenotypingRecord::len'
vt-0.57721/complex_genotyping_record.h:67:17: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'indel' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:70:17: note: Parent variable 'GenotypingRecord::indel'
vt-0.57721/complex_genotyping_record.h:67:17: note: Derived variable 'ComplexGenotypingRecord::indel'
vt-0.57721/complex_genotyping_record.h:70:17: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'motif' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:73:17: note: Parent variable 'GenotypingRecord::motif'
vt-0.57721/complex_genotyping_record.h:70:17: note: Derived variable 'ComplexGenotypingRecord::motif'
vt-0.57721/complex_genotyping_record.h:76:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'nsamples' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:100:13: note: Parent variable 'GenotypingRecord::nsamples'
vt-0.57721/complex_genotyping_record.h:76:13: note: Derived variable 'ComplexGenotypingRecord::nsamples'
vt-0.57721/complex_genotyping_record.h:77:15: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'alleles' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:101:15: note: Parent variable 'GenotypingRecord::alleles'
vt-0.57721/complex_genotyping_record.h:77:15: note: Derived variable 'ComplexGenotypingRecord::alleles'
vt-0.57721/complex_genotyping_record.h:78:30: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'v_alleles' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:102:30: note: Parent variable 'GenotypingRecord::v_alleles'
vt-0.57721/complex_genotyping_record.h:78:30: note: Derived variable 'ComplexGenotypingRecord::v_alleles'
vt-0.57721/complex_genotyping_record.h:79:14: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'n_filter' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:103:14: note: Parent variable 'GenotypingRecord::n_filter'
vt-0.57721/complex_genotyping_record.h:79:14: note: Derived variable 'ComplexGenotypingRecord::n_filter'
vt-0.57721/complex_genotyping_record.h:81:14: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'pls' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:105:14: note: Parent variable 'GenotypingRecord::pls'
vt-0.57721/complex_genotyping_record.h:81:14: note: Derived variable 'ComplexGenotypingRecord::pls'
vt-0.57721/complex_genotyping_record.h:82:14: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'ads' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:106:14: note: Parent variable 'GenotypingRecord::ads'
vt-0.57721/complex_genotyping_record.h:82:14: note: Derived variable 'ComplexGenotypingRecord::ads'
vt-0.57721/complex_genotyping_record.h:85:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'bqr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:109:11: note: Parent variable 'GenotypingRecord::bqr_num'
vt-0.57721/complex_genotyping_record.h:85:11: note: Derived variable 'ComplexGenotypingRecord::bqr_num'
vt-0.57721/complex_genotyping_record.h:85:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'bqr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:109:20: note: Parent variable 'GenotypingRecord::bqr_den'
vt-0.57721/complex_genotyping_record.h:85:20: note: Derived variable 'ComplexGenotypingRecord::bqr_den'
vt-0.57721/complex_genotyping_record.h:86:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'mqr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:110:11: note: Parent variable 'GenotypingRecord::mqr_num'
vt-0.57721/complex_genotyping_record.h:86:11: note: Derived variable 'ComplexGenotypingRecord::mqr_num'
vt-0.57721/complex_genotyping_record.h:86:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'mqr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:110:20: note: Parent variable 'GenotypingRecord::mqr_den'
vt-0.57721/complex_genotyping_record.h:86:20: note: Derived variable 'ComplexGenotypingRecord::mqr_den'
vt-0.57721/complex_genotyping_record.h:87:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'cyr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:111:11: note: Parent variable 'GenotypingRecord::cyr_num'
vt-0.57721/complex_genotyping_record.h:87:11: note: Derived variable 'ComplexGenotypingRecord::cyr_num'
vt-0.57721/complex_genotyping_record.h:87:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'cyr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:111:20: note: Parent variable 'GenotypingRecord::cyr_den'
vt-0.57721/complex_genotyping_record.h:87:20: note: Derived variable 'ComplexGenotypingRecord::cyr_den'
vt-0.57721/complex_genotyping_record.h:88:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'str_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:112:11: note: Parent variable 'GenotypingRecord::str_num'
vt-0.57721/complex_genotyping_record.h:88:11: note: Derived variable 'ComplexGenotypingRecord::str_num'
vt-0.57721/complex_genotyping_record.h:88:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'str_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:112:20: note: Parent variable 'GenotypingRecord::str_den'
vt-0.57721/complex_genotyping_record.h:88:20: note: Derived variable 'ComplexGenotypingRecord::str_den'
vt-0.57721/complex_genotyping_record.h:89:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'nmr_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:113:11: note: Parent variable 'GenotypingRecord::nmr_num'
vt-0.57721/complex_genotyping_record.h:89:11: note: Derived variable 'ComplexGenotypingRecord::nmr_num'
vt-0.57721/complex_genotyping_record.h:89:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'nmr_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:113:20: note: Parent variable 'GenotypingRecord::nmr_den'
vt-0.57721/complex_genotyping_record.h:89:20: note: Derived variable 'ComplexGenotypingRecord::nmr_den'
vt-0.57721/complex_genotyping_record.h:90:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'ior_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:114:11: note: Parent variable 'GenotypingRecord::ior_num'
vt-0.57721/complex_genotyping_record.h:90:11: note: Derived variable 'ComplexGenotypingRecord::ior_num'
vt-0.57721/complex_genotyping_record.h:90:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'ior_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:114:20: note: Parent variable 'GenotypingRecord::ior_den'
vt-0.57721/complex_genotyping_record.h:90:20: note: Derived variable 'ComplexGenotypingRecord::ior_den'
vt-0.57721/complex_genotyping_record.h:91:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'nm0_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:115:11: note: Parent variable 'GenotypingRecord::nm0_num'
vt-0.57721/complex_genotyping_record.h:91:11: note: Derived variable 'ComplexGenotypingRecord::nm0_num'
vt-0.57721/complex_genotyping_record.h:91:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'nm0_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:115:20: note: Parent variable 'GenotypingRecord::nm0_den'
vt-0.57721/complex_genotyping_record.h:91:20: note: Derived variable 'ComplexGenotypingRecord::nm0_den'
vt-0.57721/complex_genotyping_record.h:92:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'nm1_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:116:11: note: Parent variable 'GenotypingRecord::nm1_num'
vt-0.57721/complex_genotyping_record.h:92:11: note: Derived variable 'ComplexGenotypingRecord::nm1_num'
vt-0.57721/complex_genotyping_record.h:92:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'nm1_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:116:20: note: Parent variable 'GenotypingRecord::nm1_den'
vt-0.57721/complex_genotyping_record.h:92:20: note: Derived variable 'ComplexGenotypingRecord::nm1_den'
vt-0.57721/complex_genotyping_record.h:93:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'abe_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:117:11: note: Parent variable 'GenotypingRecord::abe_num'
vt-0.57721/complex_genotyping_record.h:93:11: note: Derived variable 'ComplexGenotypingRecord::abe_num'
vt-0.57721/complex_genotyping_record.h:93:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'abe_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:117:20: note: Parent variable 'GenotypingRecord::abe_den'
vt-0.57721/complex_genotyping_record.h:93:20: note: Derived variable 'ComplexGenotypingRecord::abe_den'
vt-0.57721/complex_genotyping_record.h:94:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'abz_num' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:118:11: note: Parent variable 'GenotypingRecord::abz_num'
vt-0.57721/complex_genotyping_record.h:94:11: note: Derived variable 'ComplexGenotypingRecord::abz_num'
vt-0.57721/complex_genotyping_record.h:94:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'abz_den' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:118:20: note: Parent variable 'GenotypingRecord::abz_den'
vt-0.57721/complex_genotyping_record.h:94:20: note: Derived variable 'ComplexGenotypingRecord::abz_den'
vt-0.57721/complex_genotyping_record.h:95:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'ns_nref' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:11: note: Parent variable 'GenotypingRecord::ns_nref'
vt-0.57721/complex_genotyping_record.h:95:11: note: Derived variable 'ComplexGenotypingRecord::ns_nref'
vt-0.57721/complex_genotyping_record.h:95:20: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'dp_sum' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:20: note: Parent variable 'GenotypingRecord::dp_sum'
vt-0.57721/complex_genotyping_record.h:95:20: note: Derived variable 'ComplexGenotypingRecord::dp_sum'
vt-0.57721/complex_genotyping_record.h:95:28: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'max_gq' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:119:28: note: Parent variable 'GenotypingRecord::max_gq'
vt-0.57721/complex_genotyping_record.h:95:28: note: Derived variable 'ComplexGenotypingRecord::max_gq'
vt-0.57721/complex_genotyping_record.h:97:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_dp_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:122:13: note: Parent variable 'GenotypingRecord::tmp_dp_q20'
vt-0.57721/complex_genotyping_record.h:97:13: note: Derived variable 'ComplexGenotypingRecord::tmp_dp_q20'
vt-0.57721/complex_genotyping_record.h:98:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_dp_ra' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:123:13: note: Parent variable 'GenotypingRecord::tmp_dp_ra'
vt-0.57721/complex_genotyping_record.h:98:13: note: Derived variable 'ComplexGenotypingRecord::tmp_dp_ra'
vt-0.57721/complex_genotyping_record.h:99:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_bq_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:124:13: note: Parent variable 'GenotypingRecord::tmp_bq_s1'
vt-0.57721/complex_genotyping_record.h:99:13: note: Derived variable 'ComplexGenotypingRecord::tmp_bq_s1'
vt-0.57721/complex_genotyping_record.h:99:24: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_bq_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:124:24: note: Parent variable 'GenotypingRecord::tmp_bq_s2'
vt-0.57721/complex_genotyping_record.h:99:24: note: Derived variable 'ComplexGenotypingRecord::tmp_bq_s2'
vt-0.57721/complex_genotyping_record.h:100:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_mq_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:125:13: note: Parent variable 'GenotypingRecord::tmp_mq_s1'
vt-0.57721/complex_genotyping_record.h:100:13: note: Derived variable 'ComplexGenotypingRecord::tmp_mq_s1'
vt-0.57721/complex_genotyping_record.h:100:24: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_mq_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:125:24: note: Parent variable 'GenotypingRecord::tmp_mq_s2'
vt-0.57721/complex_genotyping_record.h:100:24: note: Derived variable 'ComplexGenotypingRecord::tmp_mq_s2'
vt-0.57721/complex_genotyping_record.h:101:11: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_cy_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:126:11: note: Parent variable 'GenotypingRecord::tmp_cy_s1'
vt-0.57721/complex_genotyping_record.h:101:11: note: Derived variable 'ComplexGenotypingRecord::tmp_cy_s1'
vt-0.57721/complex_genotyping_record.h:101:22: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_cy_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:126:22: note: Parent variable 'GenotypingRecord::tmp_cy_s2'
vt-0.57721/complex_genotyping_record.h:101:22: note: Derived variable 'ComplexGenotypingRecord::tmp_cy_s2'
vt-0.57721/complex_genotyping_record.h:102:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_st_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:127:13: note: Parent variable 'GenotypingRecord::tmp_st_s1'
vt-0.57721/complex_genotyping_record.h:102:13: note: Derived variable 'ComplexGenotypingRecord::tmp_st_s1'
vt-0.57721/complex_genotyping_record.h:102:24: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_st_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:127:24: note: Parent variable 'GenotypingRecord::tmp_st_s2'
vt-0.57721/complex_genotyping_record.h:102:24: note: Derived variable 'ComplexGenotypingRecord::tmp_st_s2'
vt-0.57721/complex_genotyping_record.h:103:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_al_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:13: note: Parent variable 'GenotypingRecord::tmp_al_s1'
vt-0.57721/complex_genotyping_record.h:103:13: note: Derived variable 'ComplexGenotypingRecord::tmp_al_s1'
vt-0.57721/complex_genotyping_record.h:103:24: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_bq_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:24: note: Parent variable 'GenotypingRecord::tmp_bq_al'
vt-0.57721/complex_genotyping_record.h:103:24: note: Derived variable 'ComplexGenotypingRecord::tmp_bq_al'
vt-0.57721/complex_genotyping_record.h:103:35: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_mq_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:128:35: note: Parent variable 'GenotypingRecord::tmp_mq_al'
vt-0.57721/complex_genotyping_record.h:103:35: note: Derived variable 'ComplexGenotypingRecord::tmp_mq_al'
vt-0.57721/complex_genotyping_record.h:104:12: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_cy_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:129:12: note: Parent variable 'GenotypingRecord::tmp_cy_al'
vt-0.57721/complex_genotyping_record.h:104:12: note: Derived variable 'ComplexGenotypingRecord::tmp_cy_al'
vt-0.57721/complex_genotyping_record.h:105:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_st_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:130:13: note: Parent variable 'GenotypingRecord::tmp_st_al'
vt-0.57721/complex_genotyping_record.h:105:13: note: Derived variable 'ComplexGenotypingRecord::tmp_st_al'
vt-0.57721/complex_genotyping_record.h:105:24: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_nm_al' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:130:24: note: Parent variable 'GenotypingRecord::tmp_nm_al'
vt-0.57721/complex_genotyping_record.h:105:24: note: Derived variable 'ComplexGenotypingRecord::tmp_nm_al'
vt-0.57721/complex_genotyping_record.h:106:13: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_nm_s1' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:131:13: note: Parent variable 'GenotypingRecord::tmp_nm_s1'
vt-0.57721/complex_genotyping_record.h:106:13: note: Derived variable 'ComplexGenotypingRecord::tmp_nm_s1'
vt-0.57721/complex_genotyping_record.h:106:24: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_nm_s2' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:131:24: note: Parent variable 'GenotypingRecord::tmp_nm_s2'
vt-0.57721/complex_genotyping_record.h:106:24: note: Derived variable 'ComplexGenotypingRecord::tmp_nm_s2'
vt-0.57721/complex_genotyping_record.h:107:12: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_oth_exp_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:132:12: note: Parent variable 'GenotypingRecord::tmp_oth_exp_q20'
vt-0.57721/complex_genotyping_record.h:107:12: note: Derived variable 'ComplexGenotypingRecord::tmp_oth_exp_q20'
vt-0.57721/complex_genotyping_record.h:107:29: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_oth_obs_q20' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:132:29: note: Parent variable 'GenotypingRecord::tmp_oth_obs_q20'
vt-0.57721/complex_genotyping_record.h:107:29: note: Derived variable 'ComplexGenotypingRecord::tmp_oth_obs_q20'
vt-0.57721/complex_genotyping_record.h:108:12: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_pls' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:133:12: note: Parent variable 'GenotypingRecord::tmp_pls'
vt-0.57721/complex_genotyping_record.h:108:12: note: Derived variable 'ComplexGenotypingRecord::tmp_pls'
vt-0.57721/complex_genotyping_record.h:109:12: warning: The class 'ComplexGenotypingRecord' defines member variable with name 'tmp_ads' also defined in its parent class 'GenotypingRecord'. [duplInheritedMember]
vt-0.57721/genotyping_record.h:134:12: note: Parent variable 'GenotypingRecord::tmp_ads'
vt-0.57721/complex_genotyping_record.h:109:12: note: Derived variable 'ComplexGenotypingRecord::tmp_ads'
vt-0.57721/complex_genotyping_record.h:128:10: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:161:18: note: Virtual function in base class
vt-0.57721/complex_genotyping_record.h:128:10: note: Function in derived class
vt-0.57721/complex_genotyping_record.h:129:10: style: The function 'clearTemp' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:166:18: note: Virtual function in base class
vt-0.57721/complex_genotyping_record.h:129:10: note: Function in derived class
vt-0.57721/complex_genotyping_record.h:130:13: style: The function 'flush_variant' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:172:21: note: Virtual function in base class
vt-0.57721/complex_genotyping_record.h:130:13: note: Function in derived class
vt-0.57721/complex_genotyping_record.h:131:10: style: The function 'flush_sample' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:177:18: note: Virtual function in base class
vt-0.57721/complex_genotyping_record.h:131:10: note: Function in derived class
vt-0.57721/complex_genotyping_record.h:132:10: style: The function 'add_allele' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:182:18: note: Virtual function in base class
vt-0.57721/complex_genotyping_record.h:132:10: note: Function in derived class
vt-0.57721/complex_genotyping_record.h:133:10: style: The function 'process_read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:187:18: note: Virtual function in base class
vt-0.57721/complex_genotyping_record.h:133:10: note: Function in derived class
vt-0.57721/complex_genotyping_record.h:138:6: style: The destructor '~ComplexGenotypingRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
vt-0.57721/genotyping_record.h:156:14: note: Virtual destructor in base class
vt-0.57721/complex_genotyping_record.h:138:6: note: Destructor in derived class
vt-0.57721/complex_genotyping_record.cpp:124:11: style: C-style pointer casting [cstyleCast]
vt-0.57721/complex_genotyping_record.cpp:125:11: style: C-style pointer casting [cstyleCast]
vt-0.57721/complex_genotyping_record.cpp:190:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/complex_genotyping_record.cpp:191:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/complex_genotyping_record.cpp:192:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/complex_genotyping_record.cpp:193:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/complex_genotyping_record.cpp:194:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/complex_genotyping_record.cpp:197:12: style: The scope of the variable 'gp' can be reduced. [variableScope]
vt-0.57721/complex_genotyping_record.cpp:197:16: style: The scope of the variable 'gp_sum' can be reduced. [variableScope]
vt-0.57721/complex_genotyping_record.cpp:197:24: style: The scope of the variable 'max_gp' can be reduced. [variableScope]
vt-0.57721/complex_genotyping_record.cpp:198:13: style: The scope of the variable 'best_gt' can be reduced. [variableScope]
vt-0.57721/complex_genotyping_record.cpp:199:13: style: The scope of the variable 'best_a1' can be reduced. [variableScope]
vt-0.57721/complex_genotyping_record.cpp:199:22: style: The scope of the variable 'best_a2' can be reduced. [variableScope]
vt-0.57721/complex_genotyping_record.cpp:528:22: style: The scope of the variable 'cycle' can be reduced. [variableScope]
vt-0.57721/complex_genotyping_record.cpp:653:22: style: The scope of the variable 'cycle' can be reduced. [variableScope]
vt-0.57721/complex_genotyping_record.cpp:110:15: style: Local variable 'motif' shadows outer variable [shadowVariable]
vt-0.57721/complex_genotyping_record.h:70:17: note: Shadowed declaration
vt-0.57721/complex_genotyping_record.cpp:110:15: note: Shadow variable
vt-0.57721/complex_genotyping_record.cpp:205:13: style: Local variable 'max_gq' shadows outer variable [shadowVariable]
vt-0.57721/complex_genotyping_record.h:95:28: note: Shadowed declaration
vt-0.57721/complex_genotyping_record.cpp:205:13: note: Shadow variable
vt-0.57721/complex_genotyping_record.cpp:206:13: style: Local variable 'dp_sum' shadows outer variable [shadowVariable]
vt-0.57721/complex_genotyping_record.h:95:20: note: Shadowed declaration
vt-0.57721/complex_genotyping_record.cpp:206:13: note: Shadow variable
vt-0.57721/complex_genotyping_record.cpp:221:18: style: Variable 'pli' can be declared as pointer to const [constVariablePointer]
vt-0.57721/complex_genotyping_record.cpp:222:30: style: Variable 'gp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:200:14: style: Unused variable: pls_i [unusedVariable]
vt-0.57721/complex_genotyping_record.cpp:522:26: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:523:27: style: Variable 'qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:528:28: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:552:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:561:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:581:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:588:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:609:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:617:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:647:26: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:648:27: style: Variable 'qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:653:28: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:677:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:686:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:706:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:713:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:734:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/complex_genotyping_record.cpp:742:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/compute_concordance.h:29:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
vt-0.57721/compute_features.cpp:103:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features.cpp:156:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features.cpp:192:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features.cpp:326:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features.cpp:336:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::imap' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:72:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features.cpp:74:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/compute_features.cpp:334:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/compute_features.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/compute_features.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/compute_features.cpp:108:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/compute_features.cpp:108:10: note: Derived function 'Igor::initialize'
vt-0.57721/compute_features.cpp:324:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/compute_features.cpp:324:10: note: Derived function 'Igor::print_options'
vt-0.57721/compute_features.cpp:334:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/compute_features.cpp:334:10: note: Derived function 'Igor::print_stats'
vt-0.57721/compute_features.cpp:41:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/compute_features.cpp:42:17: style: class member 'Igor::arg_sample_list' is never used. [unusedStructMember]
vt-0.57721/compute_features.cpp:43:12: style: class member 'Igor::samples' is never used. [unusedStructMember]
vt-0.57721/compute_features.cpp:44:14: style: class member 'Igor::imap' is never used. [unusedStructMember]
vt-0.57721/compute_features.cpp:45:13: style: class member 'Igor::nsamples' is never used. [unusedStructMember]
vt-0.57721/compute_features.cpp:218:50: style: Variable 'g[i]' is assigned a value that is never used. [unreadVariable]
vt-0.57721/compute_features.cpp:184:18: style: Variable 'printed' is assigned a value that is never used. [unreadVariable]
vt-0.57721/compute_features2.cpp:103:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features2.cpp:158:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features2.cpp:194:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features2.cpp:328:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features2.cpp:338:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::imap' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:72:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_features2.cpp:74:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/compute_features2.cpp:336:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/compute_features2.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/compute_features2.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/compute_features2.cpp:108:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/compute_features2.cpp:108:10: note: Derived function 'Igor::initialize'
vt-0.57721/compute_features2.cpp:326:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/compute_features2.cpp:326:10: note: Derived function 'Igor::print_options'
vt-0.57721/compute_features2.cpp:336:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/compute_features2.cpp:336:10: note: Derived function 'Igor::print_stats'
vt-0.57721/compute_features2.cpp:41:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/compute_features2.cpp:42:17: style: class member 'Igor::arg_sample_list' is never used. [unusedStructMember]
vt-0.57721/compute_features2.cpp:43:12: style: class member 'Igor::samples' is never used. [unusedStructMember]
vt-0.57721/compute_features2.cpp:44:14: style: class member 'Igor::imap' is never used. [unusedStructMember]
vt-0.57721/compute_features2.cpp:45:13: style: class member 'Igor::nsamples' is never used. [unusedStructMember]
vt-0.57721/compute_features2.cpp:220:50: style: Variable 'g[i]' is assigned a value that is never used. [unreadVariable]
vt-0.57721/compute_features2.cpp:186:18: style: Variable 'printed' is assigned a value that is never used. [unreadVariable]
vt-0.57721/compute_rl_dist.cpp:71:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_rl_dist.cpp:158:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_rl_dist.cpp:183:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_rl_dist.cpp:217:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/compute_rl_dist.cpp:43:5: warning: Member variable 'Igor::rs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_rl_dist.cpp:43:5: warning: Member variable 'Igor::no' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/compute_rl_dist.cpp:93:17: performance:inconclusive: Technically the member function '::Igor::canonicalize' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/compute_rl_dist.cpp:286:10: performance:inconclusive: Technically the member function '::Igor::print_options' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/compute_rl_dist.cpp:304:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/compute_rl_dist.cpp:76:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/compute_rl_dist.cpp:76:10: note: Derived function 'Igor::initialize'
vt-0.57721/compute_rl_dist.cpp:286:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/compute_rl_dist.cpp:286:10: note: Derived function 'Igor::print_options'
vt-0.57721/compute_rl_dist.cpp:304:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/compute_rl_dist.cpp:304:10: note: Derived function 'Igor::print_stats'
vt-0.57721/compute_rl_dist.cpp:93:43: style: Parameter 'motif' can be declared as reference to const [constParameterReference]
vt-0.57721/compute_rl_dist.cpp:153:35: style: Variable 'v' can be declared as reference to const [constVariableReference]
vt-0.57721/compute_rl_dist.cpp:178:35: style: Variable 'v' can be declared as reference to const [constVariableReference]
vt-0.57721/compute_rl_dist.cpp:41:14: style: class member 'Igor::no' is never used. [unusedStructMember]
vt-0.57721/config.cpp:58:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/config.cpp:91:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/config.cpp:153:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/config.cpp:63:10: performance:inconclusive: Technically the member function '::Igor::initialize' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/config.cpp:67:10: style:inconclusive: Technically the member function '::Igor::config' can be const. [functionConst]
vt-0.57721/config.cpp:151:10: style:inconclusive: Technically the member function '::Igor::print_options' can be const. [functionConst]
vt-0.57721/config.cpp:159:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/config.cpp:63:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/config.cpp:63:10: note: Derived function 'Igor::initialize'
vt-0.57721/config.cpp:151:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/config.cpp:151:10: note: Derived function 'Igor::print_options'
vt-0.57721/config.cpp:159:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/config.cpp:159:10: note: Derived function 'Igor::print_stats'
vt-0.57721/config.cpp:89:13: style: Redundant initialization for 'ret'. The initialized value is overwritten before it is read. [redundantInitialization]
vt-0.57721/config.cpp:82:20: note: ret is initialized
vt-0.57721/config.cpp:89:13: note: ret is overwritten
vt-0.57721/config.cpp:98:13: style: Variable 'ret' is reassigned a value before the old one has been used. [redundantAssignment]
vt-0.57721/config.cpp:89:13: note: ret is assigned
vt-0.57721/config.cpp:98:13: note: ret is overwritten
vt-0.57721/config.cpp:105:13: style: Variable 'ret' is reassigned a value before the old one has been used. [redundantAssignment]
vt-0.57721/config.cpp:98:13: note: ret is assigned
vt-0.57721/config.cpp:105:13: note: ret is overwritten
vt-0.57721/config.cpp:122:13: style: Variable 'ret' is reassigned a value before the old one has been used. [redundantAssignment]
vt-0.57721/config.cpp:105:13: note: ret is assigned
vt-0.57721/config.cpp:122:13: note: ret is overwritten
vt-0.57721/config.cpp:129:13: style: Variable 'ret' is reassigned a value before the old one has been used. [redundantAssignment]
vt-0.57721/config.cpp:122:13: note: ret is assigned
vt-0.57721/config.cpp:129:13: note: ret is overwritten
vt-0.57721/config.cpp:138:13: style: Variable 'ret' is reassigned a value before the old one has been used. [redundantAssignment]
vt-0.57721/config.cpp:129:13: note: ret is assigned
vt-0.57721/config.cpp:138:13: note: ret is overwritten
vt-0.57721/config.cpp:145:13: style: Variable 'ret' is reassigned a value before the old one has been used. [redundantAssignment]
vt-0.57721/config.cpp:138:13: note: ret is assigned
vt-0.57721/config.cpp:145:13: note: ret is overwritten
vt-0.57721/config.cpp:145:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/consolidate.cpp:121:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate.cpp:177:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate.cpp:232:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate.cpp:414:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate.cpp:492:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable allele [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate.cpp:847:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate.cpp:860:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::overlap_snp' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::overlap_indel' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::overlap_vntr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::overlap_snp_id' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::overlap_indel_id' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::overlap_vntr_id' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::no_total_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::no_nonoverlap_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::no_overlap_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::no_new_multiallelic_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::no_new_multiallelic_indels' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::no_new_multiallelic_vntr_indels' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::no_overlap_vntrs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:81:5: warning: Member variable 'Igor::fai' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate.cpp:129:12: performance:inconclusive: Technically the member function '::Igor::compute_glfsingle_llr' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/consolidate.cpp:845:10: style:inconclusive: Technically the member function '::Igor::print_options' can be const. [functionConst]
vt-0.57721/consolidate.cpp:858:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/consolidate.cpp:156:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/consolidate.cpp:156:10: note: Derived function 'Igor::initialize'
vt-0.57721/consolidate.cpp:845:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/consolidate.cpp:845:10: note: Derived function 'Igor::print_options'
vt-0.57721/consolidate.cpp:858:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/consolidate.cpp:858:10: note: Derived function 'Igor::print_stats'
vt-0.57721/consolidate.cpp:239:40: style: Condition 'variant->end1>=cvariant->beg1' is always true [knownConditionTrueFalse]
vt-0.57721/consolidate.cpp:230:35: note: Assuming that condition 'variant->end1<cvariant->beg1' is not redundant
vt-0.57721/consolidate.cpp:239:40: note: Condition 'variant->end1>=cvariant->beg1' is always true
vt-0.57721/consolidate.cpp:514:29: style: Variable 'alts[i]' is reassigned a value before the old one has been used. [redundantAssignment]
vt-0.57721/consolidate.cpp:512:33: note: alts[i] is assigned
vt-0.57721/consolidate.cpp:514:29: note: alts[i] is overwritten
vt-0.57721/consolidate.cpp:796:18: style: The scope of the variable 'variant' can be reduced. [variableScope]
vt-0.57721/consolidate.cpp:807:24: style: The scope of the variable 'ln_lr' can be reduced. [variableScope]
vt-0.57721/consolidate.cpp:204:15: style: Variable 'tr' can be declared as pointer to const [constVariablePointer]
vt-0.57721/consolidate.cpp:396:40: style: Parameter 'var' can be declared as pointer to const [constParameterPointer]
vt-0.57721/consolidate.cpp:79:13: style: class member 'Igor::lt' is never used. [unusedStructMember]
vt-0.57721/consolidate.cpp:205:19: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
vt-0.57721/consolidate.cpp:204:15: style: Variable 'tr' is assigned a value that is never used. [unreadVariable]
vt-0.57721/consolidate.cpp:734:22: style: Unused variable: alts [unusedVariable]
vt-0.57721/consolidate.cpp:807:30: style: Variable 'ln_lr' is assigned a value that is never used. [unreadVariable]
vt-0.57721/consolidate_adjacent_vntrs.cpp:83:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_adjacent_vntrs.cpp:121:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_adjacent_vntrs.cpp:131:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_adjacent_vntrs.cpp:48:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate_adjacent_vntrs.cpp:48:5: warning: Member variable 'Igor::vc' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_consolidator.h:52:10: style:inconclusive: Technically the member function 'CompareBasisProportion::operator()' can be const. [functionConst]
vt-0.57721/consolidate_adjacent_vntrs.cpp:129:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/consolidate_adjacent_vntrs.cpp:88:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/consolidate_adjacent_vntrs.cpp:88:10: note: Derived function 'Igor::initialize'
vt-0.57721/consolidate_adjacent_vntrs.cpp:119:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/consolidate_adjacent_vntrs.cpp:119:10: note: Derived function 'Igor::print_options'
vt-0.57721/consolidate_adjacent_vntrs.cpp:129:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/consolidate_adjacent_vntrs.cpp:129:10: note: Derived function 'Igor::print_stats'
vt-0.57721/consolidate_adjacent_vntrs.cpp:102:18: style: The scope of the variable 'variant' can be reduced. [variableScope]
vt-0.57721/vntr_consolidator.h:52:39: style: Parameter 'a' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr_consolidator.h:52:60: style: Parameter 'b' can be declared as reference to const [constParameterReference]
vt-0.57721/consolidate_multiallelics.cpp:103:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_multiallelics.cpp:132:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_multiallelics.cpp:145:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_multiallelics.cpp:69:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate_multiallelics.cpp:69:5: warning: Member variable 'Igor::mc' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate_multiallelics.cpp:69:5: warning: Member variable 'Igor::no_vntrs_annotated' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate_multiallelics.cpp:69:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate_multiallelics.cpp:69:5: warning: Member variable 'Igor::rs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate_multiallelics.cpp:71:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/consolidate_multiallelics.cpp:143:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/consolidate_multiallelics.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/consolidate_multiallelics.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/consolidate_multiallelics.cpp:112:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/consolidate_multiallelics.cpp:112:10: note: Derived function 'Igor::initialize'
vt-0.57721/consolidate_multiallelics.cpp:130:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/consolidate_multiallelics.cpp:130:10: note: Derived function 'Igor::print_options'
vt-0.57721/consolidate_multiallelics.cpp:143:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/consolidate_multiallelics.cpp:143:10: note: Derived function 'Igor::print_stats'
vt-0.57721/consolidate_multiallelics.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/consolidate_multiallelics.cpp:61:13: style: class member 'Igor::no_vntrs_annotated' is never used. [unusedStructMember]
vt-0.57721/consolidate_multiallelics.cpp:66:19: style: class member 'Igor::vm' is never used. [unusedStructMember]
vt-0.57721/consolidate_multiallelics.cpp:67:24: style: class member 'Igor::rs' is never used. [unusedStructMember]
vt-0.57721/consolidate_vntrs.cpp:83:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_vntrs.cpp:121:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_vntrs.cpp:131:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/consolidate_vntrs.cpp:48:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate_vntrs.cpp:48:5: warning: Member variable 'Igor::vc' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/consolidate_vntrs.cpp:129:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/consolidate_vntrs.cpp:88:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/consolidate_vntrs.cpp:88:10: note: Derived function 'Igor::initialize'
vt-0.57721/consolidate_vntrs.cpp:119:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/consolidate_vntrs.cpp:119:10: note: Derived function 'Igor::print_options'
vt-0.57721/consolidate_vntrs.cpp:129:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/consolidate_vntrs.cpp:129:10: note: Derived function 'Igor::print_stats'
vt-0.57721/consolidate_vntrs.cpp:102:18: style: The scope of the variable 'variant' can be reduced. [variableScope]
vt-0.57721/construct_probes.cpp:92:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/construct_probes.cpp:130:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/construct_probes.cpp:184:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/construct_probes.cpp:196:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/construct_probes.cpp:62:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/construct_probes.cpp:62:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/construct_probes.cpp:62:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/construct_probes.cpp:62:5: warning: Member variable 'Igor::no_probes_generated' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/construct_probes.cpp:62:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/construct_probes.cpp:62:5: warning: Member variable 'Igor::var_manip' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/construct_probes.cpp:194:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/construct_probes.cpp:97:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/construct_probes.cpp:97:10: note: Derived function 'Igor::initialize'
vt-0.57721/construct_probes.cpp:182:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/construct_probes.cpp:182:10: note: Derived function 'Igor::print_options'
vt-0.57721/construct_probes.cpp:194:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/construct_probes.cpp:194:10: note: Derived function 'Igor::print_stats'
vt-0.57721/decompose.cpp:107:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose.cpp:196:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose.cpp:974:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose.cpp:985:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::new_no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::no_biallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::no_multiallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::no_additional_biallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:75:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose.cpp:112:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/decompose.cpp:112:10: note: Derived function 'Igor::initialize'
vt-0.57721/decompose.cpp:972:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/decompose.cpp:972:10: note: Derived function 'Igor::print_options'
vt-0.57721/decompose.cpp:983:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/decompose.cpp:983:10: note: Derived function 'Igor::print_stats'
vt-0.57721/decompose.cpp:252:42: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:259:35: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:267:35: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:275:35: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:406:38: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:467:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:497:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:596:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:611:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:712:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:738:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:767:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:800:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:841:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:869:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:909:60: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose.cpp:715:59: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:715:59: note: Shadow variable
vt-0.57721/decompose.cpp:740:59: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:740:59: note: Shadow variable
vt-0.57721/decompose.cpp:771:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:771:63: note: Shadow variable
vt-0.57721/decompose.cpp:778:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:778:63: note: Shadow variable
vt-0.57721/decompose.cpp:804:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:804:63: note: Shadow variable
vt-0.57721/decompose.cpp:811:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:811:63: note: Shadow variable
vt-0.57721/decompose.cpp:845:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:845:63: note: Shadow variable
vt-0.57721/decompose.cpp:853:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:853:63: note: Shadow variable
vt-0.57721/decompose.cpp:873:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:873:63: note: Shadow variable
vt-0.57721/decompose.cpp:881:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:881:63: note: Shadow variable
vt-0.57721/decompose.cpp:911:59: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose.cpp:687:47: note: Shadowed declaration
vt-0.57721/decompose.cpp:911:59: note: Shadow variable
vt-0.57721/decompose.cpp:39:17: style: class member 'Igor::ref_fasta_file' is never used. [unusedStructMember]
vt-0.57721/decompose.cpp:65:14: style: class member 'Igor::new_no_variants' is never used. [unusedStructMember]
vt-0.57721/decompose.cpp:220:33: style: Variable 'rid' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose.cpp:221:34: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose.cpp:707:57: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose.cpp:734:57: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose.cpp:903:57: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose.cpp:906:64: style: Variable 'n_genotype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose2.cpp:94:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose2.cpp:214:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_FMT [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose2.cpp:936:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose2.cpp:947:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose2.cpp:66:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose2.cpp:66:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose2.cpp:66:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose2.cpp:66:5: warning: Member variable 'Igor::new_no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose2.cpp:66:5: warning: Member variable 'Igor::no_biallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose2.cpp:66:5: warning: Member variable 'Igor::no_multiallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose2.cpp:66:5: warning: Member variable 'Igor::no_additional_biallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose2.cpp:66:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose2.cpp:99:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/decompose2.cpp:99:10: note: Derived function 'Igor::initialize'
vt-0.57721/decompose2.cpp:934:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/decompose2.cpp:934:10: note: Derived function 'Igor::print_options'
vt-0.57721/decompose2.cpp:945:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/decompose2.cpp:945:10: note: Derived function 'Igor::print_stats'
vt-0.57721/decompose2.cpp:222:42: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:229:35: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:237:35: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:245:35: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:376:38: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:433:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:459:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:558:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:573:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:674:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:700:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:729:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:762:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:803:59: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:831:57: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:871:60: style: C-style pointer casting [cstyleCast]
vt-0.57721/decompose2.cpp:677:59: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:677:59: note: Shadow variable
vt-0.57721/decompose2.cpp:702:59: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:702:59: note: Shadow variable
vt-0.57721/decompose2.cpp:733:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:733:63: note: Shadow variable
vt-0.57721/decompose2.cpp:740:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:740:63: note: Shadow variable
vt-0.57721/decompose2.cpp:766:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:766:63: note: Shadow variable
vt-0.57721/decompose2.cpp:773:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:773:63: note: Shadow variable
vt-0.57721/decompose2.cpp:807:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:807:63: note: Shadow variable
vt-0.57721/decompose2.cpp:815:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:815:63: note: Shadow variable
vt-0.57721/decompose2.cpp:835:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:835:63: note: Shadow variable
vt-0.57721/decompose2.cpp:843:63: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:843:63: note: Shadow variable
vt-0.57721/decompose2.cpp:873:59: style: Local variable 'j' shadows outer variable [shadowVariable]
vt-0.57721/decompose2.cpp:649:47: note: Shadowed declaration
vt-0.57721/decompose2.cpp:873:59: note: Shadow variable
vt-0.57721/decompose2.cpp:39:17: style: class member 'Igor::ref_fasta_file' is never used. [unusedStructMember]
vt-0.57721/decompose2.cpp:56:14: style: class member 'Igor::new_no_variants' is never used. [unusedStructMember]
vt-0.57721/decompose2.cpp:64:19: style: class member 'Igor::vm' is never used. [unusedStructMember]
vt-0.57721/decompose2.cpp:190:33: style: Variable 'rid' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose2.cpp:191:34: style: Variable 'pos1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose2.cpp:669:57: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose2.cpp:696:57: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose2.cpp:865:57: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose2.cpp:868:64: style: Variable 'n_genotype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose_blocksub.cpp:112:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose_blocksub.cpp:159:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose_blocksub.cpp:362:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose_blocksub.cpp:374:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/decompose_blocksub.cpp:82:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose_blocksub.cpp:82:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose_blocksub.cpp:82:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose_blocksub.cpp:82:5: warning: Member variable 'Igor::no_additional_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose_blocksub.cpp:82:5: warning: Member variable 'Igor::no_biallelic_blocksub' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose_blocksub.cpp:82:5: warning: Member variable 'Igor::new_no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose_blocksub.cpp:82:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose_blocksub.cpp:82:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/decompose_blocksub.cpp:372:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/decompose_blocksub.cpp:117:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/decompose_blocksub.cpp:117:10: note: Derived function 'Igor::initialize'
vt-0.57721/decompose_blocksub.cpp:360:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/decompose_blocksub.cpp:360:10: note: Derived function 'Igor::print_options'
vt-0.57721/decompose_blocksub.cpp:372:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/decompose_blocksub.cpp:372:10: note: Derived function 'Igor::print_stats'
vt-0.57721/needle.h:63:5: style: Class 'NeedlemanWunsch' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/decompose_blocksub.cpp:238:29: style: The scope of the variable 'no_samples' can be reduced. [variableScope]
vt-0.57721/decompose_blocksub.cpp:223:24: style: Local variable 'allele' shadows outer variable [shadowVariable]
vt-0.57721/decompose_blocksub.cpp:162:20: note: Shadowed declaration
vt-0.57721/decompose_blocksub.cpp:223:24: note: Shadow variable
vt-0.57721/decompose_blocksub.cpp:289:24: style: Local variable 'allele' shadows outer variable [shadowVariable]
vt-0.57721/decompose_blocksub.cpp:162:20: note: Shadowed declaration
vt-0.57721/decompose_blocksub.cpp:289:24: note: Shadow variable
vt-0.57721/decompose_blocksub.cpp:56:17: style: class member 'Igor::ref_fasta_file' is never used. [unusedStructMember]
vt-0.57721/decompose_blocksub.cpp:80:19: style: class member 'Igor::vm' is never used. [unusedStructMember]
vt-0.57721/decompose_blocksub.cpp:221:29: style: Variable 'rid' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose_blocksub.cpp:259:36: style: Variable 'ploidy' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose_blocksub.cpp:284:29: style: Variable 'rid' is assigned a value that is never used. [unreadVariable]
vt-0.57721/decompose_blocksub.cpp:323:40: style: Variable 'ploidy' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:208:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:246:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reads [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:306:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:355:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reads [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:614:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:963:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:1093:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:1491:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:1502:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:1542:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:1570:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reads [valueFlowBailoutIncompleteVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::tid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::rid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::s' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::gt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_reads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_overlapping_reads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_passed_reads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_exclude_flag_reads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_low_mapq_reads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_unaligned_cigars' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_malformed_del_cigars' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_malformed_ins_cigars' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_salvageable_ins_cigars' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_ts' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_tv' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_insertions' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_deletions' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_left_soft_clips' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:111:5: warning: Member variable 'Igor::no_right_soft_clips' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/discover.cpp:552:11: performance:inconclusive: Technically the member function '::Igor::compute_indel_variant_score' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/discover.cpp:584:10: performance:inconclusive: Technically the member function '::Igor::contains_non_acgt_bases' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/discover.cpp:213:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/discover.cpp:213:10: note: Derived function 'Igor::initialize'
vt-0.57721/discover.cpp:1500:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/discover.cpp:1500:10: note: Derived function 'Igor::print_options'
vt-0.57721/discover.cpp:1540:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/discover.cpp:1540:10: note: Derived function 'Igor::print_stats'
vt-0.57721/pileup.h:178:5: style: Class 'Pileup' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/discover.cpp:1131:29: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/discover.cpp:1130:29: note: First condition
vt-0.57721/discover.cpp:1131:29: note: Second condition
vt-0.57721/discover.cpp:1132:29: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/discover.cpp:1131:29: note: First condition
vt-0.57721/discover.cpp:1132:29: note: Second condition
vt-0.57721/discover.cpp:1180:37: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/discover.cpp:1179:37: note: First condition
vt-0.57721/discover.cpp:1180:37: note: Second condition
vt-0.57721/discover.cpp:1491:17: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/discover.cpp:365:34: style: C-style pointer casting [cstyleCast]
vt-0.57721/discover.cpp:493:26: style: C-style pointer casting [cstyleCast]
vt-0.57721/discover.cpp:1574:22: style: C-style pointer casting [cstyleCast]
vt-0.57721/discover.cpp:1076:22: style: The scope of the variable 'cpos1' can be reduced. [variableScope]
vt-0.57721/discover.cpp:1077:22: style: The scope of the variable 'spos0' can be reduced. [variableScope]
vt-0.57721/discover.cpp:1080:22: style: The scope of the variable 'md_mlen_left' can be reduced. [variableScope]
vt-0.57721/discover.cpp:1342:22: style: The scope of the variable 'cpos1' can be reduced. [variableScope]
vt-0.57721/discover.cpp:1343:22: style: The scope of the variable 'spos0' can be reduced. [variableScope]
vt-0.57721/discover.cpp:1344:18: style: The scope of the variable 'seenM' can be reduced. [variableScope]
vt-0.57721/discover.cpp:288:21: style: Local variable 'chrom' shadows outer variable [shadowVariable]
vt-0.57721/discover.cpp:66:17: note: Shadowed declaration
vt-0.57721/discover.cpp:288:21: note: Shadow variable
vt-0.57721/discover.cpp:908:27: style: Local variable 's' shadows outer variable [shadowVariable]
vt-0.57721/discover.cpp:74:13: note: Shadowed declaration
vt-0.57721/discover.cpp:908:27: note: Shadow variable
vt-0.57721/discover.cpp:1059:18: style: Local variable 'tid' shadows outer variable [shadowVariable]
vt-0.57721/discover.cpp:67:13: note: Shadowed declaration
vt-0.57721/discover.cpp:1059:18: note: Shadow variable
vt-0.57721/discover.cpp:1084:27: style: Local variable 'cigar' shadows outer variable [shadowVariable]
vt-0.57721/discover.cpp:1064:19: note: Shadowed declaration
vt-0.57721/discover.cpp:1084:27: note: Shadow variable
vt-0.57721/discover.cpp:1311:41: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/discover.cpp:1088:31: note: Shadowed declaration
vt-0.57721/discover.cpp:1311:41: note: Shadow variable
vt-0.57721/discover.cpp:1348:27: style: Local variable 'cigar' shadows outer variable [shadowVariable]
vt-0.57721/discover.cpp:1064:19: note: Shadowed declaration
vt-0.57721/discover.cpp:1348:27: note: Shadow variable
vt-0.57721/discover.cpp:1399:37: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/discover.cpp:1352:31: note: Shadowed declaration
vt-0.57721/discover.cpp:1399:37: note: Shadow variable
vt-0.57721/discover.cpp:1441:41: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/discover.cpp:1352:31: note: Shadowed declaration
vt-0.57721/discover.cpp:1441:41: note: Shadow variable
vt-0.57721/discover.cpp:508:60: style: Parameter 'REF_Q' can be declared as reference to const [constParameterReference]
vt-0.57721/discover.cpp:508:90: style: Parameter 'ALT_Q' can be declared as reference to const [constParameterReference]
vt-0.57721/discover.cpp:584:47: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/discover.cpp:928:31: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
vt-0.57721/discover.cpp:1064:19: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
vt-0.57721/discover.cpp:34:11: style: struct member 'interval_t::start1' is never used. [unusedStructMember]
vt-0.57721/discover.cpp:34:19: style: struct member 'interval_t::end1' is never used. [unusedStructMember]
vt-0.57721/discover.cpp:81:14: style: class member 'Igor::gt' is never used. [unusedStructMember]
vt-0.57721/discover.cpp:299:23: style: Variable 'flag' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:411:31: style: Variable 'oplen' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:626:19: style: Variable 'N' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:627:19: style: Variable 'E' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:628:29: style: Variable 'variant_score' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:1250:37: style: Variable 'is_del' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:1059:18: style: Variable 'tid' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:1063:17: style: Variable 'l_qseq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/discover.cpp:1064:19: style: Variable 'cigar' is assigned a value that is never used. [unreadVariable]
vt-0.57721/pedigree.h:89:5: style: Class 'Pedigree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/estimate.cpp:140:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/estimate.cpp:214:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/estimate.cpp:297:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/estimate.cpp:343:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/estimate.cpp:553:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/estimate.cpp:564:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::compute_estimate' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::imap' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::no_variants_not_computed' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::no_variants_computed' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::no_variants_missing_dependencies' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::no_reference' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:160:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/estimate.cpp:162:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/estimate.cpp:562:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/estimate.cpp:43:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/estimate.cpp:43:17: note: Derived variable 'Igor::version'
vt-0.57721/estimate.cpp:219:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/estimate.cpp:219:10: note: Derived function 'Igor::initialize'
vt-0.57721/estimate.cpp:551:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/estimate.cpp:551:10: note: Derived function 'Igor::print_options'
vt-0.57721/estimate.cpp:562:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/estimate.cpp:562:10: note: Derived function 'Igor::print_stats'
vt-0.57721/estimate.cpp:370:19: style: The scope of the variable 'qual' can be reduced. [variableScope]
vt-0.57721/estimate.cpp:51:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/estimate.cpp:52:17: style: class member 'Igor::arg_sample_list' is never used. [unusedStructMember]
vt-0.57721/estimate.cpp:56:12: style: class member 'Igor::samples' is never used. [unusedStructMember]
vt-0.57721/estimate.cpp:57:14: style: class member 'Igor::imap' is never used. [unusedStructMember]
vt-0.57721/estimate.cpp:58:13: style: class member 'Igor::nsamples' is never used. [unusedStructMember]
vt-0.57721/estimate.cpp:392:58: style: Variable 'g[i]' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimate.cpp:325:18: style: Variable 'printed' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:197:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_missing [valueFlowBailoutIncompleteVar]
vt-0.57721/estimator.cpp:373:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_missing [valueFlowBailoutIncompleteVar]
vt-0.57721/estimator.cpp:543:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_missing [valueFlowBailoutIncompleteVar]
vt-0.57721/estimator.cpp:640:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_missing [valueFlowBailoutIncompleteVar]
vt-0.57721/estimator.cpp:777:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_missing [valueFlowBailoutIncompleteVar]
vt-0.57721/estimator.cpp:832:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf_int32_missing [valueFlowBailoutIncompleteVar]
vt-0.57721/estimator.cpp:589:27: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
vt-0.57721/estimator.cpp:581:27: note: Assignment 'l0i=0', assigned value is 0
vt-0.57721/estimator.cpp:582:35: note: Assuming condition is false
vt-0.57721/estimator.cpp:589:27: note: Invalid argument
vt-0.57721/estimator.cpp:590:27: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
vt-0.57721/estimator.cpp:581:34: note: Assignment 'lai=0', assigned value is 0
vt-0.57721/estimator.cpp:582:35: note: Assuming condition is false
vt-0.57721/estimator.cpp:590:27: note: Invalid argument
vt-0.57721/estimator.cpp:214:15: style: The scope of the variable 'diff' can be reduced. [variableScope]
vt-0.57721/estimator.cpp:326:19: style: The scope of the variable 'diff' can be reduced. [variableScope]
vt-0.57721/estimator.cpp:389:15: style: The scope of the variable 'diff' can be reduced. [variableScope]
vt-0.57721/estimator.cpp:489:19: style: The scope of the variable 'diff' can be reduced. [variableScope]
vt-0.57721/estimator.cpp:667:15: style: Local variable 'HWE_GF' shadows outer variable [shadowVariable]
vt-0.57721/estimator.cpp:626:11: note: Shadowed declaration
vt-0.57721/estimator.cpp:667:15: note: Shadow variable
vt-0.57721/estimator.cpp:790:27: style: Local variable 'n' shadows outer argument [shadowArgument]
vt-0.57721/estimator.cpp:740:51: note: Shadowed declaration
vt-0.57721/estimator.cpp:790:27: note: Shadow variable
vt-0.57721/estimator.cpp:179:44: style: Parameter 'pls' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:360:40: style: Parameter 'pls' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:527:42: style: Parameter 'pls' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:528:40: style: Parameter 'MLE_HWE_GF' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:528:59: style: Parameter 'MLE_GF' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:615:42: style: Parameter 'pls' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:616:39: style: Parameter 'HWE_AF' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:616:74: style: Parameter 'GF' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:737:40: style: Parameter 'pls' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:738:40: style: Parameter 'dps' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:739:38: style: Parameter 'GF' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:817:39: style: Parameter 'pls' can be declared as pointer to const [constParameterPointer]
vt-0.57721/estimator.cpp:45:18: style: Variable 'iter' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:50:30: style: Variable 'no_genotypes' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:214:20: style: Variable 'diff' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:283:20: style: Variable 'debug' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:389:20: style: Variable 'diff' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:494:30: style: Variable 'diff' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:536:21: style: Variable 'no_genotypes' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:780:34: style: Variable 'gt_index' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:779:23: style: Unused variable: prob_data [unusedVariable]
vt-0.57721/estimator.cpp:779:34: style: Unused variable: p_ref [unusedVariable]
vt-0.57721/estimator.cpp:825:21: style: Variable 'no_genotypes' is assigned a value that is never used. [unreadVariable]
vt-0.57721/estimator.cpp:850:19: style: Variable 'gq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/extract_vntrs.cpp:114:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/extract_vntrs.cpp:162:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/extract_vntrs.cpp:184:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/extract_vntrs.cpp:197:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/extract_vntrs.cpp:71:5: warning: Member variable 'Igor::vntr_classification_code' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/extract_vntrs.cpp:71:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/extract_vntrs.cpp:71:5: warning: Member variable 'Igor::ve' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/extract_vntrs.cpp:71:5: warning: Member variable 'Igor::no_vntrs_annotated' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/extract_vntrs.cpp:71:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/extract_vntrs.cpp:71:5: warning: Member variable 'Igor::rs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/extract_vntrs.cpp:73:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/extract_vntrs.cpp:195:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/extract_vntrs.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/extract_vntrs.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/extract_vntrs.cpp:123:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/extract_vntrs.cpp:123:10: note: Derived function 'Igor::initialize'
vt-0.57721/extract_vntrs.cpp:182:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/extract_vntrs.cpp:182:10: note: Derived function 'Igor::print_options'
vt-0.57721/extract_vntrs.cpp:195:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/extract_vntrs.cpp:195:10: note: Derived function 'Igor::print_stats'
vt-0.57721/extract_vntrs.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/extract_vntrs.cpp:62:13: style: class member 'Igor::no_vntrs_annotated' is never used. [unusedStructMember]
vt-0.57721/extract_vntrs.cpp:67:19: style: class member 'Igor::vm' is never used. [unusedStructMember]
vt-0.57721/extract_vntrs.cpp:69:24: style: class member 'Igor::rs' is never used. [unusedStructMember]
vt-0.57721/filter.cpp:59:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:1504:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:1528:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:1568:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:1665:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:1692:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:1748:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:1824:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:2028:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:2084:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:2152:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:2209:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter.cpp:29:7: warning: Member variable 'Node::type' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:29:7: warning: Member variable 'Node::var_length' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:29:7: warning: Member variable 'Node::number' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:29:7: warning: Member variable 'Node::index' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:29:7: warning: Member variable 'Node::value_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:29:7: warning: Member variable 'Node::b' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:29:7: warning: Member variable 'Node::i' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:29:7: warning: Member variable 'Node::f' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:42:7: warning: Member variable 'Node::var_length' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:42:7: warning: Member variable 'Node::number' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:42:7: warning: Member variable 'Node::index' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:42:7: warning: Member variable 'Node::value_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:42:7: warning: Member variable 'Node::b' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:42:7: warning: Member variable 'Node::i' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:42:7: warning: Member variable 'Node::f' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:1467:9: warning: Member variable 'Filter::h' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:1467:9: warning: Member variable 'Filter::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:1467:9: warning: Member variable 'Filter::variant' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter.cpp:34:5: performance: Variable 'tag' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/filter.cpp:35:5: performance: Variable 's' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/filter.cpp:47:5: performance: Variable 'tag' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/filter.cpp:48:5: performance: Variable 's' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/filter.h:190:10: performance:inconclusive: Technically the member function 'Filter::simplify' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/filter.cpp:1545:14: note: Technically the member function 'Filter::simplify' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:190:10: note: Technically the member function 'Filter::simplify' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:207:10: performance:inconclusive: Technically the member function 'Filter::is_literal' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/filter.cpp:1725:14: note: Technically the member function 'Filter::is_literal' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:207:10: note: Technically the member function 'Filter::is_literal' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:217:10: performance:inconclusive: Technically the member function 'Filter::is_bracketed_expression' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/filter.cpp:1677:14: note: Technically the member function 'Filter::is_bracketed_expression' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:217:10: note: Technically the member function 'Filter::is_bracketed_expression' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:226:13: performance:inconclusive: Technically the member function 'Filter::get_index_width' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/filter.cpp:1766:17: note: Technically the member function 'Filter::get_index_width' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:226:13: note: Technically the member function 'Filter::get_index_width' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:236:10: performance:inconclusive: Technically the member function 'Filter::trim_brackets' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/filter.cpp:2069:14: note: Technically the member function 'Filter::trim_brackets' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:236:10: note: Technically the member function 'Filter::trim_brackets' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:242:13: performance:inconclusive: Technically the member function 'Filter::fwd_to_closing_bracket' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/filter.cpp:2136:17: note: Technically the member function 'Filter::fwd_to_closing_bracket' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:242:13: note: Technically the member function 'Filter::fwd_to_closing_bracket' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:247:13: performance:inconclusive: Technically the member function 'Filter::peek_op' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/filter.cpp:2203:17: note: Technically the member function 'Filter::peek_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:247:13: note: Technically the member function 'Filter::peek_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:257:10: performance:inconclusive: Technically the member function 'Filter::print_filter_help' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/filter.cpp:2026:14: note: Technically the member function 'Filter::print_filter_help' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.h:257:10: note: Technically the member function 'Filter::print_filter_help' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/filter.cpp:1333:23: style: Expression '(X & 0xf) == 0x10' is always false. [comparisonError]
vt-0.57721/filter.cpp:1361:16: style: Condition 's==""' is always true [knownConditionTrueFalse]
vt-0.57721/filter.cpp:1976:15: style: Redundant initialization for 'start'. The initialized value is overwritten before it is read. [redundantInitialization]
vt-0.57721/filter.cpp:1962:27: note: start is initialized
vt-0.57721/filter.cpp:1976:15: note: start is overwritten
vt-0.57721/filter.cpp:1772:10: style: The scope of the variable 'in_digits' can be reduced. [variableScope]
vt-0.57721/filter.cpp:498:30: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:498:30: note: Shadow variable
vt-0.57721/filter.cpp:616:42: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:616:42: note: Shadow variable
vt-0.57721/filter.cpp:691:42: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:691:42: note: Shadow variable
vt-0.57721/filter.cpp:750:42: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:750:42: note: Shadow variable
vt-0.57721/filter.cpp:812:42: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:812:42: note: Shadow variable
vt-0.57721/filter.cpp:883:38: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:883:38: note: Shadow variable
vt-0.57721/filter.cpp:950:38: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:950:38: note: Shadow variable
vt-0.57721/filter.cpp:1016:38: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:1016:38: note: Shadow variable
vt-0.57721/filter.cpp:1078:38: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:119:13: note: Shadowed declaration
vt-0.57721/filter.cpp:1078:38: note: Shadow variable
vt-0.57721/filter.cpp:1358:17: style: Local variable 's' shadows outer variable [shadowVariable]
vt-0.57721/filter.h:117:15: note: Shadowed declaration
vt-0.57721/filter.cpp:1358:17: note: Shadow variable
vt-0.57721/filter.cpp:2190:19: style: Local variable 's' shadows outer variable [shadowVariable]
vt-0.57721/filter.cpp:2138:17: note: Shadowed declaration
vt-0.57721/filter.cpp:2190:19: note: Shadow variable
vt-0.57721/filter.cpp:2150:31: style: Local variable 's' shadows outer variable [shadowVariable]
vt-0.57721/filter.cpp:2138:17: note: Shadowed declaration
vt-0.57721/filter.cpp:2150:31: note: Shadow variable
vt-0.57721/filter.cpp:2163:31: style: Local variable 's' shadows outer variable [shadowVariable]
vt-0.57721/filter.cpp:2138:17: note: Shadowed declaration
vt-0.57721/filter.cpp:2163:31: note: Shadow variable
vt-0.57721/filter.cpp:1475:28: performance: Function parameter 'exp' should be passed by const reference. [passedByValue]
vt-0.57721/filter.cpp:1682:21: style: Variable 'nested' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:1771:22: style: Variable 'end_bracket' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:1772:20: style: Variable 'in_digits' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:1773:22: style: Variable 'beg_bracket' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:1780:19: style: Variable 'in_digits' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:1830:13: style: Variable 'exp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:1837:13: style: Variable 'exp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:1844:13: style: Variable 'exp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:1976:15: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter.cpp:2143:21: style: Variable 'nested' is assigned a value that is never used. [unreadVariable]
vt-0.57721/filter_overlap.cpp:92:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/filter_overlap.cpp:134:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/filter_overlap.cpp:194:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/filter_overlap.cpp:204:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/filter_overlap.cpp:63:5: warning: Member variable 'Igor::merge_by_pos' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter_overlap.cpp:63:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter_overlap.cpp:63:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter_overlap.cpp:63:5: warning: Member variable 'Igor::no_total_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter_overlap.cpp:63:5: warning: Member variable 'Igor::no_nonoverlap_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter_overlap.cpp:63:5: warning: Member variable 'Igor::no_overlap_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter_overlap.cpp:63:5: warning: Member variable 'Igor::var_manip' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/filter_overlap.cpp:202:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/filter_overlap.cpp:97:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/filter_overlap.cpp:97:10: note: Derived function 'Igor::initialize'
vt-0.57721/filter_overlap.cpp:192:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/filter_overlap.cpp:192:10: note: Derived function 'Igor::print_options'
vt-0.57721/filter_overlap.cpp:202:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/filter_overlap.cpp:202:10: note: Derived function 'Igor::print_stats'
vt-0.57721/filter_overlap.cpp:42:10: style: class member 'Igor::merge_by_pos' is never used. [unusedStructMember]
vt-0.57721/filter_overlap.cpp:49:26: style: class member 'Igor::pool' is never used. [unusedStructMember]
vt-0.57721/filter_overlap.cpp:61:19: style: class member 'Igor::var_manip' is never used. [unusedStructMember]
vt-0.57721/filter_overlap.cpp:134:26: style: Variable 'tpass_id' is assigned a value that is never used. [unreadVariable]
vt-0.57721/flank_detector.cpp:107:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/flank_detector.cpp:529:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/flank_detector.cpp:652:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::min_beg0' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::max_end0' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::no_perfect_ru' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::no_ru' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::rl' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::ll' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::trf_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::comp' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::entropy' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::kl_divergence' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::entropy2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.cpp:29:16: warning: Member variable 'FlankDetector::kl_divergence2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/flank_detector.h:116:17: performance:inconclusive: Technically the member function 'FlankDetector::shift_str' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/flank_detector.cpp:287:28: note: Technically the member function 'FlankDetector::shift_str' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/flank_detector.h:116:17: note: Technically the member function 'FlankDetector::shift_str' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/flank_detector.h:161:10: performance:inconclusive: Technically the member function 'FlankDetector::polish_repeat_tract_ends' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/flank_detector.cpp:516:21: note: Technically the member function 'FlankDetector::polish_repeat_tract_ends' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/flank_detector.h:161:10: note: Technically the member function 'FlankDetector::polish_repeat_tract_ends' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/flank_detector.cpp:50:5: warning: Class 'FlankDetector' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/flank_detector.cpp:50:5: warning: Class 'FlankDetector' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/flank_detector.cpp:360:41: warning: Identical condition 'seq.compare(0,mlen,smotif)==0', second condition is always false [identicalConditionAfterEarlyExit]
vt-0.57721/flank_detector.cpp:355:41: note: If condition 'seq.compare(0,mlen,smotif)==0' is true, the function will return/exit
vt-0.57721/flank_detector.cpp:360:41: note: Testing identical condition 'seq.compare(0,mlen,smotif)==0'
vt-0.57721/flank_detector.cpp:112:13: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/flank_detector.cpp:105:13: note: First condition
vt-0.57721/flank_detector.cpp:112:13: note: Second condition
vt-0.57721/flank_detector.cpp:182:13: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/flank_detector.cpp:173:13: note: First condition
vt-0.57721/flank_detector.cpp:182:13: note: Second condition
vt-0.57721/flank_detector.cpp:214:17: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/flank_detector.cpp:209:17: note: First condition
vt-0.57721/flank_detector.cpp:214:17: note: Second condition
vt-0.57721/flank_detector.cpp:142:51: style: Condition 'vntr.exact_repeat_tract.size()>=3' is always true [knownConditionTrueFalse]
vt-0.57721/flank_detector.cpp:118:43: note: Assuming that condition 'vntr.exact_repeat_tract.size()>2' is not redundant
vt-0.57721/flank_detector.cpp:142:51: note: Condition 'vntr.exact_repeat_tract.size()>=3' is always true
vt-0.57721/flank_detector.cpp:315:13: style: Local variable 'score' shadows outer variable [shadowVariable]
vt-0.57721/flank_detector.h:76:11: note: Shadowed declaration
vt-0.57721/flank_detector.cpp:315:13: note: Shadow variable
vt-0.57721/flank_detector.cpp:287:51: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:303:79: style: Parameter 'a' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:303:95: style: Parameter 'b' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:341:67: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:424:67: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:491:66: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:516:55: style: Parameter 'variant' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:525:59: style: Parameter 'repeat_tract' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:771:66: style: Parameter 'repeat_tract' can be declared as reference to const [constParameterReference]
vt-0.57721/flank_detector.cpp:775:13: style: Variable 'b2i' can be declared as const array [constVariable]
vt-0.57721/flank_detector.cpp:810:11: style: Variable 'p' can be declared as const array [constVariable]
vt-0.57721/flank_detector.cpp:197:17: style: Unused variable: seq_len [unusedVariable]
vt-0.57721/flank_detector.cpp:346:24: style: Variable 'best_score' is assigned a value that is never used. [unreadVariable]
vt-0.57721/flank_detector.cpp:347:28: style: Variable 'best_motif' is assigned a value that is never used. [unreadVariable]
vt-0.57721/flank_detector.cpp:348:23: style: Variable 'max_score' is assigned a value that is never used. [unreadVariable]
vt-0.57721/flank_detector.cpp:841:17: style: Variable 'log2q' is assigned a value that is never used. [unreadVariable]
vt-0.57721/fuzzy_aligner.h:54:10: performance:inconclusive: Technically the member function 'FuzzyAligner::align' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/fuzzy_aligner.cpp:29:20: note: Technically the member function 'FuzzyAligner::align' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/fuzzy_aligner.h:54:10: note: Technically the member function 'FuzzyAligner::align' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/fuzzy_aligner.h:44:5: style: Class 'FuzzyAligner' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/fuzzy_aligner.cpp:29:39: style: Parameter 'sequence' can be declared as reference to const [constParameterReference]
vt-0.57721/fuzzy_aligner.cpp:29:62: style: Parameter 'repeat_unit' can be declared as reference to const [constParameterReference]
vt-0.57721/fuzzy_partition.cpp:130:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/fuzzy_partition.cpp:190:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/fuzzy_partition.cpp:211:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/fuzzy_partition.cpp:256:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/fuzzy_partition.cpp:301:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/fuzzy_partition.cpp:452:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/fuzzy_partition.cpp:477:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/fuzzy_partition.cpp:92:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/fuzzy_partition.cpp:92:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/fuzzy_partition.cpp:92:5: warning: Member variable 'Igor::obom' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/fuzzy_partition.cpp:92:5: warning: Member variable 'Igor::a_odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/fuzzy_partition.cpp:92:5: warning: Member variable 'Igor::b_odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/fuzzy_partition.cpp:92:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/fuzzy_partition.cpp:92:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/fuzzy_partition.cpp:186:10: performance:inconclusive: Technically the member function '::Igor::increment_exact_overlap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/fuzzy_partition.cpp:207:10: performance:inconclusive: Technically the member function '::Igor::increment_fuzzy_overlap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/fuzzy_partition.cpp:254:10: performance:inconclusive: Technically the member function '::Igor::bcf_variant2string_with_motif' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/fuzzy_partition.cpp:141:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/fuzzy_partition.cpp:141:10: note: Derived function 'Igor::initialize'
vt-0.57721/fuzzy_partition.cpp:448:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/fuzzy_partition.cpp:448:10: note: Derived function 'Igor::print_options'
vt-0.57721/fuzzy_partition.cpp:473:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/fuzzy_partition.cpp:473:10: note: Derived function 'Igor::print_stats'
vt-0.57721/fuzzy_partition.cpp:483:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/fuzzy_partition.cpp:484:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/fuzzy_partition.cpp:485:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/fuzzy_partition.cpp:486:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/fuzzy_partition.cpp:487:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/fuzzy_partition.cpp:488:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/fuzzy_partition.cpp:305:21: style: The scope of the variable 'no_tr_alleles' can be reduced. [variableScope]
vt-0.57721/fuzzy_partition.cpp:303:31: style: Variable 'chrom' is assigned a value that is never used. [unreadVariable]
vt-0.57721/fuzzy_partition.cpp:401:29: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/gencode.cpp:60:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/gencode.cpp:109:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/gencode.cpp:279:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/gencode.cpp:335:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/gencode.cpp:26:16: warning: Member variable 'GENCODERecord::syn' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/gencode.cpp:104:10: warning: Member variable 'GENCODE::todr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/gencode.cpp:274:10: warning: Member variable 'GENCODE::todr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/gencode.h:115:10: style:inconclusive: Technically the member function 'GENCODERecord::feature2string' can be const. [functionConst]
vt-0.57721/gencode.cpp:79:21: note: Technically the member function 'GENCODERecord::feature2string' can be const.
vt-0.57721/gencode.h:115:10: note: Technically the member function 'GENCODERecord::feature2string' can be const.
vt-0.57721/gencode.h:165:10: performance:inconclusive: Technically the member function 'GENCODE::fill_synonymous' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/gencode.cpp:288:15: note: Technically the member function 'GENCODE::fill_synonymous' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/gencode.h:165:10: note: Technically the member function 'GENCODE::fill_synonymous' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/gencode.h:170:20: performance:inconclusive: Technically the member function 'GENCODE::parse_gencode' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/interval_tree.h:48:5: style: Class 'IntervalTreeNode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/gencode.cpp:470:41: style: C-style pointer casting [cstyleCast]
vt-0.57721/gencode.cpp:486:41: style: C-style pointer casting [cstyleCast]
vt-0.57721/gencode.cpp:342:23: style: Local variable 'todr' shadows outer variable [shadowVariable]
vt-0.57721/gencode.h:363:23: note: Shadowed declaration
vt-0.57721/gencode.cpp:342:23: note: Shadow variable
vt-0.57721/gencode.cpp:26:43: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/gencode.cpp:27:24: style: Parameter 'gene' can be declared as reference to const [constParameterReference]
vt-0.57721/gencode.cpp:104:31: style: Parameter 'gencode_gtf_file' can be declared as reference to const [constParameterReference]
vt-0.57721/gencode.cpp:104:62: style: Parameter 'ref_fasta_file' can be declared as reference to const [constParameterReference]
vt-0.57721/gencode.cpp:274:31: style: Parameter 'gencode_gtf_file' can be declared as reference to const [constParameterReference]
vt-0.57721/gencode.cpp:274:62: style: Parameter 'ref_fasta_file' can be declared as reference to const [constParameterReference]
vt-0.57721/gencode.cpp:515:39: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/gencode.cpp:538:95: style: Parameter 'str' can be declared as reference to const [constParameterReference]
vt-0.57721/gencode.cpp:288:46: style: Parameter 'g' can be declared as pointer to const [constParameterPointer]
vt-0.57721/gencode.h:170:45: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
vt-0.57721/gencode.cpp:293:17: style: Unused variable: ref_len [unusedVariable]
vt-0.57721/genome_interval.cpp:87:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/genome_interval.h:84:10: style:inconclusive: Technically the member function 'GenomeInterval::overlaps_with' can be const. [functionConst]
vt-0.57721/genome_interval.cpp:158:22: note: Technically the member function 'GenomeInterval::overlaps_with' can be const.
vt-0.57721/genome_interval.h:84:10: note: Technically the member function 'GenomeInterval::overlaps_with' can be const.
vt-0.57721/genome_interval.cpp:53:44: performance: Function parameter 'interval' should be passed by const reference. [passedByValue]
vt-0.57721/genome_interval.cpp:61:39: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/genome_interval.cpp:158:49: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/genotype.cpp:152:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/genotype.cpp:304:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reads [valueFlowBailoutIncompleteVar]
vt-0.57721/genotype.cpp:469:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/genotype.cpp:511:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/genotype.cpp:532:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/genotype.cpp:551:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/genotype.cpp:101:5: warning: Member variable 'Igor::ignore_md' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/genotype.cpp:549:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/genotype.cpp:168:9: warning: Class 'Igor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/genotype.cpp:168:9: warning: Class 'Igor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/genotype.cpp:43:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/genotype.cpp:43:17: note: Derived variable 'Igor::version'
vt-0.57721/genotype.cpp:530:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/genotype.cpp:530:10: note: Derived function 'Igor::print_options'
vt-0.57721/genotype.cpp:549:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/genotype.cpp:549:10: note: Derived function 'Igor::print_stats'
vt-0.57721/genotype.cpp:314:34: style: C-style pointer casting [cstyleCast]
vt-0.57721/genotype.cpp:436:26: style: C-style pointer casting [cstyleCast]
vt-0.57721/genotype.cpp:493:21: style: Local variable 'chrom' shadows outer variable [shadowVariable]
vt-0.57721/genotype.cpp:58:17: note: Shadowed declaration
vt-0.57721/genotype.cpp:493:21: note: Shadow variable
vt-0.57721/genotype.cpp:34:11: style: struct member 'interval_t::start1' is never used. [unusedStructMember]
vt-0.57721/genotype.cpp:34:19: style: struct member 'interval_t::end1' is never used. [unusedStructMember]
vt-0.57721/genotype.cpp:358:31: style: Variable 'oplen' is assigned a value that is never used. [unreadVariable]
vt-0.57721/genotype.cpp:504:23: style: Variable 'flag' is assigned a value that is never used. [unreadVariable]
vt-0.57721/ghmm.cpp:140:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ghmm.cpp:30:7: warning: Member variable 'GHMM::ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ghmm.cpp:30:7: warning: Member variable 'GHMM::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ghmm.cpp:30:7: warning: Member variable 'GHMM::len_ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ghmm.cpp:30:7: warning: Member variable 'GHMM::len_read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ghmm.h:64:5: style: Class 'GHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/ghmm.h:69:5: style: Class 'GHMM' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/hfilter.cpp:106:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/hfilter.cpp:145:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/hfilter.cpp:158:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/hfilter.cpp:170:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/hfilter.cpp:72:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/hfilter.cpp:72:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/hfilter.cpp:72:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/hfilter.cpp:72:5: warning: Member variable 'Igor::no_variants_filtered' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/hfilter.cpp:72:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/hfilter.cpp:72:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/hfilter.cpp:74:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/hfilter.cpp:156:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/hfilter.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/hfilter.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/hfilter.cpp:113:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/hfilter.cpp:113:10: note: Derived function 'Igor::initialize'
vt-0.57721/hfilter.cpp:143:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/hfilter.cpp:143:10: note: Derived function 'Igor::print_options'
vt-0.57721/hfilter.cpp:156:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/hfilter.cpp:156:10: note: Derived function 'Igor::print_stats'
vt-0.57721/hfilter.cpp:39:17: style: class member 'Igor::ref_fasta_file' is never used. [unusedStructMember]
vt-0.57721/hfilter.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/hfilter.cpp:43:17: style: class member 'Igor::regions_bed_file' is never used. [unusedStructMember]
vt-0.57721/hts_utils.cpp:31:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
vt-0.57721/indel_annotator.cpp:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/indel_annotator.cpp:79:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/indel_annotator.cpp:29:17: warning: Member variable 'IndelAnnotator::max_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_annotator.cpp:29:17: warning: Member variable 'IndelAnnotator::seq' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_annotator.cpp:29:17: warning: Member variable 'IndelAnnotator::factors' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_annotator.cpp:29:17: warning: Member variable 'IndelAnnotator::state' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/indel_annotator.cpp:31:5: warning: Class 'IndelAnnotator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/indel_annotator.cpp:31:5: warning: Class 'IndelAnnotator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/indel_annotator.cpp:80:13: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/indel_annotator.cpp:79:13: note: First condition
vt-0.57721/indel_annotator.cpp:80:13: note: Second condition
vt-0.57721/indel_annotator.cpp:105:13: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/indel_annotator.cpp:104:13: note: First condition
vt-0.57721/indel_annotator.cpp:105:13: note: Second condition
vt-0.57721/indel_annotator.cpp:64:11: style: The scope of the variable 'vntr' can be reduced. [variableScope]
vt-0.57721/indel_annotator.cpp:122:19: style: Local variable 'vntr' shadows outer variable [shadowVariable]
vt-0.57721/indel_annotator.cpp:64:11: note: Shadowed declaration
vt-0.57721/indel_annotator.cpp:122:19: note: Shadow variable
vt-0.57721/indel_annotator.cpp:31:14: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam]
vt-0.57721/indel_annotator.cpp:66:18: style: Variable 'h' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:303:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/indel_genotyping_record.cpp:588:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/indel_genotyping_record.cpp:354:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/indel_genotyping_record.cpp:355:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/indel_genotyping_record.cpp:356:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/indel_genotyping_record.cpp:357:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/indel_genotyping_record.cpp:88:11: style: C-style pointer casting [cstyleCast]
vt-0.57721/indel_genotyping_record.cpp:89:11: style: C-style pointer casting [cstyleCast]
vt-0.57721/indel_genotyping_record.cpp:154:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/indel_genotyping_record.cpp:155:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/indel_genotyping_record.cpp:156:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/indel_genotyping_record.cpp:157:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/indel_genotyping_record.cpp:158:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/indel_genotyping_record.cpp:161:12: style: The scope of the variable 'gp' can be reduced. [variableScope]
vt-0.57721/indel_genotyping_record.cpp:161:16: style: The scope of the variable 'gp_sum' can be reduced. [variableScope]
vt-0.57721/indel_genotyping_record.cpp:161:24: style: The scope of the variable 'max_gp' can be reduced. [variableScope]
vt-0.57721/indel_genotyping_record.cpp:162:13: style: The scope of the variable 'best_gt' can be reduced. [variableScope]
vt-0.57721/indel_genotyping_record.cpp:163:13: style: The scope of the variable 'best_a1' can be reduced. [variableScope]
vt-0.57721/indel_genotyping_record.cpp:163:22: style: The scope of the variable 'best_a2' can be reduced. [variableScope]
vt-0.57721/indel_genotyping_record.cpp:492:22: style: The scope of the variable 'cycle' can be reduced. [variableScope]
vt-0.57721/indel_genotyping_record.cpp:617:22: style: The scope of the variable 'cycle' can be reduced. [variableScope]
vt-0.57721/indel_genotyping_record.cpp:169:13: style: Local variable 'max_gq' shadows outer variable [shadowVariable]
vt-0.57721/indel_genotyping_record.h:72:28: note: Shadowed declaration
vt-0.57721/indel_genotyping_record.cpp:169:13: note: Shadow variable
vt-0.57721/indel_genotyping_record.cpp:170:13: style: Local variable 'dp_sum' shadows outer variable [shadowVariable]
vt-0.57721/indel_genotyping_record.h:72:20: note: Shadowed declaration
vt-0.57721/indel_genotyping_record.cpp:170:13: note: Shadow variable
vt-0.57721/indel_genotyping_record.cpp:185:18: style: Variable 'pli' can be declared as pointer to const [constVariablePointer]
vt-0.57721/indel_genotyping_record.cpp:186:30: style: Variable 'gp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:164:14: style: Unused variable: pls_i [unusedVariable]
vt-0.57721/indel_genotyping_record.cpp:486:26: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:487:27: style: Variable 'qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:492:28: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:516:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:525:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:545:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:552:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:573:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:581:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:611:26: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:612:27: style: Variable 'qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:617:28: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:641:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:650:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:670:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:677:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:698:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/indel_genotyping_record.cpp:706:31: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/index.cpp:64:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/index.cpp:82:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bcf [valueFlowBailoutIncompleteVar]
vt-0.57721/index.cpp:119:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/index.cpp:69:10: performance:inconclusive: Technically the member function '::Igor::initialize' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/index.cpp:115:10: style:inconclusive: Technically the member function '::Igor::print_options' can be const. [functionConst]
vt-0.57721/index.cpp:126:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/index.cpp:69:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/index.cpp:69:10: note: Derived function 'Igor::initialize'
vt-0.57721/index.cpp:115:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/index.cpp:115:10: note: Derived function 'Igor::print_options'
vt-0.57721/index.cpp:126:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/index.cpp:126:10: note: Derived function 'Igor::print_stats'
vt-0.57721/index.cpp:75:18: style: Variable 'file' can be declared as pointer to const [constVariablePointer]
vt-0.57721/index.cpp:109:13: error: Uninitialized variable: ret [legacyUninitvar]
vt-0.57721/info2tab.cpp:92:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/info2tab.cpp:143:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
vt-0.57721/info2tab.cpp:518:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/info2tab.cpp:530:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/info2tab.cpp:65:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/info2tab.cpp:65:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/info2tab.cpp:65:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/info2tab.cpp:65:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/info2tab.cpp:528:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/info2tab.cpp:110:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/info2tab.cpp:110:10: note: Derived function 'Igor::initialize'
vt-0.57721/info2tab.cpp:516:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/info2tab.cpp:516:10: note: Derived function 'Igor::print_options'
vt-0.57721/info2tab.cpp:528:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/info2tab.cpp:528:10: note: Derived function 'Igor::print_stats'
vt-0.57721/info2tab.cpp:200:44: style: Condition 'info_tag_str.size()>0' is always true [knownConditionTrueFalse]
vt-0.57721/info2tab.cpp:211:29: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/info2tab.cpp:227:29: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/info2tab.cpp:321:25: style: The scope of the variable 'num' can be reduced. [variableScope]
vt-0.57721/info2tab.cpp:402:29: style: Local variable 'no_alleles' shadows outer variable [shadowVariable]
vt-0.57721/info2tab.cpp:281:21: note: Shadowed declaration
vt-0.57721/info2tab.cpp:402:29: note: Shadow variable
vt-0.57721/info2tab.cpp:473:29: style: Local variable 'no_alleles' shadows outer variable [shadowVariable]
vt-0.57721/info2tab.cpp:281:21: note: Shadowed declaration
vt-0.57721/info2tab.cpp:473:29: note: Shadow variable
vt-0.57721/info2tab.cpp:318:28: style: Variable 'id' is assigned a value that is never used. [unreadVariable]
vt-0.57721/info2tab.cpp:403:42: style: Variable 'no_genotypes' is assigned a value that is never used. [unreadVariable]
vt-0.57721/info2tab.cpp:438:44: style: Variable 'no_alt_alleles' is assigned a value that is never used. [unreadVariable]
vt-0.57721/info2tab.cpp:473:40: style: Variable 'no_alleles' is assigned a value that is never used. [unreadVariable]
vt-0.57721/interval.h:48:10: style:inconclusive: Technically the member function 'Interval::overlaps_with' can be const. [functionConst]
vt-0.57721/interval.cpp:38:16: note: Technically the member function 'Interval::overlaps_with' can be const.
vt-0.57721/interval.h:48:10: note: Technically the member function 'Interval::overlaps_with' can be const.
vt-0.57721/interval_tree.cpp:70:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/interval_tree.cpp:220:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/interval_tree.cpp:371:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/interval_tree.cpp:401:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/interval_tree.cpp:29:19: warning: Member variable 'IntervalTreeNode::start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/interval_tree.h:63:10: style:inconclusive: Technically the member function 'IntervalTreeNode::print' can be const. [functionConst]
vt-0.57721/interval_tree.cpp:68:24: note: Technically the member function 'IntervalTreeNode::print' can be const.
vt-0.57721/interval_tree.h:63:10: note: Technically the member function 'IntervalTreeNode::print' can be const.
vt-0.57721/interval_tree.h:88:14: style:inconclusive: Technically the member function 'IntervalTree::size' can be const. [functionConst]
vt-0.57721/interval_tree.cpp:101:24: note: Technically the member function 'IntervalTree::size' can be const.
vt-0.57721/interval_tree.h:88:14: note: Technically the member function 'IntervalTree::size' can be const.
vt-0.57721/interval_tree.h:125:10: performance:inconclusive: Technically the member function 'IntervalTree::search_iter_brute' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/interval_tree.cpp:308:20: note: Technically the member function 'IntervalTree::search_iter_brute' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/interval_tree.h:125:10: note: Technically the member function 'IntervalTree::search_iter_brute' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/interval_tree.h:130:10: performance:inconclusive: Technically the member function 'IntervalTree::search_iter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/interval_tree.cpp:337:20: note: Technically the member function 'IntervalTree::search_iter' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/interval_tree.h:130:10: note: Technically the member function 'IntervalTree::search_iter' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/interval_tree.h:135:10: performance:inconclusive: Technically the member function 'IntervalTree::print_iter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/interval_tree.cpp:366:20: note: Technically the member function 'IntervalTree::print_iter' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/interval_tree.h:135:10: note: Technically the member function 'IntervalTree::print_iter' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.cpp:39:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/large_motif_tree.cpp:129:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/large_motif_tree.cpp:183:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/large_motif_tree.h:116:10: performance:inconclusive: Technically the member function 'LargeMotifTree::set_sequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/large_motif_tree.cpp:100:22: note: Technically the member function 'LargeMotifTree::set_sequence' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:116:10: note: Technically the member function 'LargeMotifTree::set_sequence' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:121:10: performance:inconclusive: Technically the member function 'LargeMotifTree::set_sequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/large_motif_tree.cpp:109:22: note: Technically the member function 'LargeMotifTree::set_sequence' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:121:10: note: Technically the member function 'LargeMotifTree::set_sequence' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:126:10: performance:inconclusive: Technically the member function 'LargeMotifTree::get_candidate_motifs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/large_motif_tree.cpp:117:22: note: Technically the member function 'LargeMotifTree::get_candidate_motifs' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:126:10: note: Technically the member function 'LargeMotifTree::get_candidate_motifs' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:153:10: performance:inconclusive: Technically the member function 'LargeMotifTree::add_suffix' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/large_motif_tree.cpp:147:22: note: Technically the member function 'LargeMotifTree::add_suffix' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:153:10: note: Technically the member function 'LargeMotifTree::add_suffix' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:158:13: performance:inconclusive: Technically the member function 'LargeMotifTree::base2index' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/large_motif_tree.cpp:155:25: note: Technically the member function 'LargeMotifTree::base2index' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:158:13: note: Technically the member function 'LargeMotifTree::base2index' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:163:10: performance:inconclusive: Technically the member function 'LargeMotifTree::print' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/large_motif_tree.cpp:179:22: note: Technically the member function 'LargeMotifTree::print' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.h:163:10: note: Technically the member function 'LargeMotifTree::print' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/large_motif_tree.cpp:94:15: error: Mismatching allocation and deallocation: LargeMotifTree::tree [mismatchAllocDealloc]
vt-0.57721/large_motif_tree.cpp:51:13: style: C-style pointer casting [cstyleCast]
vt-0.57721/large_motif_tree.cpp:181:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/large_motif_tree.cpp:117:72: style: Parameter 'candidate_motifs' can be declared as reference to const [constParameterReference]
vt-0.57721/large_motif_tree.cpp:100:41: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
vt-0.57721/large_motif_tree.cpp:109:41: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
vt-0.57721/large_motif_tree.cpp:147:39: style: Parameter 'sequence' can be declared as pointer to const [constParameterPointer]
vt-0.57721/large_motif_tree.cpp:181:14: style: Variable 'seq_ptr' can be declared as pointer to const [constVariablePointer]
vt-0.57721/large_motif_tree.cpp:78:16: error: Uninitialized variable: next_len_index [uninitvar]
vt-0.57721/large_motif_tree.cpp:53:20: style: Variable 'value' is assigned a value that is never used. [unreadVariable]
vt-0.57721/large_motif_tree.cpp:84:20: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
vt-0.57721/large_motif_tree.cpp:70:14: style: Variable 'next_len_index' is not assigned a value. [unassignedVariable]
vt-0.57721/large_motif_tree.cpp:103:18: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lfhmm.cpp:128:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:175:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:213:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:453:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:500:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:663:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:761:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:868:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:1167:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:1291:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:1310:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:1330:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:1356:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:1378:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:1426:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::rlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::plen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::lflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::lflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::motif_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::motif_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::rflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::rflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::exact_motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::motif_m' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::motif_xid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::last_motif_pos' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::frac_no_repeats' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::motif_concordance' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::trf_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::max_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::max_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::optimal_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::optimal_state' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::optimal_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::optimal_probe_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::optimal_path_ptr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.cpp:75:8: warning: Member variable 'LFHMM::optimal_path_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lfhmm.h:222:13: style:inconclusive: Technically the member function 'LFHMM::get_lflank_model_spos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:345:16: note: Technically the member function 'LFHMM::get_lflank_model_spos1' can be const.
vt-0.57721/lfhmm.h:222:13: note: Technically the member function 'LFHMM::get_lflank_model_spos1' can be const.
vt-0.57721/lfhmm.h:227:13: style:inconclusive: Technically the member function 'LFHMM::get_lflank_model_epos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:353:16: note: Technically the member function 'LFHMM::get_lflank_model_epos1' can be const.
vt-0.57721/lfhmm.h:227:13: note: Technically the member function 'LFHMM::get_lflank_model_epos1' can be const.
vt-0.57721/lfhmm.h:232:13: style:inconclusive: Technically the member function 'LFHMM::get_motif_model_spos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:361:16: note: Technically the member function 'LFHMM::get_motif_model_spos1' can be const.
vt-0.57721/lfhmm.h:232:13: note: Technically the member function 'LFHMM::get_motif_model_spos1' can be const.
vt-0.57721/lfhmm.h:237:13: style:inconclusive: Technically the member function 'LFHMM::get_motif_model_epos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:369:16: note: Technically the member function 'LFHMM::get_motif_model_epos1' can be const.
vt-0.57721/lfhmm.h:237:13: note: Technically the member function 'LFHMM::get_motif_model_epos1' can be const.
vt-0.57721/lfhmm.h:242:13: style:inconclusive: Technically the member function 'LFHMM::get_rflank_model_spos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:377:16: note: Technically the member function 'LFHMM::get_rflank_model_spos1' can be const.
vt-0.57721/lfhmm.h:242:13: note: Technically the member function 'LFHMM::get_rflank_model_spos1' can be const.
vt-0.57721/lfhmm.h:247:13: style:inconclusive: Technically the member function 'LFHMM::get_rflank_model_epos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:385:16: note: Technically the member function 'LFHMM::get_rflank_model_epos1' can be const.
vt-0.57721/lfhmm.h:247:13: note: Technically the member function 'LFHMM::get_rflank_model_epos1' can be const.
vt-0.57721/lfhmm.h:252:13: style:inconclusive: Technically the member function 'LFHMM::get_lflank_read_spos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:393:16: note: Technically the member function 'LFHMM::get_lflank_read_spos1' can be const.
vt-0.57721/lfhmm.h:252:13: note: Technically the member function 'LFHMM::get_lflank_read_spos1' can be const.
vt-0.57721/lfhmm.h:257:13: style:inconclusive: Technically the member function 'LFHMM::get_lflank_read_epos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:401:16: note: Technically the member function 'LFHMM::get_lflank_read_epos1' can be const.
vt-0.57721/lfhmm.h:257:13: note: Technically the member function 'LFHMM::get_lflank_read_epos1' can be const.
vt-0.57721/lfhmm.h:262:13: style:inconclusive: Technically the member function 'LFHMM::get_motif_read_spos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:409:16: note: Technically the member function 'LFHMM::get_motif_read_spos1' can be const.
vt-0.57721/lfhmm.h:262:13: note: Technically the member function 'LFHMM::get_motif_read_spos1' can be const.
vt-0.57721/lfhmm.h:267:13: style:inconclusive: Technically the member function 'LFHMM::get_motif_read_epos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:417:16: note: Technically the member function 'LFHMM::get_motif_read_epos1' can be const.
vt-0.57721/lfhmm.h:267:13: note: Technically the member function 'LFHMM::get_motif_read_epos1' can be const.
vt-0.57721/lfhmm.h:272:13: style:inconclusive: Technically the member function 'LFHMM::get_rflank_read_spos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:425:16: note: Technically the member function 'LFHMM::get_rflank_read_spos1' can be const.
vt-0.57721/lfhmm.h:272:13: note: Technically the member function 'LFHMM::get_rflank_read_spos1' can be const.
vt-0.57721/lfhmm.h:277:13: style:inconclusive: Technically the member function 'LFHMM::get_rflank_read_epos1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:433:16: note: Technically the member function 'LFHMM::get_rflank_read_epos1' can be const.
vt-0.57721/lfhmm.h:277:13: note: Technically the member function 'LFHMM::get_rflank_read_epos1' can be const.
vt-0.57721/lfhmm.h:304:11: performance:inconclusive: Technically the member function 'LFHMM::log10_emission_odds' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lfhmm.cpp:906:14: note: Technically the member function 'LFHMM::log10_emission_odds' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:304:11: note: Technically the member function 'LFHMM::log10_emission_odds' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:309:11: style:inconclusive: Technically the member function 'LFHMM::log10_emission_odds' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:926:14: note: Technically the member function 'LFHMM::log10_emission_odds' can be const.
vt-0.57721/lfhmm.h:309:11: note: Technically the member function 'LFHMM::log10_emission_odds' can be const.
vt-0.57721/lfhmm.h:314:17: performance:inconclusive: Technically the member function 'LFHMM::state2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lfhmm.cpp:946:20: note: Technically the member function 'LFHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:314:17: note: Technically the member function 'LFHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:319:17: performance:inconclusive: Technically the member function 'LFHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lfhmm.cpp:993:20: note: Technically the member function 'LFHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:319:17: note: Technically the member function 'LFHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:324:17: style:inconclusive: Technically the member function 'LFHMM::track2cigarstring1' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:1040:20: note: Technically the member function 'LFHMM::track2cigarstring1' can be const.
vt-0.57721/lfhmm.h:324:17: note: Technically the member function 'LFHMM::track2cigarstring1' can be const.
vt-0.57721/lfhmm.h:329:17: performance:inconclusive: Technically the member function 'LFHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lfhmm.cpp:1092:20: note: Technically the member function 'LFHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:329:17: note: Technically the member function 'LFHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:334:17: performance:inconclusive: Technically the member function 'LFHMM::component2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lfhmm.cpp:1121:20: note: Technically the member function 'LFHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:334:17: note: Technically the member function 'LFHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lfhmm.h:349:10: style:inconclusive: Technically the member function 'LFHMM::print' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:1288:13: note: Technically the member function 'LFHMM::print' can be const.
vt-0.57721/lfhmm.h:349:10: note: Technically the member function 'LFHMM::print' can be const.
vt-0.57721/lfhmm.h:354:10: style:inconclusive: Technically the member function 'LFHMM::print' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:1307:13: note: Technically the member function 'LFHMM::print' can be const.
vt-0.57721/lfhmm.h:354:10: note: Technically the member function 'LFHMM::print' can be const.
vt-0.57721/lfhmm.h:389:10: style:inconclusive: Technically the member function 'LFHMM::flanks_are_mapped' can be const. [functionConst]
vt-0.57721/lfhmm.cpp:898:13: note: Technically the member function 'LFHMM::flanks_are_mapped' can be const.
vt-0.57721/lfhmm.h:389:10: note: Technically the member function 'LFHMM::flanks_are_mapped' can be const.
vt-0.57721/lfhmm.cpp:199:28: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/lfhmm.cpp:662:12: style: The scope of the variable 'c' can be reduced. [variableScope]
vt-0.57721/lfhmm.cpp:709:13: style: The scope of the variable 'u' can be reduced. [variableScope]
vt-0.57721/lfhmm.cpp:710:13: style: The scope of the variable 'des_t' can be reduced. [variableScope]
vt-0.57721/lfhmm.cpp:448:53: style:inconclusive: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'. [funcArgNamesDifferent]
vt-0.57721/lfhmm.h:289:50: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/lfhmm.cpp:448:53: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/lfhmm.cpp:489:31: style:inconclusive: Function 'align' argument 1 names different: declaration 'y' definition 'read'. [funcArgNamesDifferent]
vt-0.57721/lfhmm.h:294:28: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/lfhmm.cpp:489:31: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/lfhmm.cpp:750:40: style:inconclusive: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'. [funcArgNamesDifferent]
vt-0.57721/lfhmm.h:374:37: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/lfhmm.cpp:750:40: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/lfhmm.cpp:750:55: style:inconclusive: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'. [funcArgNamesDifferent]
vt-0.57721/lfhmm.h:374:49: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/lfhmm.cpp:750:55: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/lfhmm.cpp:906:39: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty' [funcArgOrderDifferent]
vt-0.57721/lfhmm.h:304:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty'
vt-0.57721/lfhmm.cpp:906:39: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty'
vt-0.57721/lfhmm.cpp:926:39: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl' [funcArgOrderDifferent]
vt-0.57721/lfhmm.h:309:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/lfhmm.cpp:926:39: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/lfhmm.cpp:1178:13: style: Local variable 'qual' shadows outer variable [shadowVariable]
vt-0.57721/lfhmm.h:111:17: note: Shadowed declaration
vt-0.57721/lfhmm.cpp:1178:13: note: Shadow variable
vt-0.57721/lfhmm.cpp:1165:42: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/lfhmm.cpp:1288:26: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/lfhmm.cpp:1307:28: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/lfhmm.cpp:1354:30: style: Parameter 'U' can be declared as pointer to const [constParameterPointer]
vt-0.57721/lfhmm.cpp:1379:14: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
vt-0.57721/lfhmm.cpp:1380:12: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
vt-0.57721/lfhmm.cpp:504:15: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lfhmm.cpp:505:18: style: Variable 'maxPath' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lfhmm.cpp:1223:15: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lhmm.cpp:124:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm.cpp:344:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm.cpp:791:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm.cpp:854:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm.cpp:870:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::x' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::y' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::xlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::ylen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::matchStartX' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::matchEndX' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::matchStartY' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::matchEndY' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::matchedBases' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::mismatchedBases' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.cpp:40:7: warning: Member variable 'LHMM::noBasesAligned' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm.h:138:12: style:inconclusive: Technically the member function 'LHMM::log10_emission_odds' can be const. [functionConst]
vt-0.57721/lhmm.cpp:661:14: note: Technically the member function 'LHMM::log10_emission_odds' can be const.
vt-0.57721/lhmm.h:138:12: note: Technically the member function 'LHMM::log10_emission_odds' can be const.
vt-0.57721/lhmm.h:143:17: performance:inconclusive: Technically the member function 'LHMM::reverse' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lhmm.cpp:683:19: note: Technically the member function 'LHMM::reverse' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm.h:143:17: note: Technically the member function 'LHMM::reverse' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm.h:148:10: style:inconclusive: Technically the member function 'LHMM::deletion_start_exists' can be const. [functionConst]
vt-0.57721/lhmm.cpp:716:12: note: Technically the member function 'LHMM::deletion_start_exists' can be const.
vt-0.57721/lhmm.h:148:10: note: Technically the member function 'LHMM::deletion_start_exists' can be const.
vt-0.57721/lhmm.h:153:10: style:inconclusive: Technically the member function 'LHMM::insertion_start_exists' can be const. [functionConst]
vt-0.57721/lhmm.cpp:697:12: note: Technically the member function 'LHMM::insertion_start_exists' can be const.
vt-0.57721/lhmm.h:153:10: note: Technically the member function 'LHMM::insertion_start_exists' can be const.
vt-0.57721/lhmm.h:168:10: style:inconclusive: Technically the member function 'LHMM::print' can be const. [functionConst]
vt-0.57721/lhmm.cpp:848:12: note: Technically the member function 'LHMM::print' can be const.
vt-0.57721/lhmm.h:168:10: note: Technically the member function 'LHMM::print' can be const.
vt-0.57721/lhmm.h:173:10: style:inconclusive: Technically the member function 'LHMM::print' can be const. [functionConst]
vt-0.57721/lhmm.cpp:864:12: note: Technically the member function 'LHMM::print' can be const.
vt-0.57721/lhmm.h:173:10: note: Technically the member function 'LHMM::print' can be const.
vt-0.57721/lhmm.cpp:191:43: style:inconclusive: Function 'align' argument 2 names different: declaration '_x' definition 'x'. [funcArgNamesDifferent]
vt-0.57721/lhmm.h:117:41: note: Function 'align' argument 2 names different: declaration '_x' definition 'x'.
vt-0.57721/lhmm.cpp:191:43: note: Function 'align' argument 2 names different: declaration '_x' definition 'x'.
vt-0.57721/lhmm.cpp:191:58: style:inconclusive: Function 'align' argument 3 names different: declaration '_y' definition 'y'. [funcArgNamesDifferent]
vt-0.57721/lhmm.h:117:57: note: Function 'align' argument 3 names different: declaration '_y' definition 'y'.
vt-0.57721/lhmm.cpp:191:58: note: Function 'align' argument 3 names different: declaration '_y' definition 'y'.
vt-0.57721/lhmm.cpp:683:39: performance: Function parameter 's' should be passed by const reference. [passedByValue]
vt-0.57721/lhmm.cpp:191:26: style: Parameter 'llk' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm.cpp:744:41: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm.cpp:864:24: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/lhmm.cpp:201:16: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lhmm.cpp:202:18: style: Variable 'maxPath' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lhmm.cpp:686:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
vt-0.57721/lhmm1.cpp:99:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm1.cpp:733:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm1.cpp:1140:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm1.cpp:1153:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm1.cpp:1166:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm1.cpp:1330:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::x' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::y' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::xlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::ylen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::tsx' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::tsy' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::txi' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::txd' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::tyi' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::tyd' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::tiw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::tdw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::tiz' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::tdz' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::matchStartX' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::matchEndX' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::matchStartY' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::matchEndY' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::matchedBases' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::mismatchedBases' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.cpp:28:8: warning: Member variable 'LHMM1::noBasesAligned' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/lhmm1.h:133:10: style:inconclusive: Technically the member function 'LHMM1::containsIndel' can be const. [functionConst]
vt-0.57721/lhmm1.cpp:172:13: note: Technically the member function 'LHMM1::containsIndel' can be const.
vt-0.57721/lhmm1.h:133:10: note: Technically the member function 'LHMM1::containsIndel' can be const.
vt-0.57721/lhmm1.h:169:12: style:inconclusive: Technically the member function 'LHMM1::logEmissionOdds' can be const. [functionConst]
vt-0.57721/lhmm1.cpp:1066:15: note: Technically the member function 'LHMM1::logEmissionOdds' can be const.
vt-0.57721/lhmm1.h:169:12: note: Technically the member function 'LHMM1::logEmissionOdds' can be const.
vt-0.57721/lhmm1.h:172:12: performance:inconclusive: Technically the member function 'LHMM1::logEmission' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lhmm1.cpp:1085:15: note: Technically the member function 'LHMM1::logEmission' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:172:12: note: Technically the member function 'LHMM1::logEmission' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:174:12: performance:inconclusive: Technically the member function 'LHMM1::emission' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lhmm1.cpp:1104:15: note: Technically the member function 'LHMM1::emission' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:174:12: note: Technically the member function 'LHMM1::emission' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:176:17: performance:inconclusive: Technically the member function 'LHMM1::reverse' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lhmm1.cpp:1123:20: note: Technically the member function 'LHMM1::reverse' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:176:17: note: Technically the member function 'LHMM1::reverse' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:178:10: performance:inconclusive: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lhmm1.cpp:1134:13: note: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:178:10: note: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:180:10: performance:inconclusive: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lhmm1.cpp:1147:13: note: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:180:10: note: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:182:10: performance:inconclusive: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lhmm1.cpp:1160:13: note: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:182:10: note: Technically the member function 'LHMM1::printVector' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:190:12: performance:inconclusive: Technically the member function 'LHMM1::score' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/lhmm1.cpp:1390:15: note: Technically the member function 'LHMM1::score' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:190:12: note: Technically the member function 'LHMM1::score' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/lhmm1.h:195:10: style:inconclusive: Technically the member function 'LHMM1::deletion_start_exists' can be const. [functionConst]
vt-0.57721/lhmm1.cpp:1401:13: note: Technically the member function 'LHMM1::deletion_start_exists' can be const.
vt-0.57721/lhmm1.h:195:10: note: Technically the member function 'LHMM1::deletion_start_exists' can be const.
vt-0.57721/lhmm1.h:200:10: style:inconclusive: Technically the member function 'LHMM1::insertion_start_exists' can be const. [functionConst]
vt-0.57721/lhmm1.cpp:1420:13: note: Technically the member function 'LHMM1::insertion_start_exists' can be const.
vt-0.57721/lhmm1.h:200:10: note: Technically the member function 'LHMM1::insertion_start_exists' can be const.
vt-0.57721/lhmm1.cpp:73:24: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/lhmm1.cpp:74:30: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/lhmm1.cpp:75:24: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/lhmm1.cpp:91:24: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/lhmm1.cpp:94:30: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/lhmm1.cpp:95:24: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/lhmm1.cpp:33:32: style:inconclusive: Function 'initialize' argument 1 names different: declaration 'l' definition 'maxLength'. [funcArgNamesDifferent]
vt-0.57721/lhmm1.h:131:29: note: Function 'initialize' argument 1 names different: declaration 'l' definition 'maxLength'.
vt-0.57721/lhmm1.cpp:33:32: note: Function 'initialize' argument 1 names different: declaration 'l' definition 'maxLength'.
vt-0.57721/lhmm1.cpp:569:76: style:inconclusive: Function 'align' argument 4 names different: declaration 'qual' definition '_qual'. [funcArgNamesDifferent]
vt-0.57721/lhmm1.h:150:73: note: Function 'align' argument 4 names different: declaration 'qual' definition '_qual'.
vt-0.57721/lhmm1.cpp:569:76: note: Function 'align' argument 4 names different: declaration 'qual' definition '_qual'.
vt-0.57721/lhmm1.cpp:255:14: style: Local variable 'x' shadows outer variable [shadowVariable]
vt-0.57721/lhmm1.h:34:17: note: Shadowed declaration
vt-0.57721/lhmm1.cpp:255:14: note: Shadow variable
vt-0.57721/lhmm1.cpp:255:19: style: Local variable 'y' shadows outer variable [shadowVariable]
vt-0.57721/lhmm1.h:35:17: note: Shadowed declaration
vt-0.57721/lhmm1.cpp:255:19: note: Shadow variable
vt-0.57721/lhmm1.cpp:1123:40: performance: Function parameter 's' should be passed by const reference. [passedByValue]
vt-0.57721/lhmm1.cpp:569:27: style: Parameter 'llk' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm1.cpp:769:60: style: Parameter '_path' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm1.cpp:874:80: style: Parameter '_path' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm1.cpp:1134:60: style: Parameter 'v' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm1.cpp:1147:58: style: Parameter 'v' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm1.cpp:1160:60: style: Parameter 'v' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm1.cpp:1173:41: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm1.cpp:1274:41: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/lhmm1.cpp:585:16: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lhmm1.cpp:586:18: style: Variable 'maxPath' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lhmm1.cpp:779:14: style: Variable 'q' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lhmm1.cpp:885:14: style: Variable 'q' is assigned a value that is never used. [unreadVariable]
vt-0.57721/lhmm1.cpp:1126:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
vt-0.57721/liftover.cpp:110:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/liftover.cpp:234:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/liftover.cpp:280:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::compression_level' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::left_window' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::right_window' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::sort_window_size' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::stream_selection' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::print_header' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::print_header_only' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::print_sites_only' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::print' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::debug' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::no_subset_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:81:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/liftover.cpp:276:10: style:inconclusive: Technically the member function '::Igor::print_options' can be const. [functionConst]
vt-0.57721/liftover.cpp:288:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/liftover.cpp:115:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/liftover.cpp:115:10: note: Derived function 'Igor::initialize'
vt-0.57721/liftover.cpp:276:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/liftover.cpp:276:10: note: Derived function 'Igor::print_options'
vt-0.57721/liftover.cpp:288:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/liftover.cpp:288:10: note: Derived function 'Igor::print_stats'
vt-0.57721/liftover.cpp:206:17: style: Local variable 'variant' shadows outer variable [shadowVariable]
vt-0.57721/liftover.cpp:47:17: note: Shadowed declaration
vt-0.57721/liftover.cpp:206:17: note: Shadow variable
vt-0.57721/liftover.cpp:42:17: style: class member 'Igor::streaming_selection_bed_file' is never used. [unusedStructMember]
vt-0.57721/liftover.cpp:43:14: style: class member 'Igor::left_window' is never used. [unusedStructMember]
vt-0.57721/liftover.cpp:44:14: style: class member 'Igor::right_window' is never used. [unusedStructMember]
vt-0.57721/liftover.cpp:46:30: style: class member 'Igor::samples' is never used. [unusedStructMember]
vt-0.57721/liftover.cpp:47:17: style: class member 'Igor::variant' is never used. [unusedStructMember]
vt-0.57721/liftover.cpp:50:10: style: class member 'Igor::print_header' is never used. [unusedStructMember]
vt-0.57721/liftover.cpp:51:10: style: class member 'Igor::print_header_only' is never used. [unusedStructMember]
vt-0.57721/liftover.cpp:52:10: style: class member 'Igor::print_sites_only' is never used. [unusedStructMember]
vt-0.57721/liftover.cpp:235:35: style: Variable 'chrom' is assigned a value that is never used. [unreadVariable]
vt-0.57721/liftover.cpp:236:32: style: Variable 'start1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/liftover.cpp:237:30: style: Variable 'end1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/log_tool.cpp:60:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PL [valueFlowBailoutIncompleteVar]
vt-0.57721/log_tool.cpp:84:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PL_one_minus_p [valueFlowBailoutIncompleteVar]
vt-0.57721/log_tool.cpp:107:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOG10_VARP [valueFlowBailoutIncompleteVar]
vt-0.57721/log_tool.cpp:117:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/log_tool.cpp:137:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOGZERO [valueFlowBailoutIncompleteVar]
vt-0.57721/log_tool.cpp:147:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOGZERO [valueFlowBailoutIncompleteVar]
vt-0.57721/log_tool.cpp:178:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LOG10FACT [valueFlowBailoutIncompleteVar]
vt-0.57721/log_tool.cpp:121:45: warning: Either the condition 'x<0' is redundant or std::log10() argument nr 1 can have invalid value. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
vt-0.57721/log_tool.cpp:115:17: note: Assuming that condition 'x<0' is not redundant
vt-0.57721/log_tool.cpp:121:45: note: Invalid argument
vt-0.57721/merge.cpp:102:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/merge.cpp:153:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
vt-0.57721/merge.cpp:311:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/merge.cpp:322:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::no_candidate_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::no_candidate_indels' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::no_candidate_snpindels' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::no_other_variant_types' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:71:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge.cpp:318:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/merge.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/merge.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/merge.cpp:113:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/merge.cpp:113:10: note: Derived function 'Igor::initialize'
vt-0.57721/merge.cpp:307:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/merge.cpp:307:10: note: Derived function 'Igor::print_options'
vt-0.57721/merge.cpp:318:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/merge.cpp:318:10: note: Derived function 'Igor::print_stats'
vt-0.57721/merge.cpp:180:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/merge.cpp:181:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/merge.cpp:182:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/merge.cpp:183:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/merge.cpp:184:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/merge.cpp:96:45: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/merge.cpp:50:13: note: Shadowed declaration
vt-0.57721/merge.cpp:96:45: note: Shadow variable
vt-0.57721/merge.cpp:148:17: style: Local variable 'no_samples' shadows outer variable [shadowVariable]
vt-0.57721/merge.cpp:60:14: note: Shadowed declaration
vt-0.57721/merge.cpp:148:17: note: Shadow variable
vt-0.57721/merge.cpp:194:25: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/merge.cpp:50:13: note: Shadowed declaration
vt-0.57721/merge.cpp:194:25: note: Shadow variable
vt-0.57721/merge.cpp:206:29: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/merge.cpp:194:25: note: Shadowed declaration
vt-0.57721/merge.cpp:206:29: note: Shadow variable
vt-0.57721/merge.cpp:207:32: style: Local variable 'h' shadows outer variable [shadowVariable]
vt-0.57721/merge.cpp:195:28: note: Shadowed declaration
vt-0.57721/merge.cpp:207:32: note: Shadow variable
vt-0.57721/merge.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/merge.cpp:50:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/merge.cpp:185:20: style: Variable 'ncount' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge.cpp:187:43: style: Variable 'sample2record' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge.cpp:188:42: style: Variable 'sample2index' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge.cpp:211:36: style: Variable 'ploidy' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge.cpp:213:28: style: Variable 'ploidy' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_candidate_variants.cpp:106:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_candidate_variants.cpp:135:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_HL_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_candidate_variants.cpp:253:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_candidate_variants.cpp:347:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_candidate_variants.cpp:358:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_candidate_variants.cpp:74:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_candidate_variants.cpp:74:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_candidate_variants.cpp:74:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_candidate_variants.cpp:74:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_candidate_variants.cpp:74:5: warning: Member variable 'Igor::no_candidate_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_candidate_variants.cpp:74:5: warning: Member variable 'Igor::no_candidate_indels' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_candidate_variants.cpp:74:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_candidate_variants.cpp:356:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/merge_candidate_variants.cpp:36:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/merge_candidate_variants.cpp:36:17: note: Derived variable 'Igor::version'
vt-0.57721/merge_candidate_variants.cpp:111:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/merge_candidate_variants.cpp:111:10: note: Derived function 'Igor::initialize'
vt-0.57721/merge_candidate_variants.cpp:345:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/merge_candidate_variants.cpp:345:10: note: Derived function 'Igor::print_options'
vt-0.57721/merge_candidate_variants.cpp:356:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/merge_candidate_variants.cpp:356:10: note: Derived function 'Igor::print_stats'
vt-0.57721/merge_candidate_variants.cpp:187:21: style: The scope of the variable 'samples' can be reduced. [variableScope]
vt-0.57721/merge_candidate_variants.cpp:182:17: style: Local variable 'no_samples' shadows outer variable [shadowVariable]
vt-0.57721/merge_candidate_variants.cpp:65:14: note: Shadowed declaration
vt-0.57721/merge_candidate_variants.cpp:182:17: note: Shadow variable
vt-0.57721/merge_candidate_variants.cpp:211:25: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/merge_candidate_variants.cpp:54:13: note: Shadowed declaration
vt-0.57721/merge_candidate_variants.cpp:211:25: note: Shadow variable
vt-0.57721/merge_candidate_variants.cpp:175:18: style: Variable 'ESUM' can be declared as pointer to const [constVariablePointer]
vt-0.57721/merge_candidate_variants.cpp:176:18: style: Variable 'NSUM' can be declared as pointer to const [constVariablePointer]
vt-0.57721/merge_candidate_variants.cpp:45:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/merge_candidate_variants.cpp:54:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/merge_candidate_variants.cpp:185:22: style: Variable 'esum' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_candidate_variants.cpp:186:22: style: Variable 'nsum' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_candidate_variants.cpp:175:18: style: Variable 'ESUM' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_candidate_variants.cpp:176:18: style: Variable 'NSUM' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_candidate_variants.cpp:177:17: style: Variable 'no_ESUM' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_candidate_variants.cpp:177:30: style: Variable 'no_NSUM' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:114:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_genotypes.cpp:130:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_genotypes.cpp:278:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_genotypes.cpp:649:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_genotypes.cpp:660:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::no_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::no_indels' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::no_vntrs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:81:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/merge_genotypes.cpp:658:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/merge_genotypes.cpp:36:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/merge_genotypes.cpp:36:17: note: Derived variable 'Igor::version'
vt-0.57721/merge_genotypes.cpp:119:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/merge_genotypes.cpp:119:10: note: Derived function 'Igor::initialize'
vt-0.57721/merge_genotypes.cpp:647:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/merge_genotypes.cpp:647:10: note: Derived function 'Igor::print_options'
vt-0.57721/merge_genotypes.cpp:658:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/merge_genotypes.cpp:658:10: note: Derived function 'Igor::print_stats'
vt-0.57721/merge_genotypes.cpp:130:9: portability: %zd in format string (no. 4) requires 'ssize_t' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
vt-0.57721/merge_genotypes.cpp:278:21: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/merge_genotypes.cpp:278:21: portability: %zd in format string (no. 5) requires 'ssize_t' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
vt-0.57721/merge_genotypes.cpp:287:25: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/merge_genotypes.cpp:287:25: portability: %zd in format string (no. 5) requires 'ssize_t' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
vt-0.57721/merge_genotypes.cpp:291:25: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/merge_genotypes.cpp:291:25: portability: %zd in format string (no. 5) requires 'ssize_t' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
vt-0.57721/merge_genotypes.cpp:274:29: style: Local variable 'variant' shadows outer variable [shadowVariable]
vt-0.57721/merge_genotypes.cpp:59:15: note: Shadowed declaration
vt-0.57721/merge_genotypes.cpp:274:29: note: Shadow variable
vt-0.57721/merge_genotypes.cpp:325:25: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/merge_genotypes.cpp:53:13: note: Shadowed declaration
vt-0.57721/merge_genotypes.cpp:325:25: note: Shadow variable
vt-0.57721/merge_genotypes.cpp:240:18: style: Variable 'NSAMPLES' can be declared as pointer to const [constVariablePointer]
vt-0.57721/merge_genotypes.cpp:244:18: style: Variable 'AD' can be declared as pointer to const [constVariablePointer]
vt-0.57721/merge_genotypes.cpp:585:17: warning: Uninitialized variable: vtype [uninitvar]
vt-0.57721/merge_genotypes.cpp:322:33: note: Assuming condition is false
vt-0.57721/merge_genotypes.cpp:585:17: note: Uninitialized variable: vtype
vt-0.57721/merge_genotypes.cpp:46:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/merge_genotypes.cpp:53:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/merge_genotypes.cpp:58:26: style: class member 'Igor::file_types' is never used. [unusedStructMember]
vt-0.57721/merge_genotypes.cpp:142:30: style: Variable 'EX_MOTIF' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:143:27: style: Variable 'EX_RU' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:144:30: style: Variable 'EX_BASIS' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:145:29: style: Variable 'EX_MLEN' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:146:29: style: Variable 'EX_BLEN' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:147:37: style: Variable 'EX_REPEAT_TRACT' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:148:29: style: Variable 'EX_COMP' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:149:32: style: Variable 'EX_ENTROPY' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:150:33: style: Variable 'EX_ENTROPY2' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:151:38: style: Variable 'EX_KL_DIVERGENCE' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:152:39: style: Variable 'EX_KL_DIVERGENCE2' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:153:28: style: Variable 'EX_REF' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:154:27: style: Variable 'EX_RL' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:155:27: style: Variable 'EX_LL' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:156:34: style: Variable 'EX_RU_COUNTS' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:157:30: style: Variable 'EX_SCORE' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:158:34: style: Variable 'EX_TRF_SCORE' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:161:30: style: Variable 'FZ_MOTIF' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:162:27: style: Variable 'FZ_RU' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:163:30: style: Variable 'FZ_BASIS' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:164:29: style: Variable 'FZ_MLEN' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:165:29: style: Variable 'FZ_BLEN' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:166:37: style: Variable 'FZ_REPEAT_TRACT' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:167:29: style: Variable 'FZ_COMP' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:168:32: style: Variable 'FZ_ENTROPY' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:169:33: style: Variable 'FZ_ENTROPY2' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:170:38: style: Variable 'FZ_KL_DIVERGENCE' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:171:39: style: Variable 'FZ_KL_DIVERGENCE2' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:172:28: style: Variable 'FZ_REF' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:173:27: style: Variable 'FZ_RL' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:174:27: style: Variable 'FZ_LL' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:175:34: style: Variable 'FZ_RU_COUNTS' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:176:30: style: Variable 'FZ_SCORE' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:177:34: style: Variable 'FZ_TRF_SCORE' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:179:30: style: Variable 'FLANKSEQ' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:180:40: style: Variable 'EXACT_RU_AMBIGUOUS' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:182:27: style: Variable 'MOTIF' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:183:24: style: Variable 'RU' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:184:28: style: Variable 'FLANKS' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:185:31: style: Variable 'FZ_FLANKS' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:629:19: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:240:18: style: Variable 'NSAMPLES' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:241:17: style: Variable 'no_NSAMPLES' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:244:18: style: Variable 'AD' is assigned a value that is never used. [unreadVariable]
vt-0.57721/merge_genotypes.cpp:253:17: style: Variable 'no_AD' is assigned a value that is never used. [unreadVariable]
vt-0.57721/milk_filter.cpp:132:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/milk_filter.cpp:145:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/milk_filter.cpp:401:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/milk_filter.cpp:868:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/milk_filter.cpp:878:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/milk_filter.cpp:663:28: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/milk_filter.cpp:667:48: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/milk_filter.cpp:73:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/milk_filter.cpp:73:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/milk_filter.cpp:73:5: warning: Member variable 'Igor::ped' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/nuclear_pedigree.h:66:10: style:inconclusive: Technically the member function 'NuclearFamilyPerson::hasSample' can be const. [functionConst]
vt-0.57721/milk_filter.cpp:277:11: performance:inconclusive: Technically the member function '::Igor::logSumPosterior' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/milk_filter.cpp:305:10: style:inconclusive: Technically the member function '::Igor::addDupJoint' can be const. [functionConst]
vt-0.57721/milk_filter.cpp:319:10: style:inconclusive: Technically the member function '::Igor::addTrioJoint' can be const. [functionConst]
vt-0.57721/milk_filter.cpp:328:10: performance:inconclusive: Technically the member function '::Igor::getPersonGTstr' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/milk_filter.cpp:333:11: performance:inconclusive: Technically the member function '::Igor::logGL' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/milk_filter.cpp:347:9: performance:inconclusive: Technically the member function '::Igor::getPersonGenoDepth' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/milk_filter.cpp:864:10: style:inconclusive: Technically the member function '::Igor::print_options' can be const. [functionConst]
vt-0.57721/milk_filter.cpp:874:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/milk_filter.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/milk_filter.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/milk_filter.cpp:137:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/milk_filter.cpp:137:10: note: Derived function 'Igor::initialize'
vt-0.57721/milk_filter.cpp:864:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/milk_filter.cpp:864:10: note: Derived function 'Igor::print_options'
vt-0.57721/milk_filter.cpp:874:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/milk_filter.cpp:874:10: note: Derived function 'Igor::print_stats'
vt-0.57721/nuclear_pedigree.h:56:5: style: Class 'NuclearFamilySample' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/nuclear_pedigree.h:64:5: style: Class 'NuclearFamilyPerson' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/nuclear_pedigree.h:96:5: style: Class 'NuclearFamily' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/nuclear_pedigree.h:105:5: style: Class 'NuclearPedigree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/milk_filter.cpp:390:26: style: C-style pointer casting [cstyleCast]
vt-0.57721/milk_filter.cpp:448:39: style: C-style pointer casting [cstyleCast]
vt-0.57721/milk_filter.cpp:589:20: style: C-style pointer casting [cstyleCast]
vt-0.57721/milk_filter.cpp:590:20: style: C-style pointer casting [cstyleCast]
vt-0.57721/milk_filter.cpp:591:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/milk_filter.cpp:718:32: style: C-style pointer casting [cstyleCast]
vt-0.57721/milk_filter.cpp:116:45: style: Local variable 'exclude_fam_ids' shadows outer variable [shadowVariable]
vt-0.57721/milk_filter.cpp:38:30: note: Shadowed declaration
vt-0.57721/milk_filter.cpp:116:45: note: Shadow variable
vt-0.57721/milk_filter.cpp:484:15: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/milk_filter.cpp:471:9: note: Shadowed declaration
vt-0.57721/milk_filter.cpp:484:15: note: Shadow variable
vt-0.57721/milk_filter.cpp:517:15: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/milk_filter.cpp:471:9: note: Shadowed declaration
vt-0.57721/milk_filter.cpp:517:15: note: Shadow variable
vt-0.57721/milk_filter.cpp:553:13: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/milk_filter.cpp:471:9: note: Shadowed declaration
vt-0.57721/milk_filter.cpp:553:13: note: Shadow variable
vt-0.57721/milk_filter.cpp:559:13: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/milk_filter.cpp:471:9: note: Shadowed declaration
vt-0.57721/milk_filter.cpp:559:13: note: Shadow variable
vt-0.57721/milk_filter.cpp:277:37: style: Parameter 'pls' can be declared as pointer to const [constParameterPointer]
vt-0.57721/milk_filter.cpp:277:79: style: Parameter 'priors' can be declared as pointer to const [constParameterPointer]
vt-0.57721/milk_filter.cpp:333:27: style: Parameter 'pls' can be declared as pointer to const [constParameterPointer]
vt-0.57721/milk_filter.cpp:347:38: style: Parameter 'gts' can be declared as pointer to const [constParameterPointer]
vt-0.57721/milk_filter.cpp:38:30: style: class member 'Igor::exclude_fam_ids' is never used. [unusedStructMember]
vt-0.57721/motif_map.cpp:38:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/motif_map.cpp:186:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/motif_map.h:62:14: performance:inconclusive: Technically the member function 'MotifMap::canonical' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/motif_map.cpp:91:20: note: Technically the member function 'MotifMap::canonical' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_map.h:62:14: note: Technically the member function 'MotifMap::canonical' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_map.h:67:10: performance:inconclusive: Technically the member function 'MotifMap::is_aperiodic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/motif_map.cpp:111:16: note: Technically the member function 'MotifMap::is_aperiodic' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_map.h:67:10: note: Technically the member function 'MotifMap::is_aperiodic' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_map.h:72:14: style:inconclusive: Technically the member function 'MotifMap::index2seq' can be const. [functionConst]
vt-0.57721/motif_map.cpp:144:20: note: Technically the member function 'MotifMap::index2seq' can be const.
vt-0.57721/motif_map.h:72:14: note: Technically the member function 'MotifMap::index2seq' can be const.
vt-0.57721/motif_map.h:77:14: style:inconclusive: Technically the member function 'MotifMap::seq2index' can be const. [functionConst]
vt-0.57721/motif_map.cpp:168:20: note: Technically the member function 'MotifMap::seq2index' can be const.
vt-0.57721/motif_map.h:77:14: note: Technically the member function 'MotifMap::seq2index' can be const.
vt-0.57721/motif_map.h:82:10: performance:inconclusive: Technically the member function 'MotifMap::print_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/motif_map.cpp:182:16: note: Technically the member function 'MotifMap::print_seq' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_map.h:82:10: note: Technically the member function 'MotifMap::print_seq' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_map.h:87:17: performance:inconclusive: Technically the member function 'MotifMap::seq2str' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/motif_map.cpp:194:23: note: Technically the member function 'MotifMap::seq2str' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_map.h:87:17: note: Technically the member function 'MotifMap::seq2str' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_map.cpp:38:9: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/motif_map.cpp:91:39: style:inconclusive: Function 'canonical' argument 1 names different: declaration 'motif' definition 'seq'. [funcArgNamesDifferent]
vt-0.57721/motif_map.h:62:33: note: Function 'canonical' argument 1 names different: declaration 'motif' definition 'seq'.
vt-0.57721/motif_map.cpp:91:39: note: Function 'canonical' argument 1 names different: declaration 'motif' definition 'seq'.
vt-0.57721/motif_tree.cpp:119:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/motif_tree.cpp:282:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/motif_tree.cpp:406:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/motif_tree.cpp:35:12: warning: Member variable 'MotifTree::cmax_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/motif_tree.h:166:17: performance:inconclusive: Technically the member function 'MotifTree::shift_str' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/motif_tree.cpp:197:24: note: Technically the member function 'MotifTree::shift_str' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_tree.h:166:17: note: Technically the member function 'MotifTree::shift_str' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_tree.h:199:13: performance:inconclusive: Technically the member function 'MotifTree::base2index' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/motif_tree.cpp:380:20: note: Technically the member function 'MotifTree::base2index' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_tree.h:199:13: note: Technically the member function 'MotifTree::base2index' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/motif_tree.cpp:38:5: warning: Class 'MotifTree' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/motif_tree.cpp:38:5: warning: Class 'MotifTree' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/motif_tree.cpp:66:15: error: Mismatching allocation and deallocation: MotifTree::tree [mismatchAllocDealloc]
vt-0.57721/motif_tree.cpp:44:13: style: C-style pointer casting [cstyleCast]
vt-0.57721/motif_tree.cpp:252:11: style: The scope of the variable 't' can be reduced. [variableScope]
vt-0.57721/motif_tree.cpp:290:18: style: Local variable 'len' shadows outer argument [shadowArgument]
vt-0.57721/motif_tree.cpp:278:61: note: Shadowed declaration
vt-0.57721/motif_tree.cpp:290:18: note: Shadow variable
vt-0.57721/motif_tree.cpp:197:47: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/motif_tree.cpp:211:47: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/motif_tree.cpp:73:39: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
vt-0.57721/motif_tree.cpp:239:11: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
vt-0.57721/motif_tree.cpp:54:24: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
vt-0.57721/motif_tree.cpp:223:20: style: Variable 's' is assigned a value that is never used. [unreadVariable]
vt-0.57721/motif_tree.cpp:252:13: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/motif_tree.cpp:320:22: style: Variable 'sthreshold' is assigned a value that is never used. [unreadVariable]
vt-0.57721/multi_partition.cpp:133:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/multi_partition.cpp:215:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/multi_partition.cpp:242:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/multi_partition.cpp:108:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/multi_partition.cpp:108:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/multi_partition.cpp:108:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/multi_partition.cpp:76:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/multi_partition.cpp:76:17: note: Derived variable 'Igor::version'
vt-0.57721/multi_partition.cpp:144:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/multi_partition.cpp:144:10: note: Derived function 'Igor::initialize'
vt-0.57721/multi_partition.cpp:213:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/multi_partition.cpp:213:10: note: Derived function 'Igor::print_options'
vt-0.57721/multi_partition.cpp:229:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/multi_partition.cpp:229:10: note: Derived function 'Igor::print_stats'
vt-0.57721/multi_partition.cpp:44:5: style: Class 'OverlapStats' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/multi_partition.cpp:242:13: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/multi_partition.cpp:266:13: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/multi_partition.cpp:269:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/multi_partition.cpp:252:25: style: Local variable 'partition' shadows outer function [shadowFunction]
vt-0.57721/multi_partition.cpp:168:10: note: Shadowed declaration
vt-0.57721/multi_partition.cpp:252:25: note: Shadow variable
vt-0.57721/multi_partition.cpp:196:34: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
vt-0.57721/multi_partition.cpp:34:27: style: class member 'OverlapStats::total' is never used. [unusedStructMember]
vt-0.57721/multi_partition.cpp:81:17: style: class member 'Igor::filters' is never used. [unusedStructMember]
vt-0.57721/multi_partition.cpp:84:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/multi_partition.cpp:174:41: style: Unused variable: out [unusedVariable]
vt-0.57721/multi_partition.cpp:178:21: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/multiallelics_consolidator.cpp:388:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/multiallelics_consolidator.cpp:26:28: warning: Member variable 'MultiallelicsConsolidator::debug' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/multiallelics_consolidator.h:159:14: performance:inconclusive: Technically the member function 'MultiallelicsConsolidator::create_or_update_multiallelic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/multiallelics_consolidator.cpp:263:37: note: Technically the member function 'MultiallelicsConsolidator::create_or_update_multiallelic' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/multiallelics_consolidator.h:159:14: note: Technically the member function 'MultiallelicsConsolidator::create_or_update_multiallelic' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/multiallelics_consolidator.cpp:35:5: warning: Class 'MultiallelicsConsolidator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/multiallelics_consolidator.cpp:35:5: warning: Class 'MultiallelicsConsolidator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/multiallelics_consolidator.cpp:44:15: style: C-style pointer casting [cstyleCast]
vt-0.57721/multiallelics_consolidator.cpp:94:49: style:inconclusive: Function 'insert' argument 1 names different: declaration 'variant' definition 'var'. [funcArgNamesDifferent]
vt-0.57721/multiallelics_consolidator.h:110:26: note: Function 'insert' argument 1 names different: declaration 'variant' definition 'var'.
vt-0.57721/multiallelics_consolidator.cpp:94:49: note: Function 'insert' argument 1 names different: declaration 'variant' definition 'var'.
vt-0.57721/multiallelics_consolidator.cpp:369:75: style:inconclusive: Function 'update_multiallelic_for_printing' argument 1 names different: declaration 'var' definition 'mvar'. [funcArgNamesDifferent]
vt-0.57721/multiallelics_consolidator.h:164:52: note: Function 'update_multiallelic_for_printing' argument 1 names different: declaration 'var' definition 'mvar'.
vt-0.57721/multiallelics_consolidator.cpp:369:75: note: Function 'update_multiallelic_for_printing' argument 1 names different: declaration 'var' definition 'mvar'.
vt-0.57721/multiallelics_consolidator.cpp:26:67: style: Parameter 'input_vcf_file' can be declared as reference to const [constParameterReference]
vt-0.57721/multiallelics_consolidator.cpp:26:136: style: Parameter 'output_vcf_file' can be declared as reference to const [constParameterReference]
vt-0.57721/multiallelics_consolidator.cpp:26:166: style: Parameter 'fexp' can be declared as reference to const [constParameterReference]
vt-0.57721/multiallelics_consolidator.cpp:156:18: style: Variable 'nvar' can be declared as reference to const [constVariableReference]
vt-0.57721/multiallelics_consolidator.cpp:162:22: style: Variable 'cvar' can be declared as reference to const [constVariableReference]
vt-0.57721/multiallelics_consolidator.cpp:100:19: style: Variable 'inserted' is assigned a value that is never used. [unreadVariable]
vt-0.57721/multiallelics_consolidator.cpp:191:17: style: Variable 'var' is assigned a value that is never used. [unreadVariable]
vt-0.57721/needle.cpp:141:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/needle.cpp:31:18: warning: Member variable 'NeedlemanWunsch::ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/needle.cpp:31:18: warning: Member variable 'NeedlemanWunsch::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/needle.cpp:31:18: warning: Member variable 'NeedlemanWunsch::len_ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/needle.cpp:31:18: warning: Member variable 'NeedlemanWunsch::len_read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:128:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/normalize.cpp:190:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/normalize.cpp:336:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/normalize.cpp:359:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_refs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_lt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_rt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_lt_rt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_rt_la' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_la' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_multi_lt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_multi_rt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_multi_lt_rt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_multi_rt_la' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::no_multi_la' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:85:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/normalize.cpp:351:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/normalize.cpp:133:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/normalize.cpp:133:10: note: Derived function 'Igor::initialize'
vt-0.57721/normalize.cpp:332:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/normalize.cpp:332:10: note: Derived function 'Igor::print_options'
vt-0.57721/normalize.cpp:351:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/normalize.cpp:351:10: note: Derived function 'Igor::print_stats'
vt-0.57721/nuclear_pedigree.cpp:53:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/nuclear_pedigree.cpp:112:60: style:inconclusive: Function 'setSampleIndex' argument 2 names different: declaration 'index' definition '_index'. [funcArgNamesDifferent]
vt-0.57721/nuclear_pedigree.h:107:47: note: Function 'setSampleIndex' argument 2 names different: declaration 'index' definition '_index'.
vt-0.57721/nuclear_pedigree.cpp:112:60: note: Function 'setSampleIndex' argument 2 names different: declaration 'index' definition '_index'.
vt-0.57721/nuclear_pedigree.cpp:133:15: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:93:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:222:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:335:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:479:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:501:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:542:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:578:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:29:27: warning: Member variable 'OrderedBCFOverlapMatcher::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:29:27: warning: Member variable 'OrderedBCFOverlapMatcher::end_of_file' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:29:27: warning: Member variable 'OrderedBCFOverlapMatcher::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:47:27: warning: Member variable 'OrderedBCFOverlapMatcher::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:47:27: warning: Member variable 'OrderedBCFOverlapMatcher::end_of_file' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:49:5: warning: Class 'OrderedBCFOverlapMatcher' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:49:5: warning: Class 'OrderedBCFOverlapMatcher' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:170:67: style:inconclusive: Function 'overlaps_with' argument 2 names different: declaration 'start1' definition 'beg1'. [funcArgNamesDifferent]
vt-0.57721/ordered_bcf_overlap_matcher.h:93:45: note: Function 'overlaps_with' argument 2 names different: declaration 'start1' definition 'beg1'.
vt-0.57721/ordered_bcf_overlap_matcher.cpp:170:67: note: Function 'overlaps_with' argument 2 names different: declaration 'start1' definition 'beg1'.
vt-0.57721/ordered_bcf_overlap_matcher.cpp:47:123: performance: Function parameter 'fexp' should be passed by const reference. [passedByValue]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:29:65: style: Parameter 'file' can be declared as reference to const [constParameterReference]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:47:65: style: Parameter 'file' can be declared as reference to const [constParameterReference]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:77:59: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/ordered_bcf_overlap_matcher.cpp:624:96: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/ordered_region_overlap_matcher.cpp:29:30: warning: Member variable 'OrderedRegionOverlapMatcher::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ordered_region_overlap_matcher.cpp:29:30: warning: Member variable 'OrderedRegionOverlapMatcher::end_of_file' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/ordered_region_overlap_matcher.cpp:31:5: warning: Class 'OrderedRegionOverlapMatcher' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/ordered_region_overlap_matcher.cpp:31:5: warning: Class 'OrderedRegionOverlapMatcher' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/ordered_region_overlap_matcher.cpp:45:62: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/partition.cpp:119:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/partition.cpp:302:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/partition.cpp:331:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/partition.cpp:95:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/partition.cpp:95:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/partition.cpp:95:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/partition.cpp:62:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/partition.cpp:62:17: note: Derived variable 'Igor::version'
vt-0.57721/partition.cpp:139:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/partition.cpp:139:10: note: Derived function 'Igor::initialize'
vt-0.57721/partition.cpp:300:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/partition.cpp:300:10: note: Derived function 'Igor::print_options'
vt-0.57721/partition.cpp:329:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/partition.cpp:329:10: note: Derived function 'Igor::print_stats'
vt-0.57721/partition.cpp:331:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/partition.cpp:332:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/partition.cpp:335:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/partition.cpp:336:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/partition.cpp:337:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/partition.cpp:224:34: style: Variable 'alleles' can be declared as reference to const [constVariableReference]
vt-0.57721/partition.cpp:268:53: style: Parameter 'presence' can be declared as reference to const [constParameterReference]
vt-0.57721/partition.cpp:69:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/partition.cpp:202:21: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste.cpp:98:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/paste.cpp:145:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
vt-0.57721/paste.cpp:348:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/paste.cpp:358:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/paste.cpp:61:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/paste.cpp:354:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/paste.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/paste.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/paste.cpp:109:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/paste.cpp:109:10: note: Derived function 'Igor::initialize'
vt-0.57721/paste.cpp:344:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/paste.cpp:344:10: note: Derived function 'Igor::print_options'
vt-0.57721/paste.cpp:354:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/paste.cpp:354:10: note: Derived function 'Igor::print_stats'
vt-0.57721/paste.cpp:246:37: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste.cpp:275:35: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste.cpp:304:35: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste.cpp:161:20: style: Variable 'ncount' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste.cpp:163:43: style: Variable 'sample2record' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste.cpp:164:42: style: Variable 'sample2index' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste.cpp:252:35: style: Variable 'b' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste.cpp:281:35: style: Variable 'b' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste.cpp:311:35: style: Variable 'b' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste.cpp:160:30: style: Unused variable: current_recs [unusedVariable]
vt-0.57721/paste.cpp:174:34: style: Unused variable: genotype_fields [unusedVariable]
vt-0.57721/paste_and_compute_features_sequential.cpp:108:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_and_compute_features_sequential.cpp:129:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_and_compute_features_sequential.cpp:273:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_and_compute_features_sequential.cpp:740:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_and_compute_features_sequential.cpp:750:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_and_compute_features_sequential.cpp:539:28: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/paste_and_compute_features_sequential.cpp:540:28: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/paste_and_compute_features_sequential.cpp:541:28: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/paste_and_compute_features_sequential.cpp:542:28: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/paste_and_compute_features_sequential.cpp:66:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/paste_and_compute_features_sequential.cpp:66:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/paste_and_compute_features_sequential.cpp:183:11: performance:inconclusive: Technically the member function '::Igor::compute_correlation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/paste_and_compute_features_sequential.cpp:190:11: performance:inconclusive: Technically the member function '::Igor::compute_correlation_f' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/paste_and_compute_features_sequential.cpp:746:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/paste_and_compute_features_sequential.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/paste_and_compute_features_sequential.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/paste_and_compute_features_sequential.cpp:120:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/paste_and_compute_features_sequential.cpp:120:10: note: Derived function 'Igor::initialize'
vt-0.57721/paste_and_compute_features_sequential.cpp:736:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/paste_and_compute_features_sequential.cpp:736:10: note: Derived function 'Igor::print_options'
vt-0.57721/paste_and_compute_features_sequential.cpp:746:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/paste_and_compute_features_sequential.cpp:746:10: note: Derived function 'Igor::print_stats'
vt-0.57721/paste_and_compute_features_sequential.cpp:308:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_and_compute_features_sequential.cpp:309:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_and_compute_features_sequential.cpp:310:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_and_compute_features_sequential.cpp:311:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_and_compute_features_sequential.cpp:312:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_and_compute_features_sequential.cpp:612:14: style: The scope of the variable 'gp' can be reduced. [variableScope]
vt-0.57721/paste_and_compute_features_sequential.cpp:612:18: style: The scope of the variable 'gp_sum' can be reduced. [variableScope]
vt-0.57721/paste_and_compute_features_sequential.cpp:612:26: style: The scope of the variable 'max_gp' can be reduced. [variableScope]
vt-0.57721/paste_and_compute_features_sequential.cpp:613:15: style: The scope of the variable 'best_gt' can be reduced. [variableScope]
vt-0.57721/paste_and_compute_features_sequential.cpp:614:15: style: The scope of the variable 'best_a1' can be reduced. [variableScope]
vt-0.57721/paste_and_compute_features_sequential.cpp:614:24: style: The scope of the variable 'best_a2' can be reduced. [variableScope]
vt-0.57721/paste_and_compute_features_sequential.cpp:615:16: style: The scope of the variable 'pls_i' can be reduced. [variableScope]
vt-0.57721/paste_and_compute_features_sequential.cpp:615:16: style: Variable 'pls_i' can be declared as pointer to const [constVariablePointer]
vt-0.57721/paste_and_compute_features_sequential.cpp:690:16: style: Variable 'MLE_AF_PTR' can be declared as pointer to const [constVariablePointer]
vt-0.57721/paste_and_compute_features_sequential.cpp:626:30: style: Variable 'gp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste_and_compute_features_sequential.cpp:690:27: style: Variable 'MLE_AF_PTR' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste_genotypes.cpp:115:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_genotypes.cpp:134:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_genotypes.cpp:278:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_genotypes.cpp:772:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_genotypes.cpp:782:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/paste_genotypes.cpp:559:26: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/paste_genotypes.cpp:560:26: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/paste_genotypes.cpp:561:26: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/paste_genotypes.cpp:562:26: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/paste_genotypes.cpp:69:5: warning: Member variable 'Igor::contam_fixed' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/paste_genotypes.cpp:69:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/paste_genotypes.cpp:69:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/paste_genotypes.cpp:188:11: performance:inconclusive: Technically the member function '::Igor::compute_correlation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/paste_genotypes.cpp:195:11: performance:inconclusive: Technically the member function '::Igor::compute_correlation_f' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/paste_genotypes.cpp:778:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/paste_genotypes.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/paste_genotypes.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/paste_genotypes.cpp:126:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/paste_genotypes.cpp:126:10: note: Derived function 'Igor::initialize'
vt-0.57721/paste_genotypes.cpp:768:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/paste_genotypes.cpp:768:10: note: Derived function 'Igor::print_options'
vt-0.57721/paste_genotypes.cpp:778:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/paste_genotypes.cpp:778:10: note: Derived function 'Igor::print_stats'
vt-0.57721/paste_genotypes.cpp:313:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_genotypes.cpp:314:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_genotypes.cpp:315:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_genotypes.cpp:316:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_genotypes.cpp:317:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/paste_genotypes.cpp:640:14: style: The scope of the variable 'gp' can be reduced. [variableScope]
vt-0.57721/paste_genotypes.cpp:640:18: style: The scope of the variable 'gp_sum' can be reduced. [variableScope]
vt-0.57721/paste_genotypes.cpp:640:26: style: The scope of the variable 'max_gp' can be reduced. [variableScope]
vt-0.57721/paste_genotypes.cpp:641:15: style: The scope of the variable 'best_gt' can be reduced. [variableScope]
vt-0.57721/paste_genotypes.cpp:642:15: style: The scope of the variable 'best_a1' can be reduced. [variableScope]
vt-0.57721/paste_genotypes.cpp:642:24: style: The scope of the variable 'best_a2' can be reduced. [variableScope]
vt-0.57721/paste_genotypes.cpp:643:16: style: The scope of the variable 'pls_i' can be reduced. [variableScope]
vt-0.57721/paste_genotypes.cpp:643:16: style: Variable 'pls_i' can be declared as pointer to const [constVariablePointer]
vt-0.57721/paste_genotypes.cpp:718:16: style: Variable 'MLE_AF_PTR' can be declared as pointer to const [constVariablePointer]
vt-0.57721/paste_genotypes.cpp:44:12: style: class member 'Igor::contam_fixed' is never used. [unusedStructMember]
vt-0.57721/paste_genotypes.cpp:45:17: style: class member 'Igor::contam_file_list' is never used. [unusedStructMember]
vt-0.57721/paste_genotypes.cpp:654:30: style: Variable 'gp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/paste_genotypes.cpp:718:27: style: Variable 'MLE_AF_PTR' is assigned a value that is never used. [unreadVariable]
vt-0.57721/pedigree.cpp:76:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pedigree.h:55:10: style:inconclusive: Technically the member function 'PEDRecord::is_trio' can be const. [functionConst]
vt-0.57721/pedigree.cpp:42:17: note: Technically the member function 'PEDRecord::is_trio' can be const.
vt-0.57721/pedigree.h:55:10: note: Technically the member function 'PEDRecord::is_trio' can be const.
vt-0.57721/pedigree.h:60:10: style:inconclusive: Technically the member function 'PEDRecord::is_duplicated' can be const. [functionConst]
vt-0.57721/pedigree.cpp:50:17: note: Technically the member function 'PEDRecord::is_duplicated' can be const.
vt-0.57721/pedigree.h:60:10: note: Technically the member function 'PEDRecord::is_duplicated' can be const.
vt-0.57721/pedigree.h:65:10: style:inconclusive: Technically the member function 'PEDRecord::is_male' can be const. [functionConst]
vt-0.57721/pedigree.cpp:58:17: note: Technically the member function 'PEDRecord::is_male' can be const.
vt-0.57721/pedigree.h:65:10: note: Technically the member function 'PEDRecord::is_male' can be const.
vt-0.57721/pedigree.h:70:10: style:inconclusive: Technically the member function 'PEDRecord::is_female' can be const. [functionConst]
vt-0.57721/pedigree.cpp:66:17: note: Technically the member function 'PEDRecord::is_female' can be const.
vt-0.57721/pedigree.h:70:10: note: Technically the member function 'PEDRecord::is_female' can be const.
vt-0.57721/pedigree.cpp:79:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
vt-0.57721/pedigree.cpp:29:34: performance: Function parameter 'pedigree' should be passed by const reference. [passedByValue]
vt-0.57721/pedigree.cpp:30:34: performance: Function parameter 'father' should be passed by const reference. [passedByValue]
vt-0.57721/pedigree.cpp:30:54: performance: Function parameter 'mother' should be passed by const reference. [passedByValue]
vt-0.57721/pedigree.cpp:29:70: style: Parameter 'individual' can be declared as reference to const [constParameterReference]
vt-0.57721/pedigree.cpp:89:33: style: Parameter 'ped_file' can be declared as reference to const [constParameterReference]
vt-0.57721/peek.cpp:192:5: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_INT is a macro then please configure it. [unknownMacro]
vt-0.57721/pileup.cpp:93:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:170:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:238:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:307:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:424:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:540:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:601:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:676:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:706:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:728:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:794:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:838:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:902:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:946:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:964:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:976:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:994:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/pileup.cpp:179:9: warning: Member variable 'Pileup::fai' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pileup.h:100:10: style:inconclusive: Technically the member function 'PileupPosition::is_cleared' can be const. [functionConst]
vt-0.57721/pileup.cpp:69:22: note: Technically the member function 'PileupPosition::is_cleared' can be const.
vt-0.57721/pileup.h:100:10: note: Technically the member function 'PileupPosition::is_cleared' can be const.
vt-0.57721/pileup.h:188:14: style:inconclusive: Technically the member function 'Pileup::max_size' can be const. [functionConst]
vt-0.57721/pileup.cpp:207:18: note: Technically the member function 'Pileup::max_size' can be const.
vt-0.57721/pileup.h:188:14: note: Technically the member function 'Pileup::max_size' can be const.
vt-0.57721/pileup.h:193:14: style:inconclusive: Technically the member function 'Pileup::size' can be const. [functionConst]
vt-0.57721/pileup.cpp:215:18: note: Technically the member function 'Pileup::size' can be const.
vt-0.57721/pileup.h:193:14: note: Technically the member function 'Pileup::size' can be const.
vt-0.57721/pileup.h:198:10: style:inconclusive: Technically the member function 'Pileup::is_empty' can be const. [functionConst]
vt-0.57721/pileup.cpp:223:14: note: Technically the member function 'Pileup::is_empty' can be const.
vt-0.57721/pileup.h:198:10: note: Technically the member function 'Pileup::is_empty' can be const.
vt-0.57721/pileup.h:218:14: style:inconclusive: Technically the member function 'Pileup::get_tid' can be const. [functionConst]
vt-0.57721/pileup.cpp:263:18: note: Technically the member function 'Pileup::get_tid' can be const.
vt-0.57721/pileup.h:218:14: note: Technically the member function 'Pileup::get_tid' can be const.
vt-0.57721/pileup.h:228:17: style:inconclusive: Technically the member function 'Pileup::get_chrom' can be const. [functionConst]
vt-0.57721/pileup.cpp:279:21: note: Technically the member function 'Pileup::get_chrom' can be const.
vt-0.57721/pileup.h:228:17: note: Technically the member function 'Pileup::get_chrom' can be const.
vt-0.57721/pileup.h:233:14: style:inconclusive: Technically the member function 'Pileup::get_window_size' can be const. [functionConst]
vt-0.57721/pileup.cpp:287:18: note: Technically the member function 'Pileup::get_window_size' can be const.
vt-0.57721/pileup.h:233:14: note: Technically the member function 'Pileup::get_window_size' can be const.
vt-0.57721/pileup.h:243:14: style:inconclusive: Technically the member function 'Pileup::get_gbeg1' can be const. [functionConst]
vt-0.57721/pileup.cpp:333:18: note: Technically the member function 'Pileup::get_gbeg1' can be const.
vt-0.57721/pileup.h:243:14: note: Technically the member function 'Pileup::get_gbeg1' can be const.
vt-0.57721/pileup.h:263:14: style:inconclusive: Technically the member function 'Pileup::begin' can be const. [functionConst]
vt-0.57721/pileup.cpp:372:18: note: Technically the member function 'Pileup::begin' can be const.
vt-0.57721/pileup.h:263:14: note: Technically the member function 'Pileup::begin' can be const.
vt-0.57721/pileup.h:268:14: style:inconclusive: Technically the member function 'Pileup::end' can be const. [functionConst]
vt-0.57721/pileup.cpp:380:18: note: Technically the member function 'Pileup::end' can be const.
vt-0.57721/pileup.h:268:14: note: Technically the member function 'Pileup::end' can be const.
vt-0.57721/pileup.h:273:14: style:inconclusive: Technically the member function 'Pileup::inc' can be const. [functionConst]
vt-0.57721/pileup.cpp:317:18: note: Technically the member function 'Pileup::inc' can be const.
vt-0.57721/pileup.h:273:14: note: Technically the member function 'Pileup::inc' can be const.
vt-0.57721/pileup.h:288:14: style:inconclusive: Technically the member function 'Pileup::inc' can be const. [functionConst]
vt-0.57721/pileup.cpp:412:18: note: Technically the member function 'Pileup::inc' can be const.
vt-0.57721/pileup.h:288:14: note: Technically the member function 'Pileup::inc' can be const.
vt-0.57721/pileup.h:298:14: style:inconclusive: Technically the member function 'Pileup::diff' can be const. [functionConst]
vt-0.57721/pileup.cpp:388:18: note: Technically the member function 'Pileup::diff' can be const.
vt-0.57721/pileup.h:298:14: note: Technically the member function 'Pileup::diff' can be const.
vt-0.57721/pileup.h:379:10: performance:inconclusive: Technically the member function 'Pileup::is_normalized' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/pileup.cpp:890:14: note: Technically the member function 'Pileup::is_normalized' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/pileup.h:379:10: note: Technically the member function 'Pileup::is_normalized' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/pileup.h:391:14: performance:inconclusive: Technically the member function 'Pileup::base2index' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/pileup.cpp:918:18: note: Technically the member function 'Pileup::base2index' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/pileup.h:391:14: note: Technically the member function 'Pileup::base2index' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/pileup.h:228:17: performance: Function 'get_chrom()' should return member 'chrom' by const reference. [returnByReference]
vt-0.57721/pileup.cpp:307:13: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:307:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:559:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:559:13: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:601:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:601:13: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:676:13: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:676:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:794:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:794:13: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:838:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:838:13: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:946:9: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:964:9: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/pileup.cpp:441:29: style:inconclusive: Function 'add_M' argument 1 names different: declaration 'gpos1' definition 'mgpos1'. [funcArgNamesDifferent]
vt-0.57721/pileup.h:303:25: note: Function 'add_M' argument 1 names different: declaration 'gpos1' definition 'mgpos1'.
vt-0.57721/pileup.cpp:441:29: note: Function 'add_M' argument 1 names different: declaration 'gpos1' definition 'mgpos1'.
vt-0.57721/pileup.cpp:231:41: style: Parameter 'ref_fasta_file' can be declared as reference to const [constParameterReference]
vt-0.57721/pileup.cpp:271:37: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/pileup.cpp:890:51: style: Parameter 'indel' can be declared as reference to const [constParameterReference]
vt-0.57721/pileup.cpp:940:36: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/pileup.cpp:940:53: style: Parameter 'pos1' can be declared as reference to const [constParameterReference]
vt-0.57721/pileup.cpp:958:41: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/pileup.cpp:441:90: style: Parameter 'qual' can be declared as pointer to const [constParameterPointer]
vt-0.57721/pregex.cpp:66:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PCRE2_ZERO_TERMINATED [valueFlowBailoutIncompleteVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::crlf_is_newline' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::errornumber' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::find_all' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::i' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::namecount' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::name_entry_size' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::rc' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::utf8' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::option_bits' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::newline' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::ovector' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:29:12: warning: Member variable 'PERLregex::subject_length' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/pregex.cpp:31:4: performance: Variable 'regex' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/pregex.cpp:97:29: style: C-style pointer casting [cstyleCast]
vt-0.57721/profile_afs.cpp:111:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_afs.cpp:129:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable afs [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_afs.cpp:152:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_afs.cpp:225:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_afs.cpp:240:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_afs.cpp:289:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_afs.cpp:301:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable afs [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_afs.cpp:78:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_afs.cpp:78:5: warning: Member variable 'Igor::ret' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_afs.cpp:78:5: warning: Member variable 'Igor::is_missing' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_afs.cpp:78:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_afs.cpp:78:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_afs.cpp:78:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_afs.cpp:105:13: warning: Class 'Igor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/profile_afs.cpp:105:13: warning: Class 'Igor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/profile_afs.cpp:35:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_afs.cpp:35:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_afs.cpp:116:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_afs.cpp:116:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_afs.cpp:223:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_afs.cpp:223:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_afs.cpp:287:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_afs.cpp:287:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_afs.cpp:290:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_afs.cpp:284:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
vt-0.57721/profile_afs.cpp:56:9: note: Shadowed declaration
vt-0.57721/profile_afs.cpp:284:17: note: Shadow variable
vt-0.57721/profile_afs.cpp:46:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_afs.cpp:56:14: style: class member 'Igor::is_missing' is never used. [unusedStructMember]
vt-0.57721/profile_afs.cpp:161:25: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_afs.cpp:284:21: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_chm1.cpp:188:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chm1.cpp:241:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chm1.cpp:300:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chm1.cpp:554:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chm1.cpp:566:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::no_filters' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::no_positive_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::no_negative_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::ts' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::tv' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::syn' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::nsyn' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::ins' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::del' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::fs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::nfs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:155:5: warning: Member variable 'Igor::orom_gencode_cds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chm1.cpp:97:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_chm1.cpp:97:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_chm1.cpp:193:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_chm1.cpp:193:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_chm1.cpp:552:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_chm1.cpp:552:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_chm1.cpp:564:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_chm1.cpp:564:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_chm1.cpp:293:28: style: The scope of the variable 'k0' can be reduced. [variableScope]
vt-0.57721/profile_chm1.cpp:338:21: style: The scope of the variable 'start1' can be reduced. [variableScope]
vt-0.57721/profile_chm1.cpp:391:29: style: The scope of the variable 'y1' can be reduced. [variableScope]
vt-0.57721/profile_chm1.cpp:392:29: style: The scope of the variable 'y2' can be reduced. [variableScope]
vt-0.57721/profile_chm1.cpp:313:21: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/profile_chm1.cpp:121:13: note: Shadowed declaration
vt-0.57721/profile_chm1.cpp:313:21: note: Shadow variable
vt-0.57721/profile_chm1.cpp:357:21: style: Local variable 'ts' shadows outer variable [shadowVariable]
vt-0.57721/profile_chm1.cpp:140:13: note: Shadowed declaration
vt-0.57721/profile_chm1.cpp:357:21: note: Shadow variable
vt-0.57721/profile_chm1.cpp:358:21: style: Local variable 'tv' shadows outer variable [shadowVariable]
vt-0.57721/profile_chm1.cpp:141:13: note: Shadowed declaration
vt-0.57721/profile_chm1.cpp:358:21: note: Shadow variable
vt-0.57721/profile_chm1.cpp:359:21: style: Local variable 'ins' shadows outer variable [shadowVariable]
vt-0.57721/profile_chm1.cpp:144:13: note: Shadowed declaration
vt-0.57721/profile_chm1.cpp:359:21: note: Shadow variable
vt-0.57721/profile_chm1.cpp:360:21: style: Local variable 'del' shadows outer variable [shadowVariable]
vt-0.57721/profile_chm1.cpp:145:13: note: Shadowed declaration
vt-0.57721/profile_chm1.cpp:360:21: note: Shadow variable
vt-0.57721/profile_chm1.cpp:611:21: style: Local variable 'concordance' shadows outer variable [shadowVariable]
vt-0.57721/profile_chm1.cpp:136:35: note: Shadowed declaration
vt-0.57721/profile_chm1.cpp:611:21: note: Shadow variable
vt-0.57721/profile_chm1.cpp:612:26: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/profile_chm1.cpp:607:22: note: Shadowed declaration
vt-0.57721/profile_chm1.cpp:612:26: note: Shadow variable
vt-0.57721/profile_chm1.cpp:106:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_chm1.cpp:121:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/profile_chm1.cpp:140:13: style: class member 'Igor::ts' is never used. [unusedStructMember]
vt-0.57721/profile_chm1.cpp:141:13: style: class member 'Igor::tv' is never used. [unusedStructMember]
vt-0.57721/profile_chm1.cpp:142:13: style: class member 'Igor::syn' is never used. [unusedStructMember]
vt-0.57721/profile_chm1.cpp:143:13: style: class member 'Igor::nsyn' is never used. [unusedStructMember]
vt-0.57721/profile_chm1.cpp:144:13: style: class member 'Igor::ins' is never used. [unusedStructMember]
vt-0.57721/profile_chm1.cpp:145:13: style: class member 'Igor::del' is never used. [unusedStructMember]
vt-0.57721/profile_chm1.cpp:371:23: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_chm1.cpp:391:32: style: Variable 'y1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_chm1.cpp:392:32: style: Variable 'y2' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_chm1.cpp:519:27: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_chm1.cpp:283:32: style: Unused variable: overlaps [unusedVariable]
vt-0.57721/profile_chm1.cpp:308:17: style: Variable 'discordance_filter' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_chm1.cpp:315:21: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_chrom.cpp:105:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chrom.cpp:123:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chrom.cpp:145:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chrom.cpp:198:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chrom.cpp:211:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chrom.cpp:275:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chrom.cpp:312:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_chrom.cpp:76:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chrom.cpp:76:5: warning: Member variable 'Igor::ret' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chrom.cpp:76:5: warning: Member variable 'Igor::is_missing' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chrom.cpp:76:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chrom.cpp:76:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chrom.cpp:76:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_chrom.cpp:35:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_chrom.cpp:35:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_chrom.cpp:110:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_chrom.cpp:110:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_chrom.cpp:196:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_chrom.cpp:196:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_chrom.cpp:273:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_chrom.cpp:273:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_chrom.cpp:241:12: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/profile_chrom.cpp:240:12: note: First condition
vt-0.57721/profile_chrom.cpp:241:12: note: Second condition
vt-0.57721/profile_chrom.cpp:306:12: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/profile_chrom.cpp:305:12: note: First condition
vt-0.57721/profile_chrom.cpp:306:12: note: Second condition
vt-0.57721/profile_chrom.cpp:276:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_chrom.cpp:270:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
vt-0.57721/profile_chrom.cpp:54:9: note: Shadowed declaration
vt-0.57721/profile_chrom.cpp:270:17: note: Shadow variable
vt-0.57721/profile_chrom.cpp:44:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_chrom.cpp:54:14: style: class member 'Igor::is_missing' is never used. [unusedStructMember]
vt-0.57721/profile_chrom.cpp:154:25: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_chrom.cpp:270:21: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_fic_hwe.cpp:111:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_fic_hwe.cpp:129:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable afs [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_fic_hwe.cpp:152:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_fic_hwe.cpp:213:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_fic_hwe.cpp:228:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_fic_hwe.cpp:277:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_fic_hwe.cpp:289:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable afs [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_fic_hwe.cpp:78:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_fic_hwe.cpp:78:5: warning: Member variable 'Igor::ret' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_fic_hwe.cpp:78:5: warning: Member variable 'Igor::is_missing' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_fic_hwe.cpp:78:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_fic_hwe.cpp:78:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_fic_hwe.cpp:78:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_fic_hwe.cpp:105:13: warning: Class 'Igor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/profile_fic_hwe.cpp:105:13: warning: Class 'Igor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/profile_fic_hwe.cpp:35:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_fic_hwe.cpp:35:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_fic_hwe.cpp:116:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_fic_hwe.cpp:116:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_fic_hwe.cpp:211:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_fic_hwe.cpp:211:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_fic_hwe.cpp:275:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_fic_hwe.cpp:275:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_fic_hwe.cpp:278:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_fic_hwe.cpp:272:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
vt-0.57721/profile_fic_hwe.cpp:56:9: note: Shadowed declaration
vt-0.57721/profile_fic_hwe.cpp:272:17: note: Shadow variable
vt-0.57721/profile_fic_hwe.cpp:46:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_fic_hwe.cpp:56:14: style: class member 'Igor::is_missing' is never used. [unusedStructMember]
vt-0.57721/profile_fic_hwe.cpp:163:25: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_fic_hwe.cpp:272:21: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_hwe.cpp:117:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_hwe.cpp:156:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_hwe.cpp:207:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_hwe.cpp:222:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_hwe.cpp:292:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_hwe.cpp:84:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_hwe.cpp:84:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_hwe.cpp:84:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_hwe.cpp:84:5: warning: Member variable 'Igor::pedigree' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_hwe.cpp:84:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_hwe.cpp:111:13: warning: Class 'Igor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/profile_hwe.cpp:111:13: warning: Class 'Igor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/profile_hwe.cpp:43:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_hwe.cpp:43:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_hwe.cpp:122:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_hwe.cpp:122:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_hwe.cpp:205:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_hwe.cpp:205:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_hwe.cpp:290:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_hwe.cpp:290:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_hwe.cpp:54:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_hwe.cpp:81:15: style: class member 'Igor::pedigree' is never used. [unusedStructMember]
vt-0.57721/profile_hwe.cpp:160:25: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_hwe.cpp:287:21: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_indels.cpp:143:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_indels.cpp:202:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_indels.cpp:347:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_indels.cpp:366:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_indels.cpp:425:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::no_filters' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::no_indels' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::nfs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::fs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::lcplx' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::orom_lcplx' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:106:5: warning: Member variable 'Igor::orom_gencode_cds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_indels.cpp:53:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_indels.cpp:53:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_indels.cpp:148:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_indels.cpp:148:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_indels.cpp:345:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_indels.cpp:345:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_indels.cpp:423:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_indels.cpp:423:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_indels.cpp:383:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:383:9: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:383:9: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:403:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:403:13: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:403:13: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:404:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:404:13: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:404:13: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:405:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:405:13: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:405:13: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:435:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:436:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:437:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_indels.cpp:257:21: style: The scope of the variable 'start1' can be reduced. [variableScope]
vt-0.57721/profile_indels.cpp:258:21: style: The scope of the variable 'end1' can be reduced. [variableScope]
vt-0.57721/profile_indels.cpp:252:21: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/profile_indels.cpp:80:13: note: Shadowed declaration
vt-0.57721/profile_indels.cpp:252:21: note: Shadow variable
vt-0.57721/profile_indels.cpp:65:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_indels.cpp:80:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/profile_indels.cpp:243:32: style: Unused variable: overlaps [unusedVariable]
vt-0.57721/profile_indels.cpp:254:21: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_indels.cpp:366:21: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_indels.cpp:371:28: style: Variable 'g2s' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_indels.cpp:420:25: style: Variable 'sys_ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_len.cpp:117:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_len.cpp:157:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_ALL [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_len.cpp:220:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_len.cpp:235:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_len.cpp:307:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_len.cpp:84:5: warning: Member variable 'Igor::GENCODE_NFS' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_len.cpp:84:5: warning: Member variable 'Igor::GENCODE_FS' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_len.cpp:84:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_len.cpp:84:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_len.cpp:84:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_len.cpp:84:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_len.cpp:111:13: warning: Class 'Igor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/profile_len.cpp:111:13: warning: Class 'Igor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/profile_len.cpp:41:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_len.cpp:41:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_len.cpp:122:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_len.cpp:122:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_len.cpp:218:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_len.cpp:218:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_len.cpp:305:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_len.cpp:305:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_len.cpp:308:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_len.cpp:151:21: style: C-style pointer casting [cstyleCast]
vt-0.57721/profile_len.cpp:152:21: style: C-style pointer casting [cstyleCast]
vt-0.57721/profile_len.cpp:51:17: style: class member 'Igor::GENCODE_NFS' is never used. [unusedStructMember]
vt-0.57721/profile_len.cpp:52:17: style: class member 'Igor::GENCODE_FS' is never used. [unusedStructMember]
vt-0.57721/profile_len.cpp:55:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_len.cpp:301:25: style: Variable 'cmd' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:153:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:167:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:274:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:841:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:1166:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRWXU [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:1284:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:1352:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:1392:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:1409:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:1459:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_mendelian.cpp:1114:24: warning: Either the condition 'a==-1' is redundant or the array 'gt[3][3]' is accessed at index gt[-1][*], which is out of bounds. [negativeIndex]
vt-0.57721/profile_mendelian.cpp:1112:14: note: Assuming that condition 'a==-1' is not redundant
vt-0.57721/profile_mendelian.cpp:1114:24: note: Negative array index
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::no_trios' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::no_dups' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::no_biallelic_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::no_biallelic_variants_dups' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::no_multiallelic_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::duplicate_biallelic_vntr_genotypes_concordant' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::duplicate_biallelic_vntr_genotypes_disconcordant' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::no_failed_min_depth' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::trio_genotypes' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::trio_multiallelic_genotypes' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::duplicate_genotypes' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::pedigree' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:111:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_mendelian.cpp:853:10: performance:inconclusive: Technically the member function '::Igor::is_mendelian_discordant' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/profile_mendelian.cpp:859:10: performance:inconclusive: Technically the member function '::Igor::is_duplicate_discordant' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/profile_mendelian.cpp:864:11: performance:inconclusive: Technically the member function '::Igor::get_error_rate' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/profile_mendelian.cpp:996:11: performance:inconclusive: Technically the member function '::Igor::get_homhet_ratio' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/profile_mendelian.cpp:1051:11: performance:inconclusive: Technically the member function '::Igor::get_homhet_proportion' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/profile_mendelian.cpp:1106:11: performance:inconclusive: Technically the member function '::Igor::get_dups_error_rate' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/profile_mendelian.cpp:46:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_mendelian.cpp:46:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_mendelian.cpp:158:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_mendelian.cpp:158:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_mendelian.cpp:839:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_mendelian.cpp:839:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_mendelian.cpp:1270:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_mendelian.cpp:1270:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_mendelian.cpp:762:36: style: Expression is always true because 'else if' condition is opposite to previous condition at line 757. [multiCondition]
vt-0.57721/profile_mendelian.cpp:757:36: note: first condition
vt-0.57721/profile_mendelian.cpp:762:36: note: else if condition is opposite to first condition
vt-0.57721/profile_mendelian.cpp:789:36: style: Expression is always true because 'else if' condition is opposite to previous condition at line 784. [multiCondition]
vt-0.57721/profile_mendelian.cpp:784:36: note: first condition
vt-0.57721/profile_mendelian.cpp:789:36: note: else if condition is opposite to first condition
vt-0.57721/profile_mendelian.cpp:1254:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1255:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1341:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1342:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1344:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1381:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1382:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1384:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1442:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1443:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:1445:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_mendelian.cpp:339:24: style: C-style pointer casting [cstyleCast]
vt-0.57721/profile_mendelian.cpp:993:20: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/profile_mendelian.cpp:1048:30: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/profile_mendelian.cpp:1103:36: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/profile_mendelian.cpp:1157:24: style: Same expression on both sides of '/'. [duplicateExpression]
vt-0.57721/profile_mendelian.cpp:260:17: style: Local variable 'variant' shadows outer variable [shadowVariable]
vt-0.57721/profile_mendelian.cpp:72:15: note: Shadowed declaration
vt-0.57721/profile_mendelian.cpp:260:17: note: Shadow variable
vt-0.57721/profile_mendelian.cpp:1117:29: style: Local variable 'b' shadows outer argument [shadowArgument]
vt-0.57721/profile_mendelian.cpp:1106:68: note: Shadowed declaration
vt-0.57721/profile_mendelian.cpp:1117:29: note: Shadow variable
vt-0.57721/profile_mendelian.cpp:1131:26: style: Local variable 'b' shadows outer argument [shadowArgument]
vt-0.57721/profile_mendelian.cpp:1106:68: note: Shadowed declaration
vt-0.57721/profile_mendelian.cpp:1131:26: note: Shadow variable
vt-0.57721/profile_mendelian.cpp:1142:26: style: Local variable 'a' shadows outer argument [shadowArgument]
vt-0.57721/profile_mendelian.cpp:1106:57: note: Shadowed declaration
vt-0.57721/profile_mendelian.cpp:1142:26: note: Shadow variable
vt-0.57721/profile_mendelian.cpp:748:45: error: Uninitialized variable: min_dp [legacyUninitvar]
vt-0.57721/profile_mendelian.cpp:775:45: error: Uninitialized variable: min_dp [legacyUninitvar]
vt-0.57721/profile_mendelian.cpp:57:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_mendelian.cpp:99:54: style: class member 'Igor::trios_multiallelic_genotypes' is never used. [unusedStructMember]
vt-0.57721/profile_mendelian.cpp:496:27: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:587:42: style: Variable 'variant_used' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:719:23: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:748:36: style: Variable 'min_dp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:775:36: style: Variable 'min_dp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:334:17: style: Variable 'missing' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:335:17: style: Variable 'mendel_homalt_err' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:367:25: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:605:21: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:1166:21: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:1267:25: style: Variable 'sys_ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:1430:20: style: Variable 'rr' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:1431:20: style: Variable 'ra' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_mendelian.cpp:1432:20: style: Variable 'aa' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_na12878.cpp:209:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_na12878.cpp:264:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_na12878.cpp:385:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_SAMPLE [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_na12878.cpp:840:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_na12878.cpp:852:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::no_filters' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::no_positive_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::no_negative_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::ts' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::tv' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::syn' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::nsyn' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::ins' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::del' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::fs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::nfs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:170:5: warning: Member variable 'Igor::orom_gencode_cds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_na12878.cpp:102:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_na12878.cpp:102:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_na12878.cpp:214:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_na12878.cpp:214:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_na12878.cpp:838:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_na12878.cpp:838:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_na12878.cpp:850:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_na12878.cpp:850:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_na12878.cpp:432:21: style: The scope of the variable 'start1' can be reduced. [variableScope]
vt-0.57721/profile_na12878.cpp:505:29: style: The scope of the variable 'y1' can be reduced. [variableScope]
vt-0.57721/profile_na12878.cpp:505:33: style: The scope of the variable 'y2' can be reduced. [variableScope]
vt-0.57721/profile_na12878.cpp:405:21: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:130:13: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:405:21: note: Shadow variable
vt-0.57721/profile_na12878.cpp:453:21: style: Local variable 'ts' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:149:13: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:453:21: note: Shadow variable
vt-0.57721/profile_na12878.cpp:454:21: style: Local variable 'tv' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:150:13: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:454:21: note: Shadow variable
vt-0.57721/profile_na12878.cpp:455:21: style: Local variable 'ins' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:153:13: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:455:21: note: Shadow variable
vt-0.57721/profile_na12878.cpp:456:21: style: Local variable 'del' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:154:13: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:456:21: note: Shadow variable
vt-0.57721/profile_na12878.cpp:517:31: style: Local variable 'ts' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:453:21: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:517:31: note: Shadow variable
vt-0.57721/profile_na12878.cpp:518:33: style: Local variable 'n' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:377:17: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:518:33: note: Shadow variable
vt-0.57721/profile_na12878.cpp:910:25: style: Local variable 'concordance' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:145:35: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:910:25: note: Shadow variable
vt-0.57721/profile_na12878.cpp:911:30: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/profile_na12878.cpp:904:22: note: Shadowed declaration
vt-0.57721/profile_na12878.cpp:911:30: note: Shadow variable
vt-0.57721/profile_na12878.cpp:112:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_na12878.cpp:130:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/profile_na12878.cpp:149:13: style: class member 'Igor::ts' is never used. [unusedStructMember]
vt-0.57721/profile_na12878.cpp:150:13: style: class member 'Igor::tv' is never used. [unusedStructMember]
vt-0.57721/profile_na12878.cpp:151:13: style: class member 'Igor::syn' is never used. [unusedStructMember]
vt-0.57721/profile_na12878.cpp:152:13: style: class member 'Igor::nsyn' is never used. [unusedStructMember]
vt-0.57721/profile_na12878.cpp:153:13: style: class member 'Igor::ins' is never used. [unusedStructMember]
vt-0.57721/profile_na12878.cpp:154:13: style: class member 'Igor::del' is never used. [unusedStructMember]
vt-0.57721/profile_na12878.cpp:682:31: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_na12878.cpp:757:31: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_na12878.cpp:367:32: style: Unused variable: overlaps [unusedVariable]
vt-0.57721/profile_na12878.cpp:378:28: style: Unused variable: k0 [unusedVariable]
vt-0.57721/profile_na12878.cpp:398:17: style: Variable 'discordance_filter' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_na12878.cpp:407:21: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_snps.cpp:138:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_snps.cpp:200:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_snps.cpp:337:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_snps.cpp:349:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::no_filters' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::no_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::nonsyn' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::syn' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::lcplx' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::orom_lcplx' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:105:5: warning: Member variable 'Igor::orom_gencode_cds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_snps.cpp:53:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_snps.cpp:53:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_snps.cpp:143:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_snps.cpp:143:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_snps.cpp:335:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_snps.cpp:335:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_snps.cpp:347:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_snps.cpp:347:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_snps.cpp:351:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_snps.cpp:353:9: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_snps.cpp:359:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_snps.cpp:360:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_snps.cpp:361:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_snps.cpp:180:25: style: Local variable 'line' shadows outer variable [shadowVariable]
vt-0.57721/profile_snps.cpp:79:15: note: Shadowed declaration
vt-0.57721/profile_snps.cpp:180:25: note: Shadow variable
vt-0.57721/profile_snps.cpp:249:21: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/profile_snps.cpp:78:13: note: Shadowed declaration
vt-0.57721/profile_snps.cpp:249:21: note: Shadow variable
vt-0.57721/profile_snps.cpp:63:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/profile_snps.cpp:78:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/profile_snps.cpp:240:32: style: Unused variable: overlaps [unusedVariable]
vt-0.57721/profile_snps.cpp:251:21: style: Variable 'vtype' is assigned a value that is never used. [unreadVariable]
vt-0.57721/profile_vntrs.cpp:133:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_vntrs.cpp:165:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_vntrs.cpp:249:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_vntrs.cpp:350:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_vntrs.cpp:361:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::orom_lcplx' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::orom_gencode_cds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::no_lcplx' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::no_cds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::no_vntrs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::no_redundant' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:104:5: warning: Member variable 'Igor::vntr_tree' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/profile_vntrs.cpp:53:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/profile_vntrs.cpp:53:17: note: Derived variable 'Igor::version'
vt-0.57721/profile_vntrs.cpp:138:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/profile_vntrs.cpp:138:10: note: Derived function 'Igor::initialize'
vt-0.57721/profile_vntrs.cpp:348:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/profile_vntrs.cpp:348:10: note: Derived function 'Igor::print_options'
vt-0.57721/profile_vntrs.cpp:359:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/profile_vntrs.cpp:359:10: note: Derived function 'Igor::print_stats'
vt-0.57721/profile_vntrs.cpp:362:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:363:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:364:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:365:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:376:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:377:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:378:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:379:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:380:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:381:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/profile_vntrs.cpp:304:22: style: The scope of the variable 'exact' can be reduced. [variableScope]
vt-0.57721/profile_vntrs.cpp:60:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/program.cpp:28:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:54:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:128:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:219:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:271:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:282:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:293:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:304:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:319:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:343:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.cpp:368:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/program.h:78:10: performance:inconclusive: Technically the member function 'Program::parse_files' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:114:15: note: Technically the member function 'Program::parse_files' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:78:10: note: Technically the member function 'Program::parse_files' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:87:10: performance:inconclusive: Technically the member function 'Program::parse_intervals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:152:15: note: Technically the member function 'Program::parse_intervals' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:87:10: note: Technically the member function 'Program::parse_intervals' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:103:10: performance:inconclusive: Technically the member function 'Program::parse_filters' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:206:15: note: Technically the member function 'Program::parse_filters' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:103:10: note: Technically the member function 'Program::parse_filters' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:111:10: performance:inconclusive: Technically the member function 'Program::parse_string_list' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:257:15: note: Technically the member function 'Program::parse_string_list' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:111:10: note: Technically the member function 'Program::parse_string_list' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:119:12: performance:inconclusive: Technically the member function 'Program::read_sample_list' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:391:17: note: Technically the member function 'Program::read_sample_list' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:119:12: note: Technically the member function 'Program::read_sample_list' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:139:10: performance:inconclusive: Technically the member function 'Program::print_ref_op' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:267:15: note: Technically the member function 'Program::print_ref_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:139:10: note: Technically the member function 'Program::print_ref_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:144:10: performance:inconclusive: Technically the member function 'Program::print_str_op' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:278:15: note: Technically the member function 'Program::print_str_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:144:10: note: Technically the member function 'Program::print_str_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:149:10: performance:inconclusive: Technically the member function 'Program::print_num_op' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:289:15: note: Technically the member function 'Program::print_num_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:149:10: note: Technically the member function 'Program::print_num_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:154:10: performance:inconclusive: Technically the member function 'Program::print_boo_op' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:300:15: note: Technically the member function 'Program::print_boo_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:154:10: note: Technically the member function 'Program::print_boo_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:159:10: performance:inconclusive: Technically the member function 'Program::print_int_op' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:315:15: note: Technically the member function 'Program::print_int_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:159:10: note: Technically the member function 'Program::print_int_op' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:164:10: performance:inconclusive: Technically the member function 'Program::print_strvec' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:339:15: note: Technically the member function 'Program::print_strvec' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:164:10: note: Technically the member function 'Program::print_strvec' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:169:10: performance:inconclusive: Technically the member function 'Program::print_ifiles' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/program.cpp:364:15: note: Technically the member function 'Program::print_ifiles' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.h:169:10: note: Technically the member function 'Program::print_ifiles' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/program.cpp:415:26: style: C-style pointer casting [cstyleCast]
vt-0.57721/program.cpp:394:36: style: The scope of the variable 'map' can be reduced. [variableScope]
vt-0.57721/program.cpp:114:115: performance: Function parameter 'file_list' should be passed by const reference. [passedByValue]
vt-0.57721/program.cpp:152:83: performance: Function parameter 'interval_list' should be passed by const reference. [passedByValue]
vt-0.57721/program.cpp:267:65: performance: Function parameter 'ref_fasta_file' should be passed by const reference. [passedByValue]
vt-0.57721/program.cpp:278:65: performance: Function parameter 'str_value' should be passed by const reference. [passedByValue]
vt-0.57721/program.cpp:391:65: performance: Function parameter 'sample_list' should be passed by const reference. [passedByValue]
vt-0.57721/program.cpp:41:21: style: Variable 'arg' can be declared as reference to const [constVariableReference]
vt-0.57721/program.cpp:70:21: style: Variable 'arg' can be declared as reference to const [constVariableReference]
vt-0.57721/program.cpp:339:79: style: Parameter 'vec' can be declared as reference to const [constParameterReference]
vt-0.57721/program.cpp:364:79: style: Parameter 'files' can be declared as reference to const [constParameterReference]
vt-0.57721/program.cpp:168:29: performance: Searching before insertion is not necessary. Instead of 'm[ss]=1' consider using 'm.try_emplace(ss, 1);'. [stlFindInsert]
vt-0.57721/program.cpp:185:23: performance: Searching before insertion is not necessary. Instead of 'm[v[i]]=1' consider using 'm.try_emplace(v[i], 1);'. [stlFindInsert]
vt-0.57721/program.cpp:407:31: performance: Searching before insertion is not necessary. Instead of 'map[ss]=1' consider using 'map.try_emplace(ss, 1);'. [stlFindInsert]
vt-0.57721/read_filter.cpp:36:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reads [valueFlowBailoutIncompleteVar]
vt-0.57721/read_filter.cpp:95:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reads [valueFlowBailoutIncompleteVar]
vt-0.57721/read_filter.cpp:225:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reads [valueFlowBailoutIncompleteVar]
vt-0.57721/read_filter.cpp:258:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/read_filter.cpp:29:13: warning: Member variable 'ReadFilter::output_annotations' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/read_filter.h:113:10: performance:inconclusive: Technically the member function 'ReadFilter::clear_reads' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/read_filter.cpp:223:18: note: Technically the member function 'ReadFilter::clear_reads' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/read_filter.h:113:10: note: Technically the member function 'ReadFilter::clear_reads' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/read_filter.cpp:105:30: style: C-style pointer casting [cstyleCast]
vt-0.57721/read_filter.cpp:229:18: style: C-style pointer casting [cstyleCast]
vt-0.57721/read_filter.cpp:240:17: style: Local variable 'chrom' shadows outer variable [shadowVariable]
vt-0.57721/read_filter.h:52:17: note: Shadowed declaration
vt-0.57721/read_filter.cpp:240:17: note: Shadow variable
vt-0.57721/read_filter.cpp:149:27: style: Variable 'oplen' is assigned a value that is never used. [unreadVariable]
vt-0.57721/read_filter.cpp:251:19: style: Variable 'flag' is assigned a value that is never used. [unreadVariable]
vt-0.57721/reference_sequence.cpp:39:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/reference_sequence.cpp:94:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/reference_sequence.cpp:112:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/reference_sequence.cpp:174:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/reference_sequence.cpp:244:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/reference_sequence.cpp:313:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/reference_sequence.cpp:31:20: warning: Member variable 'ReferenceSequence::tid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/reference_sequence.h:117:10: performance:inconclusive: Technically the member function 'ReferenceSequence::fetch_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/reference_sequence.cpp:133:25: note: Technically the member function 'ReferenceSequence::fetch_seq' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/reference_sequence.h:117:10: note: Technically the member function 'ReferenceSequence::fetch_seq' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/reference_sequence.h:154:14: style:inconclusive: Technically the member function 'ReferenceSequence::max_size' can be const. [functionConst]
vt-0.57721/reference_sequence.cpp:212:29: note: Technically the member function 'ReferenceSequence::max_size' can be const.
vt-0.57721/reference_sequence.h:154:14: note: Technically the member function 'ReferenceSequence::max_size' can be const.
vt-0.57721/reference_sequence.h:159:14: style:inconclusive: Technically the member function 'ReferenceSequence::size' can be const. [functionConst]
vt-0.57721/reference_sequence.cpp:220:29: note: Technically the member function 'ReferenceSequence::size' can be const.
vt-0.57721/reference_sequence.h:159:14: note: Technically the member function 'ReferenceSequence::size' can be const.
vt-0.57721/reference_sequence.h:164:10: style:inconclusive: Technically the member function 'ReferenceSequence::is_empty' can be const. [functionConst]
vt-0.57721/reference_sequence.cpp:228:25: note: Technically the member function 'ReferenceSequence::is_empty' can be const.
vt-0.57721/reference_sequence.h:164:10: note: Technically the member function 'ReferenceSequence::is_empty' can be const.
vt-0.57721/reference_sequence.h:184:14: style:inconclusive: Technically the member function 'ReferenceSequence::get_tid' can be const. [functionConst]
vt-0.57721/reference_sequence.cpp:269:29: note: Technically the member function 'ReferenceSequence::get_tid' can be const.
vt-0.57721/reference_sequence.h:184:14: note: Technically the member function 'ReferenceSequence::get_tid' can be const.
vt-0.57721/reference_sequence.h:194:17: style:inconclusive: Technically the member function 'ReferenceSequence::get_chrom' can be const. [functionConst]
vt-0.57721/reference_sequence.cpp:285:32: note: Technically the member function 'ReferenceSequence::get_chrom' can be const.
vt-0.57721/reference_sequence.h:194:17: note: Technically the member function 'ReferenceSequence::get_chrom' can be const.
vt-0.57721/reference_sequence.h:199:14: style:inconclusive: Technically the member function 'ReferenceSequence::get_window_size' can be const. [functionConst]
vt-0.57721/reference_sequence.cpp:293:29: note: Technically the member function 'ReferenceSequence::get_window_size' can be const.
vt-0.57721/reference_sequence.h:199:14: note: Technically the member function 'ReferenceSequence::get_window_size' can be const.
vt-0.57721/reference_sequence.h:194:17: performance: Function 'get_chrom()' should return member 'chrom' by const reference. [returnByReference]
vt-0.57721/reference_sequence.cpp:313:13: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/reference_sequence.cpp:313:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/reference_sequence.cpp:168:11: style: Local variable 'seq' shadows outer variable [shadowVariable]
vt-0.57721/reference_sequence.h:47:23: note: Shadowed declaration
vt-0.57721/reference_sequence.cpp:168:11: note: Shadow variable
vt-0.57721/reference_sequence.cpp:31:51: style: Parameter 'ref_fasta_file' can be declared as reference to const [constParameterReference]
vt-0.57721/reference_sequence.cpp:80:55: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/reference_sequence.cpp:106:49: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/reference_sequence.cpp:133:48: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/reference_sequence.cpp:140:48: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/reference_sequence.cpp:196:49: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/reference_sequence.cpp:236:52: style: Parameter 'ref_fasta_file' can be declared as reference to const [constParameterReference]
vt-0.57721/reference_sequence.cpp:277:48: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/reference_sequence.cpp:133:91: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
vt-0.57721/rfhmm.cpp:132:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:186:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:229:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:480:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:527:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:654:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:729:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:833:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:1115:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:1247:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:1266:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:1286:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:1312:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:1334:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:1382:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::rlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::plen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::lflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::lflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::motif_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::motif_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::rflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::rflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::exact_motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::motif_m' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::motif_xid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::motif_concordance' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::max_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::max_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::optimal_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::optimal_state' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::optimal_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::optimal_probe_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::optimal_path_ptr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.cpp:78:8: warning: Member variable 'RFHMM::optimal_path_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm.h:225:13: style:inconclusive: Technically the member function 'RFHMM::get_lflank_model_spos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:372:16: note: Technically the member function 'RFHMM::get_lflank_model_spos1' can be const.
vt-0.57721/rfhmm.h:225:13: note: Technically the member function 'RFHMM::get_lflank_model_spos1' can be const.
vt-0.57721/rfhmm.h:230:13: style:inconclusive: Technically the member function 'RFHMM::get_lflank_model_epos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:380:16: note: Technically the member function 'RFHMM::get_lflank_model_epos1' can be const.
vt-0.57721/rfhmm.h:230:13: note: Technically the member function 'RFHMM::get_lflank_model_epos1' can be const.
vt-0.57721/rfhmm.h:235:13: style:inconclusive: Technically the member function 'RFHMM::get_motif_model_spos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:388:16: note: Technically the member function 'RFHMM::get_motif_model_spos1' can be const.
vt-0.57721/rfhmm.h:235:13: note: Technically the member function 'RFHMM::get_motif_model_spos1' can be const.
vt-0.57721/rfhmm.h:240:13: style:inconclusive: Technically the member function 'RFHMM::get_motif_model_epos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:396:16: note: Technically the member function 'RFHMM::get_motif_model_epos1' can be const.
vt-0.57721/rfhmm.h:240:13: note: Technically the member function 'RFHMM::get_motif_model_epos1' can be const.
vt-0.57721/rfhmm.h:245:13: style:inconclusive: Technically the member function 'RFHMM::get_rflank_model_spos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:404:16: note: Technically the member function 'RFHMM::get_rflank_model_spos1' can be const.
vt-0.57721/rfhmm.h:245:13: note: Technically the member function 'RFHMM::get_rflank_model_spos1' can be const.
vt-0.57721/rfhmm.h:250:13: style:inconclusive: Technically the member function 'RFHMM::get_rflank_model_epos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:412:16: note: Technically the member function 'RFHMM::get_rflank_model_epos1' can be const.
vt-0.57721/rfhmm.h:250:13: note: Technically the member function 'RFHMM::get_rflank_model_epos1' can be const.
vt-0.57721/rfhmm.h:255:13: style:inconclusive: Technically the member function 'RFHMM::get_lflank_read_spos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:420:16: note: Technically the member function 'RFHMM::get_lflank_read_spos1' can be const.
vt-0.57721/rfhmm.h:255:13: note: Technically the member function 'RFHMM::get_lflank_read_spos1' can be const.
vt-0.57721/rfhmm.h:260:13: style:inconclusive: Technically the member function 'RFHMM::get_lflank_read_epos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:428:16: note: Technically the member function 'RFHMM::get_lflank_read_epos1' can be const.
vt-0.57721/rfhmm.h:260:13: note: Technically the member function 'RFHMM::get_lflank_read_epos1' can be const.
vt-0.57721/rfhmm.h:265:13: style:inconclusive: Technically the member function 'RFHMM::get_motif_read_spos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:436:16: note: Technically the member function 'RFHMM::get_motif_read_spos1' can be const.
vt-0.57721/rfhmm.h:265:13: note: Technically the member function 'RFHMM::get_motif_read_spos1' can be const.
vt-0.57721/rfhmm.h:270:13: style:inconclusive: Technically the member function 'RFHMM::get_motif_read_epos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:444:16: note: Technically the member function 'RFHMM::get_motif_read_epos1' can be const.
vt-0.57721/rfhmm.h:270:13: note: Technically the member function 'RFHMM::get_motif_read_epos1' can be const.
vt-0.57721/rfhmm.h:275:13: style:inconclusive: Technically the member function 'RFHMM::get_rflank_read_spos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:452:16: note: Technically the member function 'RFHMM::get_rflank_read_spos1' can be const.
vt-0.57721/rfhmm.h:275:13: note: Technically the member function 'RFHMM::get_rflank_read_spos1' can be const.
vt-0.57721/rfhmm.h:280:13: style:inconclusive: Technically the member function 'RFHMM::get_rflank_read_epos1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:460:16: note: Technically the member function 'RFHMM::get_rflank_read_epos1' can be const.
vt-0.57721/rfhmm.h:280:13: note: Technically the member function 'RFHMM::get_rflank_read_epos1' can be const.
vt-0.57721/rfhmm.h:307:11: style:inconclusive: Technically the member function 'RFHMM::log10_emission_odds' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:873:14: note: Technically the member function 'RFHMM::log10_emission_odds' can be const.
vt-0.57721/rfhmm.h:307:11: note: Technically the member function 'RFHMM::log10_emission_odds' can be const.
vt-0.57721/rfhmm.h:312:17: performance:inconclusive: Technically the member function 'RFHMM::state2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.cpp:895:20: note: Technically the member function 'RFHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm.h:312:17: note: Technically the member function 'RFHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm.h:317:17: performance:inconclusive: Technically the member function 'RFHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.cpp:942:20: note: Technically the member function 'RFHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm.h:317:17: note: Technically the member function 'RFHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm.h:322:17: style:inconclusive: Technically the member function 'RFHMM::track2cigarstring1' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:989:20: note: Technically the member function 'RFHMM::track2cigarstring1' can be const.
vt-0.57721/rfhmm.h:322:17: note: Technically the member function 'RFHMM::track2cigarstring1' can be const.
vt-0.57721/rfhmm.h:327:17: performance:inconclusive: Technically the member function 'RFHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.cpp:1041:20: note: Technically the member function 'RFHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm.h:327:17: note: Technically the member function 'RFHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm.h:332:17: performance:inconclusive: Technically the member function 'RFHMM::component2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm.cpp:1069:20: note: Technically the member function 'RFHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm.h:332:17: note: Technically the member function 'RFHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm.h:347:10: style:inconclusive: Technically the member function 'RFHMM::print' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:1244:13: note: Technically the member function 'RFHMM::print' can be const.
vt-0.57721/rfhmm.h:347:10: note: Technically the member function 'RFHMM::print' can be const.
vt-0.57721/rfhmm.h:352:10: style:inconclusive: Technically the member function 'RFHMM::print' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:1263:13: note: Technically the member function 'RFHMM::print' can be const.
vt-0.57721/rfhmm.h:352:10: note: Technically the member function 'RFHMM::print' can be const.
vt-0.57721/rfhmm.h:387:10: style:inconclusive: Technically the member function 'RFHMM::flanks_are_mapped' can be const. [functionConst]
vt-0.57721/rfhmm.cpp:865:13: note: Technically the member function 'RFHMM::flanks_are_mapped' can be const.
vt-0.57721/rfhmm.h:387:10: note: Technically the member function 'RFHMM::flanks_are_mapped' can be const.
vt-0.57721/rfhmm.cpp:653:12: style: The scope of the variable 'c' can be reduced. [variableScope]
vt-0.57721/rfhmm.cpp:675:13: style: The scope of the variable 'u' can be reduced. [variableScope]
vt-0.57721/rfhmm.cpp:307:54: style:inconclusive: Function 'set_model' argument 2 names different: declaration 'lflank' definition 'rflank'. [funcArgNamesDifferent]
vt-0.57721/rfhmm.h:190:51: note: Function 'set_model' argument 2 names different: declaration 'lflank' definition 'rflank'.
vt-0.57721/rfhmm.cpp:307:54: note: Function 'set_model' argument 2 names different: declaration 'lflank' definition 'rflank'.
vt-0.57721/rfhmm.cpp:475:53: style:inconclusive: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'. [funcArgNamesDifferent]
vt-0.57721/rfhmm.h:292:50: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/rfhmm.cpp:475:53: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/rfhmm.cpp:516:31: style:inconclusive: Function 'align' argument 1 names different: declaration 'y' definition 'read'. [funcArgNamesDifferent]
vt-0.57721/rfhmm.h:297:28: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/rfhmm.cpp:516:31: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/rfhmm.cpp:727:40: style:inconclusive: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'. [funcArgNamesDifferent]
vt-0.57721/rfhmm.h:372:37: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/rfhmm.cpp:727:40: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/rfhmm.cpp:727:55: style:inconclusive: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'. [funcArgNamesDifferent]
vt-0.57721/rfhmm.h:372:49: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/rfhmm.cpp:727:55: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/rfhmm.cpp:873:39: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl' [funcArgOrderDifferent]
vt-0.57721/rfhmm.h:307:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/rfhmm.cpp:873:39: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/rfhmm.cpp:542:20: style: Local variable 'c' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm.cpp:534:12: note: Shadowed declaration
vt-0.57721/rfhmm.cpp:542:20: note: Shadow variable
vt-0.57721/rfhmm.cpp:543:20: style: Local variable 'd' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm.cpp:534:14: note: Shadowed declaration
vt-0.57721/rfhmm.cpp:543:20: note: Shadow variable
vt-0.57721/rfhmm.cpp:544:20: style: Local variable 'u' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm.cpp:534:16: note: Shadowed declaration
vt-0.57721/rfhmm.cpp:544:20: note: Shadow variable
vt-0.57721/rfhmm.cpp:545:20: style: Local variable 'l' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm.cpp:534:18: note: Shadowed declaration
vt-0.57721/rfhmm.cpp:545:20: note: Shadow variable
vt-0.57721/rfhmm.cpp:1113:42: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/rfhmm.cpp:1244:26: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/rfhmm.cpp:1263:28: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/rfhmm.cpp:1310:30: style: Parameter 'U' can be declared as pointer to const [constParameterPointer]
vt-0.57721/rfhmm.cpp:1335:14: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
vt-0.57721/rfhmm.cpp:1336:12: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
vt-0.57721/rfhmm.cpp:222:14: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/rfhmm.cpp:531:15: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
vt-0.57721/rfhmm.cpp:532:18: style: Variable 'maxPath' is assigned a value that is never used. [unreadVariable]
vt-0.57721/rfhmm.cpp:534:12: style: Unused variable: c [unusedVariable]
vt-0.57721/rfhmm.cpp:534:14: style: Unused variable: d [unusedVariable]
vt-0.57721/rfhmm.cpp:534:16: style: Unused variable: u [unusedVariable]
vt-0.57721/rfhmm.cpp:534:18: style: Unused variable: l [unusedVariable]
vt-0.57721/rfhmm.cpp:1179:15: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/rfhmm_x.cpp:132:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:186:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:229:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:480:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable moves [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:539:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:749:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:824:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:928:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:1210:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:1342:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:1361:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:1381:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:1407:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:1429:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:1477:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::rlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::plen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::lflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::lflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::motif_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::motif_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::rflank_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::rflank_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::exact_motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::motif_m' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::motif_xid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::motif_concordance' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::max_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::max_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::optimal_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::optimal_state' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::optimal_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::optimal_probe_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::optimal_path_ptr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.cpp:78:10: warning: Member variable 'RFHMM_X::optimal_path_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rfhmm_x.h:225:13: style:inconclusive: Technically the member function 'RFHMM_X::get_lflank_model_spos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:372:18: note: Technically the member function 'RFHMM_X::get_lflank_model_spos1' can be const.
vt-0.57721/rfhmm_x.h:225:13: note: Technically the member function 'RFHMM_X::get_lflank_model_spos1' can be const.
vt-0.57721/rfhmm_x.h:230:13: style:inconclusive: Technically the member function 'RFHMM_X::get_lflank_model_epos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:380:18: note: Technically the member function 'RFHMM_X::get_lflank_model_epos1' can be const.
vt-0.57721/rfhmm_x.h:230:13: note: Technically the member function 'RFHMM_X::get_lflank_model_epos1' can be const.
vt-0.57721/rfhmm_x.h:235:13: style:inconclusive: Technically the member function 'RFHMM_X::get_motif_model_spos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:388:18: note: Technically the member function 'RFHMM_X::get_motif_model_spos1' can be const.
vt-0.57721/rfhmm_x.h:235:13: note: Technically the member function 'RFHMM_X::get_motif_model_spos1' can be const.
vt-0.57721/rfhmm_x.h:240:13: style:inconclusive: Technically the member function 'RFHMM_X::get_motif_model_epos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:396:18: note: Technically the member function 'RFHMM_X::get_motif_model_epos1' can be const.
vt-0.57721/rfhmm_x.h:240:13: note: Technically the member function 'RFHMM_X::get_motif_model_epos1' can be const.
vt-0.57721/rfhmm_x.h:245:13: style:inconclusive: Technically the member function 'RFHMM_X::get_rflank_model_spos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:404:18: note: Technically the member function 'RFHMM_X::get_rflank_model_spos1' can be const.
vt-0.57721/rfhmm_x.h:245:13: note: Technically the member function 'RFHMM_X::get_rflank_model_spos1' can be const.
vt-0.57721/rfhmm_x.h:250:13: style:inconclusive: Technically the member function 'RFHMM_X::get_rflank_model_epos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:412:18: note: Technically the member function 'RFHMM_X::get_rflank_model_epos1' can be const.
vt-0.57721/rfhmm_x.h:250:13: note: Technically the member function 'RFHMM_X::get_rflank_model_epos1' can be const.
vt-0.57721/rfhmm_x.h:255:13: style:inconclusive: Technically the member function 'RFHMM_X::get_lflank_read_spos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:420:18: note: Technically the member function 'RFHMM_X::get_lflank_read_spos1' can be const.
vt-0.57721/rfhmm_x.h:255:13: note: Technically the member function 'RFHMM_X::get_lflank_read_spos1' can be const.
vt-0.57721/rfhmm_x.h:260:13: style:inconclusive: Technically the member function 'RFHMM_X::get_lflank_read_epos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:428:18: note: Technically the member function 'RFHMM_X::get_lflank_read_epos1' can be const.
vt-0.57721/rfhmm_x.h:260:13: note: Technically the member function 'RFHMM_X::get_lflank_read_epos1' can be const.
vt-0.57721/rfhmm_x.h:265:13: style:inconclusive: Technically the member function 'RFHMM_X::get_motif_read_spos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:436:18: note: Technically the member function 'RFHMM_X::get_motif_read_spos1' can be const.
vt-0.57721/rfhmm_x.h:265:13: note: Technically the member function 'RFHMM_X::get_motif_read_spos1' can be const.
vt-0.57721/rfhmm_x.h:270:13: style:inconclusive: Technically the member function 'RFHMM_X::get_motif_read_epos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:444:18: note: Technically the member function 'RFHMM_X::get_motif_read_epos1' can be const.
vt-0.57721/rfhmm_x.h:270:13: note: Technically the member function 'RFHMM_X::get_motif_read_epos1' can be const.
vt-0.57721/rfhmm_x.h:275:13: style:inconclusive: Technically the member function 'RFHMM_X::get_rflank_read_spos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:452:18: note: Technically the member function 'RFHMM_X::get_rflank_read_spos1' can be const.
vt-0.57721/rfhmm_x.h:275:13: note: Technically the member function 'RFHMM_X::get_rflank_read_spos1' can be const.
vt-0.57721/rfhmm_x.h:280:13: style:inconclusive: Technically the member function 'RFHMM_X::get_rflank_read_epos1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:460:18: note: Technically the member function 'RFHMM_X::get_rflank_read_epos1' can be const.
vt-0.57721/rfhmm_x.h:280:13: note: Technically the member function 'RFHMM_X::get_rflank_read_epos1' can be const.
vt-0.57721/rfhmm_x.h:307:11: style:inconclusive: Technically the member function 'RFHMM_X::log10_emission_odds' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:968:16: note: Technically the member function 'RFHMM_X::log10_emission_odds' can be const.
vt-0.57721/rfhmm_x.h:307:11: note: Technically the member function 'RFHMM_X::log10_emission_odds' can be const.
vt-0.57721/rfhmm_x.h:312:17: performance:inconclusive: Technically the member function 'RFHMM_X::state2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.cpp:990:22: note: Technically the member function 'RFHMM_X::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm_x.h:312:17: note: Technically the member function 'RFHMM_X::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm_x.h:317:17: performance:inconclusive: Technically the member function 'RFHMM_X::state2cigarstring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.cpp:1037:22: note: Technically the member function 'RFHMM_X::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm_x.h:317:17: note: Technically the member function 'RFHMM_X::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm_x.h:322:17: style:inconclusive: Technically the member function 'RFHMM_X::track2cigarstring1' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:1084:22: note: Technically the member function 'RFHMM_X::track2cigarstring1' can be const.
vt-0.57721/rfhmm_x.h:322:17: note: Technically the member function 'RFHMM_X::track2cigarstring1' can be const.
vt-0.57721/rfhmm_x.h:327:17: performance:inconclusive: Technically the member function 'RFHMM_X::track2cigarstring2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.cpp:1136:22: note: Technically the member function 'RFHMM_X::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm_x.h:327:17: note: Technically the member function 'RFHMM_X::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm_x.h:332:17: performance:inconclusive: Technically the member function 'RFHMM_X::component2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/rfhmm_x.cpp:1164:22: note: Technically the member function 'RFHMM_X::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm_x.h:332:17: note: Technically the member function 'RFHMM_X::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/rfhmm_x.h:347:10: style:inconclusive: Technically the member function 'RFHMM_X::print' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:1339:15: note: Technically the member function 'RFHMM_X::print' can be const.
vt-0.57721/rfhmm_x.h:347:10: note: Technically the member function 'RFHMM_X::print' can be const.
vt-0.57721/rfhmm_x.h:352:10: style:inconclusive: Technically the member function 'RFHMM_X::print' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:1358:15: note: Technically the member function 'RFHMM_X::print' can be const.
vt-0.57721/rfhmm_x.h:352:10: note: Technically the member function 'RFHMM_X::print' can be const.
vt-0.57721/rfhmm_x.h:387:10: style:inconclusive: Technically the member function 'RFHMM_X::flanks_are_mapped' can be const. [functionConst]
vt-0.57721/rfhmm_x.cpp:960:15: note: Technically the member function 'RFHMM_X::flanks_are_mapped' can be const.
vt-0.57721/rfhmm_x.h:387:10: note: Technically the member function 'RFHMM_X::flanks_are_mapped' can be const.
vt-0.57721/rfhmm_x.cpp:748:12: style: The scope of the variable 'c' can be reduced. [variableScope]
vt-0.57721/rfhmm_x.cpp:770:13: style: The scope of the variable 'u' can be reduced. [variableScope]
vt-0.57721/rfhmm_x.cpp:307:56: style:inconclusive: Function 'set_model' argument 2 names different: declaration 'lflank' definition 'rflank'. [funcArgNamesDifferent]
vt-0.57721/rfhmm_x.h:190:51: note: Function 'set_model' argument 2 names different: declaration 'lflank' definition 'rflank'.
vt-0.57721/rfhmm_x.cpp:307:56: note: Function 'set_model' argument 2 names different: declaration 'lflank' definition 'rflank'.
vt-0.57721/rfhmm_x.cpp:475:55: style:inconclusive: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'. [funcArgNamesDifferent]
vt-0.57721/rfhmm_x.h:292:50: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/rfhmm_x.cpp:475:55: note: Function 'proc_comp' argument 3 names different: declaration 'i' definition 'index1'.
vt-0.57721/rfhmm_x.cpp:528:33: style:inconclusive: Function 'align' argument 1 names different: declaration 'y' definition 'read'. [funcArgNamesDifferent]
vt-0.57721/rfhmm_x.h:297:28: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/rfhmm_x.cpp:528:33: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/rfhmm_x.cpp:822:42: style:inconclusive: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'. [funcArgNamesDifferent]
vt-0.57721/rfhmm_x.h:372:37: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/rfhmm_x.cpp:822:42: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/rfhmm_x.cpp:822:57: style:inconclusive: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'. [funcArgNamesDifferent]
vt-0.57721/rfhmm_x.h:372:49: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/rfhmm_x.cpp:822:57: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/rfhmm_x.cpp:968:41: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl' [funcArgOrderDifferent]
vt-0.57721/rfhmm_x.h:307:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/rfhmm_x.cpp:968:41: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/rfhmm_x.cpp:553:20: style: Local variable 'c' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm_x.cpp:546:12: note: Shadowed declaration
vt-0.57721/rfhmm_x.cpp:553:20: note: Shadow variable
vt-0.57721/rfhmm_x.cpp:554:20: style: Local variable 'd' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm_x.cpp:546:14: note: Shadowed declaration
vt-0.57721/rfhmm_x.cpp:554:20: note: Shadow variable
vt-0.57721/rfhmm_x.cpp:555:20: style: Local variable 'u' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm_x.cpp:546:16: note: Shadowed declaration
vt-0.57721/rfhmm_x.cpp:555:20: note: Shadow variable
vt-0.57721/rfhmm_x.cpp:556:20: style: Local variable 'l' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm_x.cpp:546:18: note: Shadowed declaration
vt-0.57721/rfhmm_x.cpp:556:20: note: Shadow variable
vt-0.57721/rfhmm_x.cpp:636:20: style: Local variable 'c' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm_x.cpp:546:12: note: Shadowed declaration
vt-0.57721/rfhmm_x.cpp:636:20: note: Shadow variable
vt-0.57721/rfhmm_x.cpp:637:20: style: Local variable 'd' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm_x.cpp:546:14: note: Shadowed declaration
vt-0.57721/rfhmm_x.cpp:637:20: note: Shadow variable
vt-0.57721/rfhmm_x.cpp:638:20: style: Local variable 'u' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm_x.cpp:546:16: note: Shadowed declaration
vt-0.57721/rfhmm_x.cpp:638:20: note: Shadow variable
vt-0.57721/rfhmm_x.cpp:639:20: style: Local variable 'l' shadows outer variable [shadowVariable]
vt-0.57721/rfhmm_x.cpp:546:18: note: Shadowed declaration
vt-0.57721/rfhmm_x.cpp:639:20: note: Shadow variable
vt-0.57721/rfhmm_x.cpp:1208:44: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/rfhmm_x.cpp:1339:28: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/rfhmm_x.cpp:1358:30: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/rfhmm_x.cpp:1405:32: style: Parameter 'U' can be declared as pointer to const [constParameterPointer]
vt-0.57721/rfhmm_x.cpp:1430:14: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
vt-0.57721/rfhmm_x.cpp:1431:12: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
vt-0.57721/rfhmm_x.cpp:222:14: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/rfhmm_x.cpp:543:15: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
vt-0.57721/rfhmm_x.cpp:544:18: style: Variable 'maxPath' is assigned a value that is never used. [unreadVariable]
vt-0.57721/rfhmm_x.cpp:546:12: style: Unused variable: c [unusedVariable]
vt-0.57721/rfhmm_x.cpp:546:14: style: Unused variable: d [unusedVariable]
vt-0.57721/rfhmm_x.cpp:546:16: style: Unused variable: u [unusedVariable]
vt-0.57721/rfhmm_x.cpp:546:18: style: Unused variable: l [unusedVariable]
vt-0.57721/rfhmm_x.cpp:1274:15: style: Variable 't' is assigned a value that is never used. [unreadVariable]
vt-0.57721/rminfo.cpp:95:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/rminfo.cpp:104:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/rminfo.cpp:134:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/rminfo.cpp:166:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/rminfo.cpp:180:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/rminfo.cpp:61:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rminfo.cpp:61:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rminfo.cpp:61:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rminfo.cpp:61:5: warning: Member variable 'Igor::no_variants_with_removed_info' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rminfo.cpp:61:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/rminfo.cpp:176:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/rminfo.cpp:100:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/rminfo.cpp:100:10: note: Derived function 'Igor::initialize'
vt-0.57721/rminfo.cpp:162:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/rminfo.cpp:162:10: note: Derived function 'Igor::print_options'
vt-0.57721/rminfo.cpp:176:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/rminfo.cpp:176:10: note: Derived function 'Igor::print_stats'
vt-0.57721/rminfo.cpp:170:75: style: Condition '!print' is always false [knownConditionTrueFalse]
vt-0.57721/rminfo.cpp:164:13: note: Assuming that condition '!print' is not redundant
vt-0.57721/rminfo.cpp:170:75: note: Condition '!print' is always false
vt-0.57721/rminfo.cpp:59:19: style: class member 'Igor::vm' is never used. [unusedStructMember]
vt-0.57721/seq.cpp:80:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/seq.cpp:103:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/seq.cpp:112:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/seq.cpp:154:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/seq.cpp:54:5: warning: Member variable 'Igor::fai' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/seq.cpp:54:5: warning: Member variable 'Igor::reference_present' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/seq.cpp:161:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/seq.cpp:85:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/seq.cpp:85:10: note: Derived function 'Igor::initialize'
vt-0.57721/seq.cpp:150:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/seq.cpp:150:10: note: Derived function 'Igor::print_options'
vt-0.57721/seq.cpp:161:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/seq.cpp:161:10: note: Derived function 'Igor::print_stats'
vt-0.57721/seq.cpp:106:37: style: Condition 'fai!=NULL' is always true [knownConditionTrueFalse]
vt-0.57721/set_ref.cpp:108:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/set_ref.cpp:150:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/set_ref.cpp:164:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/set_ref.cpp:207:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::no_variants_with_REF_set' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::no_variants_within_bounds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::no_variants_partial_overlap' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::no_variants_no_overlap' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:74:5: warning: Member variable 'Igor::rs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/set_ref.cpp:76:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/set_ref.cpp:162:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/set_ref.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/set_ref.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/set_ref.cpp:117:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/set_ref.cpp:117:10: note: Derived function 'Igor::initialize'
vt-0.57721/set_ref.cpp:148:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/set_ref.cpp:148:10: note: Derived function 'Igor::print_options'
vt-0.57721/set_ref.cpp:162:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/set_ref.cpp:162:10: note: Derived function 'Igor::print_stats'
vt-0.57721/set_ref.cpp:236:33: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/set_ref.cpp:225:33: note: First condition
vt-0.57721/set_ref.cpp:236:33: note: Second condition
vt-0.57721/set_ref.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/snp_genotyping_record.cpp:290:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/snp_genotyping_record.cpp:547:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/snp_genotyping_record.cpp:341:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/snp_genotyping_record.cpp:342:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/snp_genotyping_record.cpp:343:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/snp_genotyping_record.cpp:344:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::h' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::rid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::pos1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::dlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::nsamples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::n_filter' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::bqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::bqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::mqr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::mqr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::cyr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::cyr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::str_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::str_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::nmr_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::nmr_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::ior_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::ior_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::nm0_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::nm0_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::nm1_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::nm1_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::abe_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::abe_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::abz_num' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::abz_den' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::ns_nref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::dp_sum' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::max_gq' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_dp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_dp_ra' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_bq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_bq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_mq_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_mq_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_cy_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_cy_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_st_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_st_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_al_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_bq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_mq_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_cy_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_st_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_nm_al' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_nm_s1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_nm_s2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_oth_exp_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_oth_obs_q20' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_pls' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:30:22: warning:inconclusive: Member variable 'SNPGenotypingRecord::tmp_ads' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/snp_genotyping_record.cpp:72:11: style: C-style pointer casting [cstyleCast]
vt-0.57721/snp_genotyping_record.cpp:73:11: style: C-style pointer casting [cstyleCast]
vt-0.57721/snp_genotyping_record.cpp:141:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/snp_genotyping_record.cpp:142:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/snp_genotyping_record.cpp:143:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/snp_genotyping_record.cpp:144:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/snp_genotyping_record.cpp:145:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/snp_genotyping_record.cpp:148:12: style: The scope of the variable 'gp' can be reduced. [variableScope]
vt-0.57721/snp_genotyping_record.cpp:148:16: style: The scope of the variable 'gp_sum' can be reduced. [variableScope]
vt-0.57721/snp_genotyping_record.cpp:148:24: style: The scope of the variable 'max_gp' can be reduced. [variableScope]
vt-0.57721/snp_genotyping_record.cpp:149:13: style: The scope of the variable 'best_gt' can be reduced. [variableScope]
vt-0.57721/snp_genotyping_record.cpp:150:13: style: The scope of the variable 'best_a1' can be reduced. [variableScope]
vt-0.57721/snp_genotyping_record.cpp:150:22: style: The scope of the variable 'best_a2' can be reduced. [variableScope]
vt-0.57721/snp_genotyping_record.cpp:156:13: style: Local variable 'max_gq' shadows outer variable [shadowVariable]
vt-0.57721/snp_genotyping_record.h:94:28: note: Shadowed declaration
vt-0.57721/snp_genotyping_record.cpp:156:13: note: Shadow variable
vt-0.57721/snp_genotyping_record.cpp:157:13: style: Local variable 'dp_sum' shadows outer variable [shadowVariable]
vt-0.57721/snp_genotyping_record.h:94:20: note: Shadowed declaration
vt-0.57721/snp_genotyping_record.cpp:157:13: note: Shadow variable
vt-0.57721/snp_genotyping_record.cpp:172:18: style: Variable 'pli' can be declared as pointer to const [constVariablePointer]
vt-0.57721/snp_genotyping_record.cpp:173:30: style: Variable 'gp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/snp_genotyping_record.cpp:151:14: style: Unused variable: pls_i [unusedVariable]
vt-0.57721/snp_genotyping_record.cpp:471:22: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/snp_genotyping_record.cpp:559:22: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/sort.cpp:120:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/sort.cpp:175:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/sort.cpp:348:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/sort.cpp:362:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/sort.cpp:72:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/sort.cpp:72:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/sort.cpp:72:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/sort.cpp:344:10: style:inconclusive: Technically the member function '::Igor::print_options' can be const. [functionConst]
vt-0.57721/sort.cpp:358:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/sort.cpp:130:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/sort.cpp:130:10: note: Derived function 'Igor::initialize'
vt-0.57721/sort.cpp:344:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/sort.cpp:344:10: note: Derived function 'Igor::print_options'
vt-0.57721/sort.cpp:358:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/sort.cpp:358:10: note: Derived function 'Igor::print_stats'
vt-0.57721/sort.cpp:354:70: style: Condition 'print' is always true [knownConditionTrueFalse]
vt-0.57721/sort.cpp:346:13: note: Assuming that condition '!print' is not redundant
vt-0.57721/sort.cpp:354:70: note: Condition 'print' is always true
vt-0.57721/sort.cpp:32:18: style: C-style pointer casting [cstyleCast]
vt-0.57721/sort.cpp:33:18: style: C-style pointer casting [cstyleCast]
vt-0.57721/sort.cpp:32:13: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
vt-0.57721/sort.cpp:33:13: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
vt-0.57721/sort.cpp:157:24: style: Variable 'h' can be declared as pointer to const [constVariablePointer]
vt-0.57721/sort.cpp:186:24: style: Variable 'h' can be declared as pointer to const [constVariablePointer]
vt-0.57721/sort.cpp:157:26: style: Variable 'h' is assigned a value that is never used. [unreadVariable]
vt-0.57721/sort.cpp:186:26: style: Variable 'h' is assigned a value that is never used. [unreadVariable]
vt-0.57721/subset.cpp:105:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/subset.cpp:149:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/subset.cpp:226:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/subset.cpp:237:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::imap' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::no_subset_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::no_subset_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:73:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/subset.cpp:75:9: performance: Variable 'version' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/subset.cpp:235:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/subset.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/subset.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/subset.cpp:110:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/subset.cpp:110:10: note: Derived function 'Igor::initialize'
vt-0.57721/subset.cpp:224:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/subset.cpp:224:10: note: Derived function 'Igor::print_options'
vt-0.57721/subset.cpp:235:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/subset.cpp:235:10: note: Derived function 'Igor::print_stats'
vt-0.57721/subset.cpp:119:16: style: C-style pointer casting [cstyleCast]
vt-0.57721/subset.cpp:41:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/sv_tree.cpp:123:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/sv_tree.cpp:188:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m [valueFlowBailoutIncompleteVar]
vt-0.57721/sv_tree.cpp:230:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m [valueFlowBailoutIncompleteVar]
vt-0.57721/sv_tree.cpp:285:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m [valueFlowBailoutIncompleteVar]
vt-0.57721/sv_tree.h:86:17: performance:inconclusive: Technically the member function 'SVNode::sv_type2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/sv_tree.cpp:136:21: note: Technically the member function 'SVNode::sv_type2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/sv_tree.h:86:17: note: Technically the member function 'SVNode::sv_type2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/sv_tree.h:132:10: performance:inconclusive: Technically the member function 'SVTree::enumerate_dfs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/sv_tree.cpp:327:14: note: Technically the member function 'SVTree::enumerate_dfs' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/sv_tree.h:132:10: note: Technically the member function 'SVTree::enumerate_dfs' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/sv_tree.cpp:185:5: warning: Class 'SVTree' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/sv_tree.cpp:185:5: warning: Class 'SVTree' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/sv_tree.h:46:5: style: Class 'SVNode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
vt-0.57721/sv_tree.cpp:224:30: style:inconclusive: Function 'add' argument 1 names different: declaration 'desc' definition 'sv_type'. [funcArgNamesDifferent]
vt-0.57721/sv_tree.h:117:26: note: Function 'add' argument 1 names different: declaration 'desc' definition 'sv_type'.
vt-0.57721/sv_tree.cpp:224:30: note: Function 'add' argument 1 names different: declaration 'desc' definition 'sv_type'.
vt-0.57721/sv_tree.cpp:276:29: style: Parameter 'variant' can be declared as reference to const [constParameterReference]
vt-0.57721/sv_tree.cpp:279:17: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
vt-0.57721/svm_predict.cpp:94:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/svm_predict.cpp:139:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/svm_predict.cpp:68:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_predict.cpp:68:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_predict.cpp:68:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_predict.cpp:68:5: warning: Member variable 'Igor::no_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_predict.cpp:68:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_predict.cpp:147:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/svm_predict.cpp:32:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/svm_predict.cpp:32:17: note: Derived variable 'Igor::version'
vt-0.57721/svm_predict.cpp:99:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/svm_predict.cpp:99:10: note: Derived function 'Igor::initialize'
vt-0.57721/svm_predict.cpp:137:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/svm_predict.cpp:137:10: note: Derived function 'Igor::print_options'
vt-0.57721/svm_predict.cpp:147:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/svm_predict.cpp:147:10: note: Derived function 'Igor::print_stats'
vt-0.57721/svm_predict.cpp:126:17: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/svm_predict.cpp:48:13: note: Shadowed declaration
vt-0.57721/svm_predict.cpp:126:17: note: Shadow variable
vt-0.57721/svm_predict.cpp:38:30: style: class member 'Igor::input_vcf_files' is never used. [unusedStructMember]
vt-0.57721/svm_predict.cpp:40:17: style: class member 'Igor::ref_data_sets_list' is never used. [unusedStructMember]
vt-0.57721/svm_predict.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/svm_predict.cpp:48:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/svm_predict.cpp:61:13: style: class member 'Igor::no_snps' is never used. [unusedStructMember]
vt-0.57721/svm_train.cpp:100:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/svm_train.cpp:158:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
vt-0.57721/svm_train.cpp:262:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/svm_train.cpp:272:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/svm_train.cpp:67:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_train.cpp:67:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_train.cpp:67:5: warning: Member variable 'Igor::no_snps' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_train.cpp:67:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_train.cpp:67:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/svm_train.cpp:135:10: performance:inconclusive: Technically the member function '::Igor::inverse_normalize' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/svm_train.cpp:270:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/svm_train.cpp:148:18: style:inconclusive: Technically the member function '::Igor::inverse_normalize::Anonymous0::operator()' can be const. [functionConst]
vt-0.57721/svm_train.cpp:32:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/svm_train.cpp:32:17: note: Derived variable 'Igor::version'
vt-0.57721/svm_train.cpp:105:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/svm_train.cpp:105:10: note: Derived function 'Igor::initialize'
vt-0.57721/svm_train.cpp:260:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/svm_train.cpp:260:10: note: Derived function 'Igor::print_options'
vt-0.57721/svm_train.cpp:270:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/svm_train.cpp:270:10: note: Derived function 'Igor::print_stats'
vt-0.57721/svm_train.cpp:156:13: style: Condition 'debug' is always false [knownConditionTrueFalse]
vt-0.57721/svm_train.cpp:137:22: note: Assignment 'debug=false', assigned value is 0
vt-0.57721/svm_train.cpp:156:13: note: Condition 'debug' is always false
vt-0.57721/svm_train.cpp:168:13: style: Condition 'debug' is always false [knownConditionTrueFalse]
vt-0.57721/svm_train.cpp:137:22: note: Assignment 'debug=false', assigned value is 0
vt-0.57721/svm_train.cpp:168:13: note: Condition 'debug' is always false
vt-0.57721/svm_train.cpp:148:36: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
vt-0.57721/svm_train.cpp:148:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
vt-0.57721/svm_train.cpp:194:16: style: Variable 'offset' can be declared as pointer to const [constVariablePointer]
vt-0.57721/svm_train.cpp:40:17: style: class member 'Igor::model' is never used. [unusedStructMember]
vt-0.57721/svm_train.cpp:42:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/tbx_ordered_reader.cpp:53:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/tbx_ordered_reader.cpp:91:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/tbx_ordered_reader.cpp:31:19: warning: Member variable 'TBXOrderedReader::intervals_present' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/tbx_ordered_reader.cpp:40:5: performance: Variable 's' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/tbx_ordered_reader.cpp:77:5: performance: Variable 's' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/tbx_ordered_reader.cpp:31:49: style: Parameter 'hts_file' can be declared as reference to const [constParameterReference]
vt-0.57721/tbx_ordered_reader.cpp:67:49: style: Parameter 'hts_file' can be declared as reference to const [constParameterReference]
vt-0.57721/tbx_ordered_reader.cpp:67:88: style: Parameter 'intervals' can be declared as reference to const [constParameterReference]
vt-0.57721/tbx_ordered_reader.cpp:114:18: error: Out of bounds access in 'intervals[interval_index++]', if 'intervals' size is 1 and 'interval_index++' is 1 [containerOutOfBounds]
vt-0.57721/tbx_ordered_reader.cpp:112:26: note: Assignment 'interval_index=0', assigned value is 0
vt-0.57721/tbx_ordered_reader.cpp:114:19: note: interval_index is incremented', new value is 1
vt-0.57721/tbx_ordered_reader.cpp:114:18: note: Access out of bounds
vt-0.57721/test.cpp:38:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:221:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:300:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:335:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:349:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:383:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:468:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:512:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:614:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/test.cpp:73:5: warning: Member variable 'Igor::debug' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/test.cpp:73:5: warning: Member variable 'Igor::no' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/test.cpp:159:10: performance:inconclusive: Technically the member function '::Igor::compute_composition_and_entropy' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/test.cpp:333:10: performance:inconclusive: Technically the member function '::Igor::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/test.cpp:341:11: performance:inconclusive: Technically the member function '::Igor::get_sequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/test.cpp:602:10: performance:inconclusive: Technically the member function '::Igor::test_ip2g' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/test.cpp:333:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/test.cpp:333:10: note: Derived function 'Igor::print_stats'
vt-0.57721/test.cpp:349:13: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/test.cpp:449:18: style: The scope of the variable 'fai' can be reduced. [variableScope]
vt-0.57721/test.cpp:402:18: style: Local variable 'no' shadows outer variable [shadowVariable]
vt-0.57721/test.cpp:69:14: note: Shadowed declaration
vt-0.57721/test.cpp:402:18: note: Shadow variable
vt-0.57721/test.cpp:159:55: style: Parameter 'repeat_tract' can be declared as reference to const [constParameterReference]
vt-0.57721/test.cpp:341:37: style: Parameter 'chrom' can be declared as reference to const [constParameterReference]
vt-0.57721/test.cpp:169:17: style: Variable 'b2i' can be declared as const array [constVariable]
vt-0.57721/test.cpp:204:15: style: Variable 'p' can be declared as const array [constVariable]
vt-0.57721/test.cpp:341:82: style: Parameter 'fai' can be declared as pointer to const [constParameterPointer]
vt-0.57721/test.cpp:364:18: style: Variable 'fai' can be declared as pointer to const [constVariablePointer]
vt-0.57721/test.cpp:449:18: style: Variable 'fai' can be declared as pointer to const [constVariablePointer]
vt-0.57721/test.cpp:422:44: warning: Uninitialized variable: fai [uninitvar]
vt-0.57721/test.cpp:389:27: note: Assuming condition is false
vt-0.57721/test.cpp:422:44: note: Uninitialized variable: fai
vt-0.57721/test.cpp:64:17: style: class member 'Igor::method' is never used. [unusedStructMember]
vt-0.57721/test.cpp:66:17: style: class member 'Igor::sequence' is never used. [unusedStructMember]
vt-0.57721/test.cpp:68:10: style: class member 'Igor::debug' is never used. [unusedStructMember]
vt-0.57721/test.cpp:219:17: style: Variable 'comp[3]' is assigned a value that is never used. [unreadVariable]
vt-0.57721/test.cpp:232:21: style: Variable 'log2q' is assigned a value that is never used. [unreadVariable]
vt-0.57721/test.cpp:493:18: style: Unused variable: fai [unusedVariable]
vt-0.57721/union_variants.cpp:97:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/union_variants.cpp:126:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/union_variants.cpp:198:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/union_variants.cpp:207:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/union_variants.cpp:68:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/union_variants.cpp:68:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/union_variants.cpp:68:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/union_variants.cpp:68:5: warning: Member variable 'Igor::no_unique_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/union_variants.cpp:68:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/union_variants.cpp:68:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/union_variants.cpp:205:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/union_variants.cpp:33:17: warning: The class 'Igor' defines member variable with name 'version' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:62:17: note: Parent variable 'Program::version'
vt-0.57721/union_variants.cpp:33:17: note: Derived variable 'Igor::version'
vt-0.57721/union_variants.cpp:102:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/union_variants.cpp:102:10: note: Derived function 'Igor::initialize'
vt-0.57721/union_variants.cpp:196:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/union_variants.cpp:196:10: note: Derived function 'Igor::print_options'
vt-0.57721/union_variants.cpp:205:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/union_variants.cpp:205:10: note: Derived function 'Igor::print_stats'
vt-0.57721/union_variants.cpp:175:21: style: Local variable 'v' shadows outer variable [shadowVariable]
vt-0.57721/union_variants.cpp:50:13: note: Shadowed declaration
vt-0.57721/union_variants.cpp:175:21: note: Shadow variable
vt-0.57721/union_variants.cpp:43:17: style: class member 'Igor::interval_list' is never used. [unusedStructMember]
vt-0.57721/union_variants.cpp:50:13: style: class member 'Igor::v' is never used. [unusedStructMember]
vt-0.57721/union_variants.cpp:146:25: style: Variable 'ncenter' is assigned a value that is never used. [unreadVariable]
vt-0.57721/uniq.cpp:86:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/uniq.cpp:161:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/uniq.cpp:170:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/uniq.cpp:59:5: warning: Member variable 'Igor::sr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/uniq.cpp:59:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/uniq.cpp:59:5: warning: Member variable 'Igor::no_total_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/uniq.cpp:59:5: warning: Member variable 'Igor::no_unique_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/uniq.cpp:59:5: warning: Member variable 'Igor::var_manip' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/uniq.cpp:168:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/uniq.cpp:91:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/uniq.cpp:91:10: note: Derived function 'Igor::initialize'
vt-0.57721/uniq.cpp:159:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/uniq.cpp:159:10: note: Derived function 'Igor::print_options'
vt-0.57721/uniq.cpp:168:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/uniq.cpp:168:10: note: Derived function 'Igor::print_stats'
vt-0.57721/uniq.cpp:46:26: style: class member 'Igor::pool' is never used. [unusedStructMember]
vt-0.57721/uniq.cpp:57:19: style: class member 'Igor::var_manip' is never used. [unusedStructMember]
vt-0.57721/utils.cpp:173:80: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __FUNCTION__ [valueFlowBailoutIncompleteVar]
vt-0.57721/utils.cpp:49:10: style: The scope of the variable 'isDelim' can be reduced. [variableScope]
vt-0.57721/utils.cpp:96:10: style: The scope of the variable 'isDelim' can be reduced. [variableScope]
vt-0.57721/utils.cpp:123:61: performance: Function parameter 'delim' should be passed by const reference. [passedByValue]
vt-0.57721/utils.cpp:138:67: performance: Function parameter 'delim' should be passed by const reference. [passedByValue]
vt-0.57721/utils.cpp:29:76: style: Parameter 'str' can be declared as reference to const [constParameterReference]
vt-0.57721/utils.cpp:123:44: style: Parameter 'vec' can be declared as reference to const [constParameterReference]
vt-0.57721/utils.cpp:138:50: style: Parameter 'map' can be declared as reference to const [constParameterReference]
vt-0.57721/utils.cpp:155:29: style: Parameter 's' can be declared as reference to const [constParameterReference]
vt-0.57721/utils.cpp:166:32: style: Parameter 's' can be declared as reference to const [constParameterReference]
vt-0.57721/utils.cpp:182:30: style: Parameter 's' can be declared as reference to const [constParameterReference]
vt-0.57721/utils.cpp:193:30: style: Parameter 's' can be declared as reference to const [constParameterReference]
vt-0.57721/utils.cpp:204:35: style: Parameter 's' can be declared as reference to const [constParameterReference]
vt-0.57721/utils.cpp:49:18: style: Variable 'isDelim' is assigned a value that is never used. [unreadVariable]
vt-0.57721/utils.cpp:96:18: style: Variable 'isDelim' is assigned a value that is never used. [unreadVariable]
vt-0.57721/validate.cpp:90:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/validate.cpp:120:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/validate.cpp:134:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/validate.cpp:191:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/validate.cpp:201:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/validate.cpp:60:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/validate.cpp:60:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/validate.cpp:60:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/validate.cpp:60:5: warning: Member variable 'Igor::no_unordered' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/validate.cpp:60:5: warning: Member variable 'Igor::no_unordered_chrom' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/validate.cpp:60:5: warning: Member variable 'Igor::no_inconsistent_ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/validate.cpp:60:5: warning: Member variable 'Igor::fai' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/validate.cpp:199:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/validate.cpp:95:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/validate.cpp:95:10: note: Derived function 'Igor::initialize'
vt-0.57721/validate.cpp:189:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/validate.cpp:189:10: note: Derived function 'Igor::print_options'
vt-0.57721/validate.cpp:199:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/validate.cpp:199:10: note: Derived function 'Igor::print_stats'
vt-0.57721/validate.cpp:160:29: style: Local variable 'chrom' shadows outer variable [shadowVariable]
vt-0.57721/validate.cpp:137:25: note: Shadowed declaration
vt-0.57721/validate.cpp:160:29: note: Shadow variable
vt-0.57721/variant.cpp:86:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/variant.cpp:212:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/variant.cpp:623:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/variant.cpp:650:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::h' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::ts' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::tv' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::ins' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::del' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::max_dlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::min_dlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::is_new_multiallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::is_involved_in_a_multiallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::associated_new_multiallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::updated_multiallelic' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:96:10: warning: Member variable 'Variant::contains_N' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant.cpp:100:5: performance: Variable 'chrom' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
vt-0.57721/variant.cpp:375:21: style: Local variable 'ts' shadows outer variable [shadowVariable]
vt-0.57721/variant.h:72:13: note: Shadowed declaration
vt-0.57721/variant.cpp:375:21: note: Shadow variable
vt-0.57721/variant.cpp:376:21: style: Local variable 'tv' shadows outer variable [shadowVariable]
vt-0.57721/variant.h:73:13: note: Shadowed declaration
vt-0.57721/variant.cpp:376:21: note: Shadow variable
vt-0.57721/variant.cpp:219:18: style: Variable 'pos0' is assigned a value that is never used. [unreadVariable]
vt-0.57721/variant.cpp:455:16: style: Variable 'ts' is assigned a value that is never used. [unreadVariable]
vt-0.57721/variant.cpp:456:16: style: Variable 'tv' is assigned a value that is never used. [unreadVariable]
vt-0.57721/variant.cpp:488:19: style: Variable 'allele' is assigned a value that is never used. [unreadVariable]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::reference_bias' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::snp_baseq_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::snp_e_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::snp_f_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::snp_desired_type_I_error' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::snp_desired_type_II_error' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::deletion_e_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::deletion_f_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::deletion_desired_type_I_error' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::deletion_desired_type_II_error' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::insertion_e_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::insertion_f_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::insertion_desired_type_I_error' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::insertion_desired_type_II_error' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::sclip_mq_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.cpp:26:16: warning: Member variable 'VariantFilter::sclip_u_cutoff' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_filter.h:108:11: style:inconclusive: Technically the member function 'VariantFilter::get_reference_bias' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:118:22: note: Technically the member function 'VariantFilter::get_reference_bias' can be const.
vt-0.57721/variant_filter.h:108:11: note: Technically the member function 'VariantFilter::get_reference_bias' can be const.
vt-0.57721/variant_filter.h:115:11: style:inconclusive: Technically the member function 'VariantFilter::get_lr_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:131:22: note: Technically the member function 'VariantFilter::get_lr_cutoff' can be const.
vt-0.57721/variant_filter.h:115:11: note: Technically the member function 'VariantFilter::get_lr_cutoff' can be const.
vt-0.57721/variant_filter.h:130:14: style:inconclusive: Technically the member function 'VariantFilter::get_snp_baseq_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:164:25: note: Technically the member function 'VariantFilter::get_snp_baseq_cutoff' can be const.
vt-0.57721/variant_filter.h:130:14: note: Technically the member function 'VariantFilter::get_snp_baseq_cutoff' can be const.
vt-0.57721/variant_filter.h:132:14: style:inconclusive: Technically the member function 'VariantFilter::get_snp_e_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:169:25: note: Technically the member function 'VariantFilter::get_snp_e_cutoff' can be const.
vt-0.57721/variant_filter.h:132:14: note: Technically the member function 'VariantFilter::get_snp_e_cutoff' can be const.
vt-0.57721/variant_filter.h:134:11: style:inconclusive: Technically the member function 'VariantFilter::get_snp_f_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:174:22: note: Technically the member function 'VariantFilter::get_snp_f_cutoff' can be const.
vt-0.57721/variant_filter.h:134:11: note: Technically the member function 'VariantFilter::get_snp_f_cutoff' can be const.
vt-0.57721/variant_filter.h:136:11: style:inconclusive: Technically the member function 'VariantFilter::get_snp_desired_type_I_error' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:179:22: note: Technically the member function 'VariantFilter::get_snp_desired_type_I_error' can be const.
vt-0.57721/variant_filter.h:136:11: note: Technically the member function 'VariantFilter::get_snp_desired_type_I_error' can be const.
vt-0.57721/variant_filter.h:138:11: style:inconclusive: Technically the member function 'VariantFilter::get_snp_desired_type_II_error' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:184:22: note: Technically the member function 'VariantFilter::get_snp_desired_type_II_error' can be const.
vt-0.57721/variant_filter.h:138:11: note: Technically the member function 'VariantFilter::get_snp_desired_type_II_error' can be const.
vt-0.57721/variant_filter.h:151:14: style:inconclusive: Technically the member function 'VariantFilter::get_deletion_e_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:212:25: note: Technically the member function 'VariantFilter::get_deletion_e_cutoff' can be const.
vt-0.57721/variant_filter.h:151:14: note: Technically the member function 'VariantFilter::get_deletion_e_cutoff' can be const.
vt-0.57721/variant_filter.h:153:11: style:inconclusive: Technically the member function 'VariantFilter::get_deletion_f_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:217:22: note: Technically the member function 'VariantFilter::get_deletion_f_cutoff' can be const.
vt-0.57721/variant_filter.h:153:11: note: Technically the member function 'VariantFilter::get_deletion_f_cutoff' can be const.
vt-0.57721/variant_filter.h:155:11: style:inconclusive: Technically the member function 'VariantFilter::get_deletion_desired_type_I_error' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:222:22: note: Technically the member function 'VariantFilter::get_deletion_desired_type_I_error' can be const.
vt-0.57721/variant_filter.h:155:11: note: Technically the member function 'VariantFilter::get_deletion_desired_type_I_error' can be const.
vt-0.57721/variant_filter.h:157:11: style:inconclusive: Technically the member function 'VariantFilter::get_deletion_desired_type_II_error' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:227:22: note: Technically the member function 'VariantFilter::get_deletion_desired_type_II_error' can be const.
vt-0.57721/variant_filter.h:157:11: note: Technically the member function 'VariantFilter::get_deletion_desired_type_II_error' can be const.
vt-0.57721/variant_filter.h:170:14: style:inconclusive: Technically the member function 'VariantFilter::get_insertion_e_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:255:25: note: Technically the member function 'VariantFilter::get_insertion_e_cutoff' can be const.
vt-0.57721/variant_filter.h:170:14: note: Technically the member function 'VariantFilter::get_insertion_e_cutoff' can be const.
vt-0.57721/variant_filter.h:172:11: style:inconclusive: Technically the member function 'VariantFilter::get_insertion_f_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:260:22: note: Technically the member function 'VariantFilter::get_insertion_f_cutoff' can be const.
vt-0.57721/variant_filter.h:172:11: note: Technically the member function 'VariantFilter::get_insertion_f_cutoff' can be const.
vt-0.57721/variant_filter.h:174:11: style:inconclusive: Technically the member function 'VariantFilter::get_insertion_desired_type_I_error' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:265:22: note: Technically the member function 'VariantFilter::get_insertion_desired_type_I_error' can be const.
vt-0.57721/variant_filter.h:174:11: note: Technically the member function 'VariantFilter::get_insertion_desired_type_I_error' can be const.
vt-0.57721/variant_filter.h:176:11: style:inconclusive: Technically the member function 'VariantFilter::get_insertion_desired_type_II_error' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:270:22: note: Technically the member function 'VariantFilter::get_insertion_desired_type_II_error' can be const.
vt-0.57721/variant_filter.h:176:11: note: Technically the member function 'VariantFilter::get_insertion_desired_type_II_error' can be const.
vt-0.57721/variant_filter.h:185:11: style:inconclusive: Technically the member function 'VariantFilter::get_sclip_mq_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:288:22: note: Technically the member function 'VariantFilter::get_sclip_mq_cutoff' can be const.
vt-0.57721/variant_filter.h:185:11: note: Technically the member function 'VariantFilter::get_sclip_mq_cutoff' can be const.
vt-0.57721/variant_filter.h:187:14: style:inconclusive: Technically the member function 'VariantFilter::get_sclip_u_cutoff' can be const. [functionConst]
vt-0.57721/variant_filter.cpp:293:25: note: Technically the member function 'VariantFilter::get_sclip_u_cutoff' can be const.
vt-0.57721/variant_filter.h:187:14: note: Technically the member function 'VariantFilter::get_sclip_u_cutoff' can be const.
vt-0.57721/variant_manip.cpp:38:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/variant_manip.cpp:72:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/variant_manip.cpp:234:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/variant_manip.cpp:568:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/variant_manip.cpp:48:15: warning: Member variable 'VariantManip::fai' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/variant_manip.h:56:13: performance:inconclusive: Technically the member function 'VariantManip::classify_variant' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/variant_manip.cpp:227:23: note: Technically the member function 'VariantManip::classify_variant' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/variant_manip.h:56:13: note: Technically the member function 'VariantManip::classify_variant' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/variant_manip.h:66:13: style:inconclusive: Technically the member function 'VariantManip::is_not_ref_consistent' can be const. [functionConst]
vt-0.57721/variant_manip.cpp:61:23: note: Technically the member function 'VariantManip::is_not_ref_consistent' can be const.
vt-0.57721/variant_manip.h:66:13: note: Technically the member function 'VariantManip::is_not_ref_consistent' can be const.
vt-0.57721/variant_manip.h:72:10: performance:inconclusive: Technically the member function 'VariantManip::is_normalized' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/variant_manip.cpp:109:20: note: Technically the member function 'VariantManip::is_normalized' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/variant_manip.h:72:10: note: Technically the member function 'VariantManip::is_normalized' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/variant_manip.h:77:10: performance:inconclusive: Technically the member function 'VariantManip::contains_N' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/variant_manip.cpp:202:20: note: Technically the member function 'VariantManip::contains_N' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/variant_manip.h:77:10: note: Technically the member function 'VariantManip::contains_N' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/variant_manip.h:82:10: style:inconclusive: Technically the member function 'VariantManip::right_trim_or_left_extend' can be const. [functionConst]
vt-0.57721/variant_manip.cpp:513:20: note: Technically the member function 'VariantManip::right_trim_or_left_extend' can be const.
vt-0.57721/variant_manip.h:82:10: note: Technically the member function 'VariantManip::right_trim_or_left_extend' can be const.
vt-0.57721/variant_manip.h:104:10: style:inconclusive: Technically the member function 'VariantManip::generate_probes' can be const. [functionConst]
vt-0.57721/variant_manip.cpp:733:20: note: Technically the member function 'VariantManip::generate_probes' can be const.
vt-0.57721/variant_manip.h:104:10: note: Technically the member function 'VariantManip::generate_probes' can be const.
vt-0.57721/variant_manip.cpp:41:33: style: Condition 'fai!=NULL' is always true [knownConditionTrueFalse]
vt-0.57721/variant_manip.cpp:72:9: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/variant_manip.cpp:72:9: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/variant_manip.cpp:96:8: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/variant_manip.cpp:96:8: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
vt-0.57721/variant_manip.cpp:118:12: style: The scope of the variable 'rlen' can be reduced. [variableScope]
vt-0.57721/variant_manip.cpp:118:18: style: The scope of the variable 'alen' can be reduced. [variableScope]
vt-0.57721/variant_manip.cpp:118:24: style: The scope of the variable 'len' can be reduced. [variableScope]
vt-0.57721/variant_manip.cpp:705:15: style: The scope of the variable 'base' can be reduced. [variableScope]
vt-0.57721/variant_manip.cpp:227:74: style:inconclusive: Function 'classify_variant' argument 3 names different: declaration 'variant' definition 'var'. [funcArgNamesDifferent]
vt-0.57721/variant_manip.h:56:64: note: Function 'classify_variant' argument 3 names different: declaration 'variant' definition 'var'.
vt-0.57721/variant_manip.cpp:227:74: note: Function 'classify_variant' argument 3 names different: declaration 'variant' definition 'var'.
vt-0.57721/variant_manip.cpp:670:23: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/variant_manip.cpp:647:18: note: Shadowed declaration
vt-0.57721/variant_manip.cpp:670:23: note: Shadow variable
vt-0.57721/variant_manip.cpp:723:21: style: Local variable 'i' shadows outer variable [shadowVariable]
vt-0.57721/variant_manip.cpp:706:18: note: Shadowed declaration
vt-0.57721/variant_manip.cpp:723:21: note: Shadow variable
vt-0.57721/variant_manip.cpp:31:40: performance: Function parameter 'ref_fasta_file' should be passed by const reference. [passedByValue]
vt-0.57721/variant_manip.cpp:65:11: style: Variable 'vcf_ref' can be declared as pointer to const [constVariablePointer]
vt-0.57721/variant_manip.cpp:245:18: style: Variable 'pos0' is assigned a value that is never used. [unreadVariable]
vt-0.57721/variant_manip.cpp:334:18: style: Variable 'type' is assigned a value that is never used. [unreadVariable]
vt-0.57721/view.cpp:129:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/view.cpp:197:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_STR [valueFlowBailoutIncompleteVar]
vt-0.57721/view.cpp:241:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/view.cpp:263:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::stream_selection' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::print_sites_only' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::no_samples' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:79:5: warning: Member variable 'Igor::orom_regions' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/view.cpp:259:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/view.cpp:134:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/view.cpp:134:10: note: Derived function 'Igor::initialize'
vt-0.57721/view.cpp:237:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/view.cpp:237:10: note: Derived function 'Igor::print_options'
vt-0.57721/view.cpp:259:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/view.cpp:259:10: note: Derived function 'Igor::print_stats'
vt-0.57721/view.cpp:189:17: style: Local variable 'variant' shadows outer variable [shadowVariable]
vt-0.57721/view.cpp:44:17: note: Shadowed declaration
vt-0.57721/view.cpp:189:17: note: Shadow variable
vt-0.57721/view.cpp:43:30: style: class member 'Igor::samples' is never used. [unusedStructMember]
vt-0.57721/view.cpp:44:17: style: class member 'Igor::variant' is never used. [unusedStructMember]
vt-0.57721/vntr.cpp:290:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::rid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::mlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::blen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::comp' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::entropy' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::entropy2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::kl_divergence' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::kl_divergence2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::lref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::rl' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::ll' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::no_perfect_ru' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::no_ru' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::trf_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_mlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_blen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_comp' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_entropy' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_entropy2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_kl_divergence' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_kl_divergence2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_lref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_rl' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_ll' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_no_perfect_ru' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_no_ru' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_trf_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::exact_ru_ambiguous' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_mlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_blen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_comp' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_entropy' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_entropy2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_kl_divergence' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_kl_divergence2' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_beg1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_end1' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_ref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_lref' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_rl' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_ll' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_no_perfect_ru' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_no_ru' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::fuzzy_trf_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::is_large_repeat_tract' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.cpp:29:7: warning: Member variable 'VNTR::is_interspersed_repeat_tract' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr.h:161:10: style:inconclusive: Technically the member function 'VNTR::equals' can be const. [functionConst]
vt-0.57721/vntr.cpp:111:12: note: Technically the member function 'VNTR::equals' can be const.
vt-0.57721/vntr.h:161:10: note: Technically the member function 'VNTR::equals' can be const.
vt-0.57721/vntr.h:212:10: style:inconclusive: Technically the member function 'VNTR::print' can be const. [functionConst]
vt-0.57721/vntr.cpp:288:12: note: Technically the member function 'VNTR::print' can be const.
vt-0.57721/vntr.h:212:10: note: Technically the member function 'VNTR::print' can be const.
vt-0.57721/vntr.cpp:85:46: style: Parameter 'indel' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr.cpp:111:25: style: Parameter 'vntr' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr.cpp:124:51: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr.cpp:274:42: style: Parameter 'seq' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr.cpp:234:35: style: Parameter 'motif' can be declared as pointer to const [constParameterPointer]
vt-0.57721/vntr_annotator.cpp:36:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_annotator.cpp:79:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_annotator.cpp:29:16: warning: Member variable 'VNTRAnnotator::max_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_annotator.cpp:29:16: warning: Member variable 'VNTRAnnotator::seq' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_annotator.cpp:29:16: warning: Member variable 'VNTRAnnotator::factors' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_annotator.cpp:31:5: warning: Class 'VNTRAnnotator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/vntr_annotator.cpp:31:5: warning: Class 'VNTRAnnotator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/vntr_annotator.cpp:80:13: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/vntr_annotator.cpp:79:13: note: First condition
vt-0.57721/vntr_annotator.cpp:80:13: note: Second condition
vt-0.57721/vntr_annotator.cpp:105:13: style: The if condition is the same as the previous if condition [duplicateCondition]
vt-0.57721/vntr_annotator.cpp:104:13: note: First condition
vt-0.57721/vntr_annotator.cpp:105:13: note: Second condition
vt-0.57721/vntr_annotator.cpp:64:11: style: The scope of the variable 'vntr' can be reduced. [variableScope]
vt-0.57721/vntr_annotator.cpp:118:19: style: Local variable 'vntr' shadows outer variable [shadowVariable]
vt-0.57721/vntr_annotator.cpp:64:11: note: Shadowed declaration
vt-0.57721/vntr_annotator.cpp:118:19: note: Shadow variable
vt-0.57721/vntr_annotator.cpp:31:14: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam]
vt-0.57721/vntr_annotator.cpp:66:18: style: Variable 'h' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_consolidator.cpp:48:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_consolidator.cpp:136:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_consolidator.cpp:261:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_consolidator.cpp:327:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_consolidator.cpp:394:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_consolidator.cpp:29:19: warning: Member variable 'VNTRConsolidator::overlap_snp' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_consolidator.cpp:29:19: warning: Member variable 'VNTRConsolidator::overlap_indel' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_consolidator.cpp:29:19: warning: Member variable 'VNTRConsolidator::overlap_snp_id' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_consolidator.cpp:29:19: warning: Member variable 'VNTRConsolidator::overlap_indel_id' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_consolidator.h:176:10: performance:inconclusive: Technically the member function 'VNTRConsolidator::merge_consistent_basis_overlapping_VNTR' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/vntr_consolidator.cpp:507:24: note: Technically the member function 'VNTRConsolidator::merge_consistent_basis_overlapping_VNTR' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_consolidator.h:176:10: note: Technically the member function 'VNTRConsolidator::merge_consistent_basis_overlapping_VNTR' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_consolidator.cpp:38:5: warning: Class 'VNTRConsolidator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/vntr_consolidator.cpp:38:5: warning: Class 'VNTRConsolidator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/vntr_consolidator.cpp:146:36: style: Condition 'variant->end1>=cvariant->beg1' is always true [knownConditionTrueFalse]
vt-0.57721/vntr_consolidator.cpp:134:31: note: Assuming that condition 'variant->end1<cvariant->beg1' is not redundant
vt-0.57721/vntr_consolidator.cpp:146:36: note: Condition 'variant->end1>=cvariant->beg1' is always true
vt-0.57721/vntr_consolidator.cpp:354:19: style: Redundant initialization for 'basis'. The initialized value is overwritten before it is read. [redundantInitialization]
vt-0.57721/vntr_consolidator.cpp:350:31: note: basis is initialized
vt-0.57721/vntr_consolidator.cpp:354:19: note: basis is overwritten
vt-0.57721/vntr_consolidator.cpp:29:49: style: Parameter 'input_vcf_file' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr_consolidator.cpp:29:118: style: Parameter 'output_vcf_file' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr_consolidator.cpp:182:54: style: Parameter 'var' can be declared as pointer to const [constParameterPointer]
vt-0.57721/vntr_consolidator.cpp:507:73: style: Parameter 'variant' can be declared as pointer to const [constParameterPointer]
vt-0.57721/vntr_consolidator.cpp:338:29: style: Variable 'merged_beg1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_consolidator.cpp:339:29: style: Variable 'merged_end1' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_consolidator.cpp:341:40: style: Unused variable: motifs [unusedVariable]
vt-0.57721/vntr_extractor.cpp:179:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_extractor.cpp:222:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_extractor.cpp:510:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_extractor.cpp:26:16: warning: Member variable 'VNTRExtractor::debug' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_extractor.h:174:10: performance:inconclusive: Technically the member function 'VNTRExtractor::copy_exact_vntr_features_to_final_vntr_features' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/vntr_extractor.cpp:315:21: note: Technically the member function 'VNTRExtractor::copy_exact_vntr_features_to_final_vntr_features' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_extractor.h:174:10: note: Technically the member function 'VNTRExtractor::copy_exact_vntr_features_to_final_vntr_features' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_extractor.h:179:10: performance:inconclusive: Technically the member function 'VNTRExtractor::copy_fuzzy_vntr_features_to_final_vntr_features' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/vntr_extractor.cpp:344:21: note: Technically the member function 'VNTRExtractor::copy_fuzzy_vntr_features_to_final_vntr_features' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_extractor.h:179:10: note: Technically the member function 'VNTRExtractor::copy_fuzzy_vntr_features_to_final_vntr_features' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_extractor.h:189:17: style:inconclusive: Technically the member function 'VNTRExtractor::vntr_code_2_str' can be const. [functionConst]
vt-0.57721/vntr_extractor.cpp:564:28: note: Technically the member function 'VNTRExtractor::vntr_code_2_str' can be const.
vt-0.57721/vntr_extractor.h:189:17: note: Technically the member function 'VNTRExtractor::vntr_code_2_str' can be const.
vt-0.57721/vntr_extractor.cpp:37:5: warning: Class 'VNTRExtractor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
vt-0.57721/vntr_extractor.cpp:37:5: warning: Class 'VNTRExtractor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
vt-0.57721/vntr_extractor.cpp:46:15: style: C-style pointer casting [cstyleCast]
vt-0.57721/vntr_extractor.cpp:108:37: style:inconclusive: Function 'insert' argument 1 names different: declaration 'variant' definition 'var'. [funcArgNamesDifferent]
vt-0.57721/vntr_extractor.h:130:26: note: Function 'insert' argument 1 names different: declaration 'variant' definition 'var'.
vt-0.57721/vntr_extractor.cpp:108:37: note: Function 'insert' argument 1 names different: declaration 'variant' definition 'var'.
vt-0.57721/vntr_extractor.cpp:26:43: style: Parameter 'input_vcf_file' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr_extractor.cpp:26:112: style: Parameter 'output_vcf_file' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr_extractor.cpp:26:142: style: Parameter 'fexp' can be declared as reference to const [constParameterReference]
vt-0.57721/vntr_extractor.cpp:201:18: style: Variable 'nvar' can be declared as reference to const [constVariableReference]
vt-0.57721/vntr_extractor.cpp:207:22: style: Variable 'cvar' can be declared as reference to const [constVariableReference]
vt-0.57721/vntr_extractor.cpp:241:17: style: Variable 'var' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:283:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_DT_ID [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_genotyping_record.cpp:546:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_genotyping_record.cpp:338:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/vntr_genotyping_record.cpp:339:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/vntr_genotyping_record.cpp:340:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/vntr_genotyping_record.cpp:341:22: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
vt-0.57721/vntr_genotyping_record.cpp:64:11: style: C-style pointer casting [cstyleCast]
vt-0.57721/vntr_genotyping_record.cpp:65:11: style: C-style pointer casting [cstyleCast]
vt-0.57721/vntr_genotyping_record.cpp:134:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/vntr_genotyping_record.cpp:135:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/vntr_genotyping_record.cpp:136:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/vntr_genotyping_record.cpp:137:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/vntr_genotyping_record.cpp:138:19: style: C-style pointer casting [cstyleCast]
vt-0.57721/vntr_genotyping_record.cpp:141:12: style: The scope of the variable 'gp' can be reduced. [variableScope]
vt-0.57721/vntr_genotyping_record.cpp:141:16: style: The scope of the variable 'gp_sum' can be reduced. [variableScope]
vt-0.57721/vntr_genotyping_record.cpp:141:24: style: The scope of the variable 'max_gp' can be reduced. [variableScope]
vt-0.57721/vntr_genotyping_record.cpp:142:13: style: The scope of the variable 'best_gt' can be reduced. [variableScope]
vt-0.57721/vntr_genotyping_record.cpp:143:13: style: The scope of the variable 'best_a1' can be reduced. [variableScope]
vt-0.57721/vntr_genotyping_record.cpp:143:22: style: The scope of the variable 'best_a2' can be reduced. [variableScope]
vt-0.57721/vntr_genotyping_record.cpp:573:26: style: The scope of the variable 'cycle' can be reduced. [variableScope]
vt-0.57721/vntr_genotyping_record.cpp:149:13: style: Local variable 'max_gq' shadows outer variable [shadowVariable]
vt-0.57721/vntr_genotyping_record.h:78:28: note: Shadowed declaration
vt-0.57721/vntr_genotyping_record.cpp:149:13: note: Shadow variable
vt-0.57721/vntr_genotyping_record.cpp:150:13: style: Local variable 'dp_sum' shadows outer variable [shadowVariable]
vt-0.57721/vntr_genotyping_record.h:78:20: note: Shadowed declaration
vt-0.57721/vntr_genotyping_record.cpp:150:13: note: Shadow variable
vt-0.57721/vntr_genotyping_record.cpp:165:18: style: Variable 'pli' can be declared as pointer to const [constVariablePointer]
vt-0.57721/vntr_genotyping_record.cpp:166:30: style: Variable 'gp' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:144:14: style: Unused variable: pls_i [unusedVariable]
vt-0.57721/vntr_genotyping_record.cpp:470:26: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:567:30: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:568:31: style: Variable 'qual' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:573:32: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:597:35: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:606:35: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:626:35: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:633:35: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:654:35: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_genotyping_record.cpp:662:35: style: Variable 'cycle' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntr_tree.cpp:166:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntr_tree.cpp:25:11: warning:inconclusive: Member variable 'VNTRNode::exact_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_tree.cpp:25:11: warning:inconclusive: Member variable 'VNTRNode::fuzzy_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntr_tree.h:60:10: performance:inconclusive: Technically the member function 'VNTRNode::clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/vntr_tree.cpp:51:16: note: Technically the member function 'VNTRNode::clear' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_tree.h:60:10: note: Technically the member function 'VNTRNode::clear' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_tree.h:65:10: performance:inconclusive: Technically the member function 'VNTRNode::print' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/vntr_tree.cpp:58:16: note: Technically the member function 'VNTRNode::print' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_tree.h:65:10: note: Technically the member function 'VNTRNode::print' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/vntr_tree.cpp:33:32: performance: Function parameter 'motif' should be passed by const reference. [passedByValue]
vt-0.57721/vntr_tree.cpp:33:51: performance: Function parameter 'basis' should be passed by const reference. [passedByValue]
vt-0.57721/vntr_tree.cpp:175:31: style: Variable 'vntr_node' can be declared as reference to const [constVariableReference]
vt-0.57721/vntr_tree.cpp:197:31: style: Variable 'vntr_node' can be declared as reference to const [constVariableReference]
vt-0.57721/vntr_tree.cpp:219:31: style: Variable 'vntr_node' can be declared as reference to const [constVariableReference]
vt-0.57721/vntrize.cpp:112:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/vntrize.cpp:202:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BCF_UN_INFO [valueFlowBailoutIncompleteVar]
vt-0.57721/vntrize.cpp:263:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/vntrize.cpp:279:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
vt-0.57721/vntrize.cpp:74:5: warning: Member variable 'Igor::filter_exists' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntrize.cpp:74:5: warning: Member variable 'Igor::odr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntrize.cpp:74:5: warning: Member variable 'Igor::odw' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntrize.cpp:74:5: warning: Member variable 'Igor::v' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntrize.cpp:74:5: warning: Member variable 'Igor::no_variants' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntrize.cpp:74:5: warning: Member variable 'Igor::no_variants_vntrized' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntrize.cpp:74:5: warning: Member variable 'Igor::vm' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntrize.cpp:74:5: warning: Member variable 'Igor::orom_vntrs' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/vntrize.cpp:275:10: style:inconclusive: Technically the member function '::Igor::print_stats' can be const. [functionConst]
vt-0.57721/vntrize.cpp:117:10: warning: The class 'Igor' defines member function with name 'initialize' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:124:10: note: Parent function 'Program::initialize'
vt-0.57721/vntrize.cpp:117:10: note: Derived function 'Igor::initialize'
vt-0.57721/vntrize.cpp:259:10: warning: The class 'Igor' defines member function with name 'print_options' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:129:10: note: Parent function 'Program::print_options'
vt-0.57721/vntrize.cpp:259:10: note: Derived function 'Igor::print_options'
vt-0.57721/vntrize.cpp:275:10: warning: The class 'Igor' defines member function with name 'print_stats' also defined in its parent class 'Program'. [duplInheritedMember]
vt-0.57721/program.h:134:10: note: Parent function 'Program::print_stats'
vt-0.57721/vntrize.cpp:275:10: note: Derived function 'Igor::print_stats'
vt-0.57721/vntrize.cpp:204:31: style: Variable 'chrom' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntrize.cpp:178:18: style: Variable 'left_extended' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntrize.cpp:179:18: style: Variable 'left_trimmed' is assigned a value that is never used. [unreadVariable]
vt-0.57721/vntrize.cpp:180:18: style: Variable 'right_trimmed' is assigned a value that is never used. [unreadVariable]
vt-0.57721/wdp_ahmm.cpp:124:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/wdp_ahmm.cpp:157:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
vt-0.57721/wdp_ahmm.cpp:288:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
vt-0.57721/wdp_ahmm.cpp:793:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/wdp_ahmm.cpp:907:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/wdp_ahmm.cpp:926:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::rlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::motif_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::motif_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::exact_motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::motif_m' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::motif_xid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::frac_no_repeats' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::motif_concordance' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::trf_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::max_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::max_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::optimal_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::optimal_state' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::optimal_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::optimal_probe_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::optimal_path_ptr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::optimal_path_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:44:11: warning: Member variable 'WDP_AHMM::lt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::read' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::qual' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::rlen' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::motif_start' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::motif_end' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::exact_motif_count' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::motif_m' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::motif_xid' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::frac_no_repeats' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::motif_concordance' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::maxLogOdds' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::trf_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::max_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::max_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::optimal_score' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::optimal_state' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::optimal_track' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::optimal_probe_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::optimal_path_ptr' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::optimal_path_len' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.cpp:53:11: warning: Member variable 'WDP_AHMM::lt' is not initialized in the constructor. [uninitMemberVar]
vt-0.57721/wdp_ahmm.h:178:13: performance:inconclusive: Technically the member function 'WDP_AHMM::get_motif_model_spos1' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:222:19: note: Technically the member function 'WDP_AHMM::get_motif_model_spos1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:178:13: note: Technically the member function 'WDP_AHMM::get_motif_model_spos1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:183:13: performance:inconclusive: Technically the member function 'WDP_AHMM::get_motif_model_epos1' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:230:19: note: Technically the member function 'WDP_AHMM::get_motif_model_epos1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:183:13: note: Technically the member function 'WDP_AHMM::get_motif_model_epos1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:188:13: performance:inconclusive: Technically the member function 'WDP_AHMM::get_motif_read_spos1' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:238:19: note: Technically the member function 'WDP_AHMM::get_motif_read_spos1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:188:13: note: Technically the member function 'WDP_AHMM::get_motif_read_spos1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:193:13: performance:inconclusive: Technically the member function 'WDP_AHMM::get_motif_read_epos1' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:246:19: note: Technically the member function 'WDP_AHMM::get_motif_read_epos1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:193:13: note: Technically the member function 'WDP_AHMM::get_motif_read_epos1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:198:11: style:inconclusive: Technically the member function 'WDP_AHMM::get_motif_concordance' can be const. [functionConst]
vt-0.57721/wdp_ahmm.cpp:254:17: note: Technically the member function 'WDP_AHMM::get_motif_concordance' can be const.
vt-0.57721/wdp_ahmm.h:198:11: note: Technically the member function 'WDP_AHMM::get_motif_concordance' can be const.
vt-0.57721/wdp_ahmm.h:203:14: style:inconclusive: Technically the member function 'WDP_AHMM::get_exact_motif_count' can be const. [functionConst]
vt-0.57721/wdp_ahmm.cpp:262:20: note: Technically the member function 'WDP_AHMM::get_exact_motif_count' can be const.
vt-0.57721/wdp_ahmm.h:203:14: note: Technically the member function 'WDP_AHMM::get_exact_motif_count' can be const.
vt-0.57721/wdp_ahmm.h:208:14: style:inconclusive: Technically the member function 'WDP_AHMM::get_motif_count' can be const. [functionConst]
vt-0.57721/wdp_ahmm.cpp:270:20: note: Technically the member function 'WDP_AHMM::get_motif_count' can be const.
vt-0.57721/wdp_ahmm.h:208:14: note: Technically the member function 'WDP_AHMM::get_motif_count' can be const.
vt-0.57721/wdp_ahmm.h:218:10: performance:inconclusive: Technically the member function 'WDP_AHMM::trace_path' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:399:16: note: Technically the member function 'WDP_AHMM::trace_path' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:218:10: note: Technically the member function 'WDP_AHMM::trace_path' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:233:17: performance:inconclusive: Technically the member function 'WDP_AHMM::state2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:598:23: note: Technically the member function 'WDP_AHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:233:17: note: Technically the member function 'WDP_AHMM::state2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:238:17: performance:inconclusive: Technically the member function 'WDP_AHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:638:23: note: Technically the member function 'WDP_AHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:238:17: note: Technically the member function 'WDP_AHMM::state2cigarstring' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:243:17: performance:inconclusive: Technically the member function 'WDP_AHMM::track2cigarstring1' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:673:23: note: Technically the member function 'WDP_AHMM::track2cigarstring1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:243:17: note: Technically the member function 'WDP_AHMM::track2cigarstring1' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:248:17: performance:inconclusive: Technically the member function 'WDP_AHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:726:23: note: Technically the member function 'WDP_AHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:248:17: note: Technically the member function 'WDP_AHMM::track2cigarstring2' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:253:17: performance:inconclusive: Technically the member function 'WDP_AHMM::component2string' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:752:23: note: Technically the member function 'WDP_AHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:253:17: note: Technically the member function 'WDP_AHMM::component2string' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:263:10: style:inconclusive: Technically the member function 'WDP_AHMM::print_alignment' can be const. [functionConst]
vt-0.57721/wdp_ahmm.cpp:789:16: note: Technically the member function 'WDP_AHMM::print_alignment' can be const.
vt-0.57721/wdp_ahmm.h:263:10: note: Technically the member function 'WDP_AHMM::print_alignment' can be const.
vt-0.57721/wdp_ahmm.h:268:10: style:inconclusive: Technically the member function 'WDP_AHMM::print' can be const. [functionConst]
vt-0.57721/wdp_ahmm.cpp:904:16: note: Technically the member function 'WDP_AHMM::print' can be const.
vt-0.57721/wdp_ahmm.h:268:10: note: Technically the member function 'WDP_AHMM::print' can be const.
vt-0.57721/wdp_ahmm.h:273:10: style:inconclusive: Technically the member function 'WDP_AHMM::print' can be const. [functionConst]
vt-0.57721/wdp_ahmm.cpp:923:16: note: Technically the member function 'WDP_AHMM::print' can be const.
vt-0.57721/wdp_ahmm.h:273:10: note: Technically the member function 'WDP_AHMM::print' can be const.
vt-0.57721/wdp_ahmm.h:278:10: performance:inconclusive: Technically the member function 'WDP_AHMM::print_T' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:942:16: note: Technically the member function 'WDP_AHMM::print_T' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:278:10: note: Technically the member function 'WDP_AHMM::print_T' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:283:10: performance:inconclusive: Technically the member function 'WDP_AHMM::print_U' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:973:16: note: Technically the member function 'WDP_AHMM::print_U' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:283:10: note: Technically the member function 'WDP_AHMM::print_U' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:288:10: performance:inconclusive: Technically the member function 'WDP_AHMM::print_trace' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:995:16: note: Technically the member function 'WDP_AHMM::print_trace' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:288:10: note: Technically the member function 'WDP_AHMM::print_trace' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:293:10: performance:inconclusive: Technically the member function 'WDP_AHMM::collect_statistics' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:475:16: note: Technically the member function 'WDP_AHMM::collect_statistics' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:293:10: note: Technically the member function 'WDP_AHMM::collect_statistics' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:298:10: performance:inconclusive: Technically the member function 'WDP_AHMM::clear_statistics' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:534:16: note: Technically the member function 'WDP_AHMM::clear_statistics' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:298:10: note: Technically the member function 'WDP_AHMM::clear_statistics' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:308:10: performance:inconclusive: Technically the member function 'WDP_AHMM::print_track' can be static (but you may consider moving to unnamed namespace). [functionStatic]
vt-0.57721/wdp_ahmm.cpp:1022:16: note: Technically the member function 'WDP_AHMM::print_track' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.h:308:10: note: Technically the member function 'WDP_AHMM::print_track' can be static (but you may consider moving to unnamed namespace).
vt-0.57721/wdp_ahmm.cpp:278:34: style:inconclusive: Function 'align' argument 1 names different: declaration 'y' definition 'read'. [funcArgNamesDifferent]
vt-0.57721/wdp_ahmm.h:213:28: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/wdp_ahmm.cpp:278:34: note: Function 'align' argument 1 names different: declaration 'y' definition 'read'.
vt-0.57721/wdp_ahmm.cpp:475:43: style:inconclusive: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'. [funcArgNamesDifferent]
vt-0.57721/wdp_ahmm.h:293:37: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/wdp_ahmm.cpp:475:43: note: Function 'collect_statistics' argument 1 names different: declaration 't1' definition 'src_t'.
vt-0.57721/wdp_ahmm.cpp:475:58: style:inconclusive: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'. [funcArgNamesDifferent]
vt-0.57721/wdp_ahmm.h:293:49: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/wdp_ahmm.cpp:475:58: note: Function 'collect_statistics' argument 2 names different: declaration 't2' definition 'des_t'.
vt-0.57721/wdp_ahmm.cpp:558:42: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty' [funcArgOrderDifferent]
vt-0.57721/wdp_ahmm.h:223:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty'
vt-0.57721/wdp_ahmm.cpp:558:42: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl, mismatch_penalty' definition 'probe_base, read_base, pl, mismatch_penalty'
vt-0.57721/wdp_ahmm.cpp:578:42: warning: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl' [funcArgOrderDifferent]
vt-0.57721/wdp_ahmm.h:228:36: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/wdp_ahmm.cpp:578:42: note: Function 'log10_emission_odds' argument order different: declaration 'read_base, probe_base, pl' definition 'probe_base, read_base, pl'
vt-0.57721/wdp_ahmm.cpp:789:45: style: Parameter 'pad' can be declared as reference to const [constParameterReference]
vt-0.57721/wdp_ahmm.cpp:904:29: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/wdp_ahmm.cpp:923:31: style: Parameter 'v' can be declared as pointer to const [constParameterPointer]
vt-0.57721/wdp_ahmm.cpp:973:33: style: Parameter 'U' can be declared as pointer to const [constParameterPointer]
vt-0.57721/wdp_ahmm.cpp:150:22: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
vt-0.57721/motif_tree.h:51:9: error: The one definition rule is violated, different classes/structs have the same name 'node' [ctuOneDefinitionRuleViolation]
vt-0.57721/large_motif_tree.h:44:9: note: The one definition rule is violated, different classes/structs have the same name 'node'
vt-0.57721/motif_tree.h:51:9: note: The one definition rule is violated, different classes/structs have the same name 'node'
diff:


DONE