2024-04-22 06:45
ftp://ftp.de.debian.org/debian/pool/main/s/spaln/spaln_3.0.2+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib  --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: ea2e716 (2024-04-21 15:59:20 +0200)
count: 1890 1890
elapsed-time: 322.9 321.0
head-timing-info:

old-timing-info:

head results:
spaln-ver3.0.2/src/adddef.h:178:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:105:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable X [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:174:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:279:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hz [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:617:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:631:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:644:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:656:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:676:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:1034:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hz [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.h:199:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.h:376:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.h:479:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MSF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.h:640:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.h:844:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/aln.h:221:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/aln.h:323:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/aln2.cc:74:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SkipLongGap [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/aln2.cc:90:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SkipLongGap [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/aln2.cc:153:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/aln2.cc:359:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AllowdOverlap [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/aln2.cc:407:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NoOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/aln2.cc:424:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NoOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/gsinfo.h:321:2: warning: Member variable 'Vulgar::rec' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/gsinfo.h:409:2: warning: Member variable 'Gsinfo::fd' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/seq.h:348:7: style: 'operator=' should return reference to 'this' instance. [operatorEqRetRefThis]
spaln-ver3.0.2/src/clib.h:467:6: style:inconclusive: Technically the member function 'PrQueue::find' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:551:21: note: Technically the member function 'PrQueue::find' can be const.
spaln-ver3.0.2/src/clib.h:467:6: note: Technically the member function 'PrQueue::find' can be const.
spaln-ver3.0.2/src/clib.h:721:6: style:inconclusive: Technically the member function 'PrQueue_idx::gettop_idx' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:724:7: style:inconclusive: Technically the member function 'PrQueue_idx::empty' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:725:6: style:inconclusive: Technically the member function 'PrQueue_idx::size' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:726:7: style:inconclusive: Technically the member function 'PrQueue_idx::lt' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:1186:6: style:inconclusive: Technically the member function 'PutIntoBins::step' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:1190:6: style:inconclusive: Technically the member function 'PutIntoBins::samples' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:1212:6: style:inconclusive: Technically the member function 'RandNumGen::get' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:1221:15: style:inconclusive: Technically the member function 'AddExt::add_ext' can be const. [functionConst]
spaln-ver3.0.2/src/mfile.h:40:9: style:inconclusive: Technically the member function 'Mfile::size' can be const. [functionConst]
spaln-ver3.0.2/src/gsinfo.h:229:8: style:inconclusive: Technically the member function 'PfqItr::match_score' can be const. [functionConst]
spaln-ver3.0.2/src/codepot.h:233:9: performance:inconclusive: Technically the member function 'IntronPenalty::ProbDist' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/seq.h:220:6: style:inconclusive: Technically the member function 'PolyA::getthr' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:283:7: performance:inconclusive: Technically the member function 'Seq::isGap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/seq.h:326:7: style:inconclusive: Technically the member function 'Seq::fullrange' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:357:7: style:inconclusive: Technically the member function 'Seq::tron2aa' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:1195:6: style:inconclusive: Technically the member function 'SeqServer::getmolc' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:1313:7: style:inconclusive: Technically the member function 'SeqItr::operator==' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:1314:7: style:inconclusive: Technically the member function 'SeqItr::operator<' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:1315:7: style:inconclusive: Technically the member function 'SeqItr::operator>' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:1316:7: style:inconclusive: Technically the member function 'SeqItr::operator<=' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:1317:7: style:inconclusive: Technically the member function 'SeqItr::operator>=' can be const. [functionConst]
spaln-ver3.0.2/src/seq.h:1318:7: style:inconclusive: Technically the member function 'SeqItr::dullend' can be const. [functionConst]
spaln-ver3.0.2/src/aln.h:215:7: performance:inconclusive: Technically the member function 'Colonies::detectoverlap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/aln2.cc:356:16: note: Technically the member function 'Colonies::detectoverlap' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/aln.h:215:7: note: Technically the member function 'Colonies::detectoverlap' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/aln.h:315:6: style:inconclusive: Technically the member function 'AlnOutModes::end' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:998:6: style:inconclusive: Technically the member function 'StrHash < int >::size' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:1002:8: style:inconclusive: Technically the member function 'StrHash < int >::undef' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:252:8: style:inconclusive: Technically the member function 'Dhash < int , int >::undef' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:253:7: style:inconclusive: Technically the member function 'Dhash < int , int >::write_binary' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:287:27: note: Technically the member function 'Dhash < int , int >::write_binary' can be const.
spaln-ver3.0.2/src/clib.h:253:7: note: Technically the member function 'Dhash < int , int >::write_binary' can be const.
spaln-ver3.0.2/src/clib.h:370:6: warning: Class 'Queue' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:410:6: warning: Class 'Queue2' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:602:2: warning: Class 'PrQueue_wh' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:602:2: warning: Class 'PrQueue_wh' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:736:2: warning: Class 'PrQueue_idx' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:736:2: warning: Class 'PrQueue_idx' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:843:20: warning: Class 'Stack' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:843:20: warning: Class 'Stack' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:925:2: warning: Class 'Strlist' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/sets.h:36:6: warning: Struct 'Subset' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/gsinfo.h:81:2: warning: Struct 'SigII' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/gsinfo.h:302:11: warning: Class 'Cigar' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/gsinfo.h:302:11: warning: Class 'Cigar' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/gsinfo.h:321:12: warning: Class 'Vulgar' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/gsinfo.h:321:12: warning: Class 'Vulgar' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/aln2.cc:427:2: warning: Class 'Colonies' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/aln2.cc:427:2: warning: Class 'Colonies' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/aln2.cc:125:6: warning: Struct 'PwdB' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/aln2.cc:125:6: warning: Struct 'PwdB' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:1035:2: warning: Class 'StrHash < int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:263:6: warning: Class 'Dhash < int , int >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:263:6: warning: Class 'Dhash < int , int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:369:2: style: Class 'Queue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:409:2: style: Class 'Queue2' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:839:2: style: Class 'Stack' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:886:2: style: Class 'Strlist' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:891:2: style: Class 'Strlist' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:1175:2: style: Class 'PutIntoBins' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:1200:2: style: Class 'Dixon' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/mfile.h:33:2: style: Class 'Mfile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/sets.h:33:2: style: Struct 'Subset' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/gsinfo.h:47:2: style: Struct 'SigII' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/gsinfo.h:50:2: style: Struct 'SigII' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/gsinfo.h:131:2: style: Class 'Cip_score' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/gsinfo.h:228:2: style: Class 'PfqItr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/gsinfo.h:231:2: style: Class 'PfqItr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/gsinfo.h:344:2: style: Class 'Eijnc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/gsinfo.h:409:2: style: Class 'Gsinfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/codepot.h:60:2: style: Class 'Premat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/utilseq.h:74:2: style: Class 'PatMat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/utilseq.h:75:2: style: Class 'PatMat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/utilseq.h:120:2: style: Class 'ExinPot' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/utilseq.h:123:2: style: Class 'ExinPot' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/utilseq.h:178:2: style: Struct 'EijPat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/seq.h:217:2: style: Class 'PolyA' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/seq.h:428:2: style: Class 'Seq' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/seq.h:429:2: style: Class 'Seq' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/seq.h:431:2: style: Class 'Seq' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/seq.h:1207:2: style: Class 'StrPhrases' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/seq.h:1335:2: style: Class 'SeqItr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/seq.h:1344:2: style: Class 'PrintMember' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/aln.h:211:2: style: Class 'Colonies' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/aln.h:265:2: style: Struct 'PwdB' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:945:2: style: Class 'StrHash < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:949:2: style: Class 'StrHash < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:205:2: style: Class 'Dhash < int , int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/adddef.h:104:20: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/adddef.h:111:22: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/clib.h:112:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/clib.h:119:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/clib.h:1221:43: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/gsinfo.h:310:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/gsinfo.h:330:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/gsinfo.h:349:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/seq.h:629:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/seq.h:886:11: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/seq.h:1058:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/seq.h:1063:12: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/aln2.cc:303:23: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/aln2.cc:332:23: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/aln2.cc:375:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/aln2.cc:384:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/aln2.cc:387:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/aln2.cc:406:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/aln2.cc:409:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/adddef.h:106:13: style: Checking if unsigned expression 'rv' is less than zero. [unsignedLessThanZero]
spaln-ver3.0.2/src/adddef.h:113:13: style: Checking if unsigned expression 'rv' is less than zero. [unsignedLessThanZero]
spaln-ver3.0.2/src/clib.h:481:42: style:inconclusive: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:456:27: note: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'.
spaln-ver3.0.2/src/clib.h:481:42: note: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'.
spaln-ver3.0.2/src/clib.h:607:45: style:inconclusive: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:581:27: note: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'.
spaln-ver3.0.2/src/clib.h:607:45: note: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'.
spaln-ver3.0.2/src/clib.h:742:46: style:inconclusive: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:713:27: note: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'.
spaln-ver3.0.2/src/clib.h:742:46: note: Function 'downheap' argument 2 names different: declaration 'kk' definition 'kmax'.
spaln-ver3.0.2/src/clib.h:807:39: style:inconclusive: Function 'shift_idx' argument 1 names different: declaration 'x' definition 'j'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:718:20: note: Function 'shift_idx' argument 1 names different: declaration 'x' definition 'j'.
spaln-ver3.0.2/src/clib.h:807:39: note: Function 'shift_idx' argument 1 names different: declaration 'x' definition 'j'.
spaln-ver3.0.2/src/seq.h:675:53: style:inconclusive: Function 'get_nat_aln' argument 3 names different: declaration 'pcr' definition 'qcr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:382:49: note: Function 'get_nat_aln' argument 3 names different: declaration 'pcr' definition 'qcr'.
spaln-ver3.0.2/src/seq.h:675:53: note: Function 'get_nat_aln' argument 3 names different: declaration 'pcr' definition 'qcr'.
spaln-ver3.0.2/src/aln2.cc:293:55: style:inconclusive: Function 'alnscore2dist' argument 3 names different: declaration 'ends' definition 'end'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/aln.h:354:62: note: Function 'alnscore2dist' argument 3 names different: declaration 'ends' definition 'end'.
spaln-ver3.0.2/src/aln2.cc:293:55: note: Function 'alnscore2dist' argument 3 names different: declaration 'ends' definition 'end'.
spaln-ver3.0.2/src/aln2.cc:293:66: style:inconclusive: Function 'alnscore2dist' argument 4 names different: declaration 'denom' definition 'denome'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/aln.h:354:78: note: Function 'alnscore2dist' argument 4 names different: declaration 'denom' definition 'denome'.
spaln-ver3.0.2/src/aln2.cc:293:66: note: Function 'alnscore2dist' argument 4 names different: declaration 'denom' definition 'denome'.
spaln-ver3.0.2/src/clib.h:1054:53: style:inconclusive: Function 'map' argument 1 names different: declaration 'ky' definition 'skey'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:959:38: note: Function 'map' argument 1 names different: declaration 'ky' definition 'skey'.
spaln-ver3.0.2/src/clib.h:1054:53: note: Function 'map' argument 1 names different: declaration 'ky' definition 'skey'.
spaln-ver3.0.2/src/clib.h:297:54: style:inconclusive: Function 'map' argument 1 names different: declaration 'ky' definition 'key'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:213:34: note: Function 'map' argument 1 names different: declaration 'ky' definition 'key'.
spaln-ver3.0.2/src/clib.h:297:54: note: Function 'map' argument 1 names different: declaration 'ky' definition 'key'.
spaln-ver3.0.2/src/seq.h:619:10: style: Local variable 'len' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/seq.h:254:6: note: Shadowed declaration
spaln-ver3.0.2/src/seq.h:619:10: note: Shadow variable
spaln-ver3.0.2/src/clib.h:373:15: style: Parameter 'q' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/clib.h:521:36: style: Parameter 'x' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/clib.h:652:39: style: Parameter 'x' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/clib.h:795:40: style: Parameter 'x' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/clib.h:1177:27: style: Parameter 'src' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/gsinfo.h:232:28: style: Parameter 'bpi' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/seq.h:348:22: style: Parameter 'src' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/seq.h:1313:26: style: Parameter 'b' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/seq.h:1314:25: style: Parameter 'b' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/seq.h:1315:25: style: Parameter 'b' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/seq.h:1316:26: style: Parameter 'b' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/seq.h:1317:26: style: Parameter 'b' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/seq.h:1336:17: style: Parameter 'src' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/aln.h:227:20: style: Parameter 'cc' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/seq.h:450:18: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.h:634:50: style: Parameter 'db' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/seq.h:787:12: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.h:1043:12: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.h:86:17: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.h:111:17: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.h:346:19: style: Parameter 'eis' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/clib.h:229:28: style: Variable 'sh' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/clib.h:345:24: style: Variable 'zold' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/clib.h:839:35: style: Parameter 'given' can be declared as pointer to const. However it seems that 'Stack' is a callback function, if 'given' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/clib.h:833:7: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/clib.h:839:35: note: Parameter 'given' can be declared as pointer to const
spaln-ver3.0.2/src/gsinfo.h:108:6: style: Variable 'wfq' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/seq.h:602:9: style: Variable 'qs' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/seq.h:1294:15: style: Variable 'temp.pos' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/seq.h:1295:15: style: Variable 'temp.res' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/seq.h:1296:22: style: Variable 'temp.bb' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/seq.h:1302:15: style: Variable 'temp.pos' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/seq.h:1303:15: style: Variable 'temp.res' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/seq.h:1304:22: style: Variable 'temp.bb' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/phyl.h:222:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/phyl.h:321:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable node_t [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:89:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable msd [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:104:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input_mode [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:133:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable catalog [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:159:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable interactive [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:175:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idx_a [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:185:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable njumble [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:229:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbs_dt [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:241:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable var_no [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:315:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable var_no [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:372:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:399:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbs_dt [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:591:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input_ns [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:614:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_t [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:628:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vararray [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:729:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vararray [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:866:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in_face [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:878:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input_ns [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/calcserv.h:647:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/calcserv.h:590:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/phyl.h:106:2: warning: Member variable 'Tnode::tname' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/autocomp.h:69:2: warning: Member variable 'AlnServer::tmpdir' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/autocomp.h:80:2: warning: Member variable 'AlnServer::tmpdir' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Seq >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Seq >::optn_job' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:363:2: warning: Member variable 'CalcServer < Seq >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:227:6: performance:inconclusive: Technically the member function 'Minvar::fget' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/phyl.h:111:10: style:inconclusive: Technically the member function 'Tnode::isleaf' can be const. [functionConst]
spaln-ver3.0.2/src/phyl.h:112:7: style:inconclusive: Technically the member function 'Tnode::isroot' can be const. [functionConst]
spaln-ver3.0.2/src/phyl.h:113:6: style:inconclusive: Technically the member function 'Tnode::ndescend' can be const. [functionConst]
spaln-ver3.0.2/src/phyl.h:134:10: style:inconclusive: Technically the member function 'Knode::isleaf' can be const. [functionConst]
spaln-ver3.0.2/src/phyl.h:135:7: style:inconclusive: Technically the member function 'Knode::isroot' can be const. [functionConst]
spaln-ver3.0.2/src/phyl.h:136:6: style:inconclusive: Technically the member function 'Knode::ndescend' can be const. [functionConst]
spaln-ver3.0.2/src/phyl.h:155:7: style:inconclusive: Technically the member function 'Btree::fill_tname' can be const. [functionConst]
spaln-ver3.0.2/src/phyl.h:188:21: note: Technically the member function 'Btree::fill_tname' can be const.
spaln-ver3.0.2/src/phyl.h:155:7: note: Technically the member function 'Btree::fill_tname' can be const.
spaln-ver3.0.2/src/phyl.h:509:6: style:inconclusive: Technically the member function 'PpPrm::normal' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:251:7: style:inconclusive: Technically the member function 'CalcServer < Seq >::initvars' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:736:26: note: Technically the member function 'CalcServer < Seq >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:251:7: note: Technically the member function 'CalcServer < Seq >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:252:7: performance:inconclusive: Technically the member function 'CalcServer < Seq >::common_usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:645:25: note: Technically the member function 'CalcServer < Seq >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:252:7: note: Technically the member function 'CalcServer < Seq >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:279:7: performance:inconclusive: Technically the member function 'CalcServer < Seq >::alias_of' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:295:6: style:inconclusive: Technically the member function 'CalcServer < Seq >::getgrp2' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:296:6: style:inconclusive: Technically the member function 'CalcServer < Seq >::getgrp22' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:299:6: style:inconclusive: Technically the member function 'CalcServer < Seq >::memsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:312:6: style:inconclusive: Technically the member function 'CalcServer < Seq >::calcsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:323:6: style:inconclusive: Technically the member function 'CalcServer < Seq >::calcnbr' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:433:7: style:inconclusive: Technically the member function 'VarLoader < Seq >::active_file' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:178:18: warning: Struct 'InFiles' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/calcserv.h:178:18: warning: Struct 'InFiles' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Seq >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Seq >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/phyl.h:89:2: style: Struct 'DistMat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/phyl.h:158:2: style: Class 'Btree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/phyl.h:420:2: style: Class 'Ktree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/phyl.h:421:2: style: Class 'Ktree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/phyl.h:422:2: style: Class 'Ktree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/phyl.h:453:2: style: Class 'DistTree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/phyl.h:454:2: style: Class 'DistTree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/phyl.h:456:2: style: Class 'DistTree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/autocomp.h:93:2: style: Class 'AlnServer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/autocomp.h:124:2: style: Class 'AlnServer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/autocomp.h:206:2: style: Class 'SeqLoader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/autocomp.h:219:2: style: Class 'MakeMsa' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:341:2: style: Class 'CalcServer < Seq >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:363:2: style: Class 'CalcServer < Seq >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:417:2: style: Class 'VarLoader < Seq >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:611:7: style: Condition 'fd' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/autocomp.h:226:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/autocomp.cc:35:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/autocomp.h:411:9: style: The scope of the variable 'k' can be reduced. [variableScope]
spaln-ver3.0.2/src/calcserv.h:586:7: style: The scope of the variable 'first' can be reduced. [variableScope]
spaln-ver3.0.2/src/autocomp.h:589:39: style:inconclusive: Function 'setshuffle' argument 1 names different: declaration 'in' definition 'ns'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/autocomp.h:154:22: note: Function 'setshuffle' argument 1 names different: declaration 'in' definition 'ns'.
spaln-ver3.0.2/src/autocomp.h:589:39: note: Function 'setshuffle' argument 1 names different: declaration 'in' definition 'ns'.
spaln-ver3.0.2/src/autocomp.h:589:47: style:inconclusive: Function 'setshuffle' argument 2 names different: declaration 'nj' definition 'jmbl'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/autocomp.h:154:30: note: Function 'setshuffle' argument 2 names different: declaration 'nj' definition 'jmbl'.
spaln-ver3.0.2/src/autocomp.h:589:47: note: Function 'setshuffle' argument 2 names different: declaration 'nj' definition 'jmbl'.
spaln-ver3.0.2/src/autocomp.h:589:57: style:inconclusive: Function 'setshuffle' argument 3 names different: declaration 'wh' definition 'wch'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/autocomp.h:154:38: note: Function 'setshuffle' argument 3 names different: declaration 'wh' definition 'wch'.
spaln-ver3.0.2/src/autocomp.h:589:57: note: Function 'setshuffle' argument 3 names different: declaration 'wh' definition 'wch'.
spaln-ver3.0.2/src/autocomp.h:124:17: style: Parameter 'argc' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/autocomp.h:289:12: style: Variable 'sdb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/autocomp.h:882:18: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/calcserv.h:147:36: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/calcserv.h:150:38: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/calcserv.h:227:17: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/phyl.h:157:22: style: Parameter 'node' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/phyl.h:311:9: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/phyl.h:334:9: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/phyl.h:469:21: style: Parameter 'node' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/autocomp.h:901:9: style: Variable 'ps' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/bitpat.cc:341:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/bitpat.cc:271:10: warning:inconclusive: Member variable 'WordTab::p' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
spaln-ver3.0.2/src/bitpat.cc:75:2: warning: Class 'ReducWord' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/bitpat.cc:127:6: warning: Class 'Bitpat' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/bitpat.cc:159:2: warning: Class 'Bitpat_wq' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/bitpat.cc:232:2: warning: Class 'WordTab' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/bitpat.h:55:2: style: Class 'ReducWord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/bitpat.h:77:2: style: Class 'Bitpat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/bitpat.h:112:2: style: Struct 'WordState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/bitpat.cc:341:3: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/bitpat.cc:341:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/bitpat.cc:341:3: portability: %d in format string (no. 3) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/bitpat.h:158:12: style: Local variable 'p' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/bitpat.h:128:6: note: Shadowed declaration
spaln-ver3.0.2/src/bitpat.h:158:12: note: Shadow variable
spaln-ver3.0.2/src/bitpat.h:162:12: style: Local variable 'p' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/bitpat.h:128:6: note: Shadowed declaration
spaln-ver3.0.2/src/bitpat.h:162:12: note: Shadow variable
spaln-ver3.0.2/src/bitpat.cc:197:7: style: Variable 'exm' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.h:148:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQ_DELIM [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.h:164:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DbsRec [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.h:520:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seqlen [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.h:543:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut2 [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:110:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut2 [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:196:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out_file [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:222:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable entptr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:232:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out_file [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:247:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out_file [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:260:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DbsRec [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:288:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gzipped [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:306:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQ_DELIM [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:365:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:376:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:400:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable prelude [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:610:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BKA_EXT [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:727:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BKA_EXT [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:988:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:1048:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DbsRec [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:1070:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LUN_EXT [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:1085:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:1274:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQ_DELIM [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:1340:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQ_DELIM [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:1846:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALN_DBS [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:2018:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FQUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:2127:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbs_dt [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:2188:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:2342:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut2 [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:2643:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut2 [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:3101:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:3140:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:3213:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:3314:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable supself [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:602:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hpos [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:609:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:627:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:642:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:654:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:669:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable front [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:693:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable front [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:477:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable front [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:483:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:499:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:512:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:523:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:537:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable front [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:553:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable front [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:561:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable front [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/blksrc.cc:2597:24: error:inconclusive: Array 'bh4->sigw[2]' accessed at index bh4->sigw[*][-1], which is out of bounds. [negativeIndex]
spaln-ver3.0.2/src/blksrc.cc:2595:21: note: Assignment 'i=0', assigned value is 0
spaln-ver3.0.2/src/blksrc.cc:2597:24: note: Negative array index
spaln-ver3.0.2/src/wln.h:104:2: warning: Member variable 'JxtQueue::kq' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:187:10: warning: Member variable 'MakeDbs::maxlen' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:187:10: warning: Member variable 'MakeDbs::entrystr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:345:10: warning: Member variable 'ContBlk::AvrScr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:345:10: warning: Member variable 'ContBlk::MaxBlk' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:345:10: warning: Member variable 'ContBlk::BytBlk' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2731:8: warning: Member variable 'Bhit4::sigm' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2731:8: warning: Member variable 'Bhit4::sign' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2731:8: warning: Member variable 'Bhit4::maxs' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2731:8: warning: Member variable 'Bhit4::nhit' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2731:8: warning: Member variable 'Bhit4::mmct' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2731:8: warning: Member variable 'Bhit4::bend' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2731:8: warning: Member variable 'Bhit4::testword' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:3112:8: warning: Member variable 'Bhit2::hpos' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2081:10: warning: Member variable 'SrchBlk::seqs' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2081:10: warning: Member variable 'SrchBlk::query' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2081:10: warning: Member variable 'SrchBlk::gener' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2081:10: warning: Member variable 'SrchBlk::lstgr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2081:10: warning: Member variable 'SrchBlk::curgr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2081:10: warning: Member variable 'SrchBlk::critjscr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2081:10: warning: Member variable 'SrchBlk::MinGeneLen' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2100:10: warning: Member variable 'SrchBlk::seqs' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2100:10: warning: Member variable 'SrchBlk::query' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2100:10: warning: Member variable 'SrchBlk::gener' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2100:10: warning: Member variable 'SrchBlk::lstgr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2100:10: warning: Member variable 'SrchBlk::curgr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2100:10: warning: Member variable 'SrchBlk::critjscr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/blksrc.cc:2100:10: warning: Member variable 'SrchBlk::MinGeneLen' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/wln.h:218:8: style:inconclusive: Technically the member function 'Wlprms::sim2' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.h:112:7: style:inconclusive: Technically the member function 'MakeDbs::putsq' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.h:131:6: style:inconclusive: Technically the member function 'MakeDbs::max_dbseq_len' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.h:142:7: style:inconclusive: Technically the member function 'MakeDbs::write_odr' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.cc:266:15: note: Technically the member function 'MakeDbs::write_odr' can be const.
spaln-ver3.0.2/src/blksrc.h:142:7: note: Technically the member function 'MakeDbs::write_odr' can be const.
spaln-ver3.0.2/src/blksrc.h:176:7: style:inconclusive: Technically the member function 'PreScan::scan_genome' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.cc:983:15: note: Technically the member function 'PreScan::scan_genome' can be const.
spaln-ver3.0.2/src/blksrc.h:176:7: note: Technically the member function 'PreScan::scan_genome' can be const.
spaln-ver3.0.2/src/blksrc.cc:365:24: debug: CheckClass::isMemberVar found used member variable 'hash' with varid 0 [varid0]
spaln-ver3.0.2/src/blksrc.cc:366:14: debug: CheckClass::isMemberVar found used member variable 'hz' with varid 0 [varid0]
spaln-ver3.0.2/src/blksrc.h:234:7: style:inconclusive: Technically the member function 'Chash::countBlk' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.cc:363:13: note: Technically the member function 'Chash::countBlk' can be const.
spaln-ver3.0.2/src/blksrc.h:234:7: note: Technically the member function 'Chash::countBlk' can be const.
spaln-ver3.0.2/src/blksrc.cc:376:29: debug: CheckClass::isMemberVar found used member variable 'hash' with varid 0 [varid0]
spaln-ver3.0.2/src/blksrc.cc:376:39: debug: CheckClass::isMemberVar found used member variable 'hz' with varid 0 [varid0]
spaln-ver3.0.2/src/blksrc.h:235:7: style:inconclusive: Technically the member function 'Chash::registBlk' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.cc:374:13: note: Technically the member function 'Chash::registBlk' can be const.
spaln-ver3.0.2/src/blksrc.h:235:7: note: Technically the member function 'Chash::registBlk' can be const.
spaln-ver3.0.2/src/blksrc.h:298:6: style:inconclusive: Technically the member function 'MakeBlk::chrblk' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.h:301:6: style:inconclusive: Technically the member function 'MakeBlk::encode' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.h:515:6: style:inconclusive: Technically the member function 'SrchBlk::chrblk' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.h:518:6: style:inconclusive: Technically the member function 'SrchBlk::chrsize' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.h:551:6: performance:inconclusive: Technically the member function 'SrchBlk::MinQuery' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/blksrc.cc:1983:14: note: Technically the member function 'SrchBlk::MinQuery' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/blksrc.h:551:6: note: Technically the member function 'SrchBlk::MinQuery' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/blksrc.h:552:6: performance:inconclusive: Technically the member function 'SrchBlk::MaxGene' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/blksrc.cc:1987:14: note: Technically the member function 'SrchBlk::MaxGene' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/blksrc.h:552:6: note: Technically the member function 'SrchBlk::MaxGene' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/blksrc.h:561:7: style:inconclusive: Technically the member function 'SrchBlk::grngoverlap' can be const. [functionConst]
spaln-ver3.0.2/src/blksrc.cc:2052:15: note: Technically the member function 'SrchBlk::grngoverlap' can be const.
spaln-ver3.0.2/src/blksrc.h:561:7: note: Technically the member function 'SrchBlk::grngoverlap' can be const.
spaln-ver3.0.2/src/clib.h:252:8: style:inconclusive: Technically the member function 'Dhash < unsigned int , int >::undef' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:253:7: style:inconclusive: Technically the member function 'Dhash < unsigned int , int >::write_binary' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:287:27: note: Technically the member function 'Dhash < unsigned int , int >::write_binary' can be const.
spaln-ver3.0.2/src/clib.h:253:7: note: Technically the member function 'Dhash < unsigned int , int >::write_binary' can be const.
spaln-ver3.0.2/src/wln.h:105:6: warning: Class 'JxtQueue' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/wln.h:105:6: warning: Class 'JxtQueue' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/blksrc.cc:191:6: warning: Class 'MakeDbs' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/blksrc.cc:191:6: warning: Class 'MakeDbs' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/blksrc.cc:403:6: warning: Class 'Block' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/blksrc.cc:403:6: warning: Class 'Block' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/blksrc.cc:503:2: warning: Class 'MakeBlk' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/blksrc.cc:503:2: warning: Class 'MakeBlk' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/blksrc.cc:2748:2: warning: Class 'Bhit4' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/blksrc.cc:2748:2: warning: Class 'Bhit4' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/blksrc.cc:3116:2: warning: Class 'Bhit2' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/blksrc.cc:3116:2: warning: Class 'Bhit2' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/blksrc.cc:2103:2: warning: Class 'SrchBlk' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/blksrc.cc:2103:2: warning: Class 'SrchBlk' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/blksrc.cc:2790:2: warning: Class 'Qwords' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/blksrc.cc:2790:2: warning: Class 'Qwords' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:263:6: warning: Class 'Dhash < unsigned int , int >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:263:6: warning: Class 'Dhash < unsigned int , int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/blksrc.h:281:12: warning: The class 'MakeBlk' defines member variable with name 'sd' also defined in its parent class 'Block'. [duplInheritedMember]
spaln-ver3.0.2/src/blksrc.h:240:12: note: Parent variable 'Block::sd'
spaln-ver3.0.2/src/blksrc.h:281:12: note: Derived variable 'MakeBlk::sd'
spaln-ver3.0.2/src/wln.h:104:2: style: Class 'JxtQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/wln.h:198:2: style: Class 'Wlp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/wln.h:216:2: style: Struct 'Wlprms' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/blksrc.h:232:2: style: Class 'Chash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/blksrc.h:318:2: style: Class 'MakeBlk' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/blksrc.h:423:2: style: Class 'Bhit4' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/blksrc.h:435:2: style: Class 'Bhit2' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:205:2: style: Class 'Dhash < unsigned int , int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/blksrc.cc:719:9: style: Suspicious condition (assignment + comparison); Clarify expression with parentheses. [clarifyCondition]
spaln-ver3.0.2/src/blksrc.cc:2994:17: style: Condition 'blk' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/blksrc.cc:2987:26: note: Assuming that condition 'blk=qwd.next_mrglist()' is not redundant
spaln-ver3.0.2/src/blksrc.cc:2994:17: note: Condition 'blk' is always true
spaln-ver3.0.2/src/blksrc.cc:1977:2: portability: %d in format string (no. 2) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/blksrc.cc:1977:2: portability: %d in format string (no. 3) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/blksrc.cc:2706:6: portability: %d in format string (no. 6) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/blksrc.cc:2706:6: portability: %d in format string (no. 7) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/blksrc.cc:2706:6: portability: %ld in format string (no. 10) requires 'long' but the argument type is 'ptrdiff_t {aka signed int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/blksrc.cc:2706:6: portability: %ld in format string (no. 11) requires 'long' but the argument type is 'ptrdiff_t {aka signed int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/blksrc.cc:2706:6: portability: %d in format string (no. 16) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/blksrc.cc:2706:6: portability: %d in format string (no. 17) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/blksrc.cc:283:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:576:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:593:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:1669:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:1671:31: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:2151:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:2298:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:2337:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:2535:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:3065:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:3084:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:3087:9: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:3222:20: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/blksrc.cc:1738:12: style: Variable 'b2.s' is reassigned a value before the old one has been used. [redundantAssignment]
spaln-ver3.0.2/src/blksrc.cc:1736:12: note: b2.s is assigned
spaln-ver3.0.2/src/blksrc.cc:1738:12: note: b2.s is overwritten
spaln-ver3.0.2/src/blksrc.cc:1745:12: style: Variable 'b2.s' is reassigned a value before the old one has been used. [redundantAssignment]
spaln-ver3.0.2/src/blksrc.cc:1742:12: note: b2.s is assigned
spaln-ver3.0.2/src/blksrc.cc:1745:12: note: b2.s is overwritten
spaln-ver3.0.2/src/blksrc.cc:2644:13: style: Redundant initialization for 'wrkbp'. The initialized value is overwritten before it is read. [redundantInitialization]
spaln-ver3.0.2/src/blksrc.cc:2576:15: note: wrkbp is initialized
spaln-ver3.0.2/src/blksrc.cc:2644:13: note: wrkbp is overwritten
spaln-ver3.0.2/src/blksrc.cc:1720:11: style: The scope of the variable 'iblk' can be reduced. [variableScope]
spaln-ver3.0.2/src/blksrc.cc:2954:6: style: The scope of the variable 'totalsign' can be reduced. [variableScope]
spaln-ver3.0.2/src/blksrc.cc:187:30: style:inconclusive: Function 'MakeDbs' argument 1 names different: declaration 'dbname' definition 'dbn'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:117:22: note: Function 'MakeDbs' argument 1 names different: declaration 'dbname' definition 'dbn'.
spaln-ver3.0.2/src/blksrc.cc:187:30: note: Function 'MakeDbs' argument 1 names different: declaration 'dbname' definition 'dbn'.
spaln-ver3.0.2/src/blksrc.cc:494:29: style:inconclusive: Function 'MakeBlk' argument 1 names different: declaration 'sd' definition 'sq'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:318:21: note: Function 'MakeBlk' argument 1 names different: declaration 'sd' definition 'sq'.
spaln-ver3.0.2/src/blksrc.cc:494:29: note: Function 'MakeBlk' argument 1 names different: declaration 'sd' definition 'sq'.
spaln-ver3.0.2/src/blksrc.cc:494:53: style:inconclusive: Function 'MakeBlk' argument 3 names different: declaration 'mkdbs' definition 'mdbs'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:318:49: note: Function 'MakeBlk' argument 3 names different: declaration 'mkdbs' definition 'mdbs'.
spaln-ver3.0.2/src/blksrc.cc:494:53: note: Function 'MakeBlk' argument 3 names different: declaration 'mkdbs' definition 'mdbs'.
spaln-ver3.0.2/src/blksrc.cc:558:51: style:inconclusive: Function 'writeBlkInfo' argument 2 names different: declaration 'fn' definition 'block_fn'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:333:43: note: Function 'writeBlkInfo' argument 2 names different: declaration 'fn' definition 'block_fn'.
spaln-ver3.0.2/src/blksrc.cc:558:51: note: Function 'writeBlkInfo' argument 2 names different: declaration 'fn' definition 'block_fn'.
spaln-ver3.0.2/src/blksrc.cc:734:64: style:inconclusive: Function 'makeblock' argument 4 names different: declaration 'mkblk' definition 'mk_blk'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:585:71: note: Function 'makeblock' argument 4 names different: declaration 'mkblk' definition 'mk_blk'.
spaln-ver3.0.2/src/blksrc.cc:734:64: note: Function 'makeblock' argument 4 names different: declaration 'mkblk' definition 'mk_blk'.
spaln-ver3.0.2/src/blksrc.cc:983:50: style:inconclusive: Function 'scan_genome' argument 2 names different: declaration 'as' definition 'sls'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:176:42: note: Function 'scan_genome' argument 2 names different: declaration 'as' definition 'sls'.
spaln-ver3.0.2/src/blksrc.cc:983:50: note: Function 'scan_genome' argument 2 names different: declaration 'as' definition 'sls'.
spaln-ver3.0.2/src/blksrc.cc:1019:46: style:inconclusive: Function 'lenStat' argument 2 names different: declaration 'av' definition 'seqdb'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:179:38: note: Function 'lenStat' argument 2 names different: declaration 'av' definition 'seqdb'.
spaln-ver3.0.2/src/blksrc.cc:1019:46: note: Function 'lenStat' argument 2 names different: declaration 'av' definition 'seqdb'.
spaln-ver3.0.2/src/blksrc.cc:1019:65: style:inconclusive: Function 'lenStat' argument 3 names different: declaration 'as' definition 'sls'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:179:54: note: Function 'lenStat' argument 3 names different: declaration 'as' definition 'sls'.
spaln-ver3.0.2/src/blksrc.cc:1019:65: note: Function 'lenStat' argument 3 names different: declaration 'as' definition 'sls'.
spaln-ver3.0.2/src/blksrc.cc:1782:50: style:inconclusive: Function 'ReadBlkInfo' argument 2 names different: declaration 'fname' definition 'fn'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:556:42: note: Function 'ReadBlkInfo' argument 2 names different: declaration 'fname' definition 'fn'.
spaln-ver3.0.2/src/blksrc.cc:1782:50: note: Function 'ReadBlkInfo' argument 2 names different: declaration 'fname' definition 'fn'.
spaln-ver3.0.2/src/blksrc.cc:1953:35: style:inconclusive: Function 'findChrNo' argument 1 names different: declaration 'n' definition 'blk'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:557:27: note: Function 'findChrNo' argument 1 names different: declaration 'n' definition 'blk'.
spaln-ver3.0.2/src/blksrc.cc:1953:35: note: Function 'findChrNo' argument 1 names different: declaration 'n' definition 'blk'.
spaln-ver3.0.2/src/blksrc.cc:2039:20: style:inconclusive: Function 'genemergin' argument 1 names different: declaration 'agap' definition 'apos'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/blksrc.h:590:27: note: Function 'genemergin' argument 1 names different: declaration 'agap' definition 'apos'.
spaln-ver3.0.2/src/blksrc.cc:2039:20: note: Function 'genemergin' argument 1 names different: declaration 'agap' definition 'apos'.
spaln-ver3.0.2/src/blksrc.cc:641:16: style: Variable 'wcp_t' can be declared as reference to const [constVariableReference]
spaln-ver3.0.2/src/blksrc.cc:650:16: style: Variable 'wcp_t' can be declared as reference to const [constVariableReference]
spaln-ver3.0.2/src/blksrc.cc:3044:15: style: Variable 'bs' can be declared as reference to const [constVariableReference]
spaln-ver3.0.2/src/blksrc.cc:576:9: style: Variable 'sblkb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:596:11: style: Variable 'iblk' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:820:14: style: Variable 'pcomp' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1058:10: style: Variable 'tidx' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1226:12: style: Variable 'ts' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1263:12: style: Variable 'ts' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1278:17: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1299:8: style: Variable 'ts' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1323:8: style: Variable 'pe' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1351:11: style: Variable 'lst' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1352:11: style: Variable 'lfq' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1719:13: style: Variable 'sblk' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:1728:13: style: Variable 'sblk' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:2797:25: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/blksrc.cc:3224:21: style: Variable 'th' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:3319:21: style: Variable 'h' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.cc:509:24: style: Variable 'molc' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/blksrc.cc:2954:16: style: Variable 'totalsign' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/boyer_moore.cc:155:13: warning: Member variable 'BoyerMoore::idx' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/boyer_moore.cc:155:13: warning: Member variable 'BoyerMoore::eqtab' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/boyer_moore.h:44:7: performance:inconclusive: Technically the member function 'BoyerMoore::eq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/boyer_moore.h:45:7: performance:inconclusive: Technically the member function 'BoyerMoore::eqa' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/boyer_moore.h:46:7: performance:inconclusive: Technically the member function 'BoyerMoore::eqn' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/boyer_moore.h:47:7: performance:inconclusive: Technically the member function 'BoyerMoore::eqta' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/boyer_moore.h:50:7: performance:inconclusive: Technically the member function 'BoyerMoore::eqtn' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/boyer_moore.h:61:6: style:inconclusive: Technically the member function 'BoyerMoore::shift_after_hit' can be const. [functionConst]
spaln-ver3.0.2/src/boyer_moore.h:70:7: style:inconclusive: Technically the member function 'BoyerMoore::finished' can be const. [functionConst]
spaln-ver3.0.2/src/boyer_moore.cc:163:2: warning: Class 'BoyerMoore' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/boyer_moore.cc:163:2: warning: Class 'BoyerMoore' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/boyer_moore.cc:156:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/boyer_moore.cc:174:58: style:inconclusive: Function 'BoyerMoore' argument 3 names different: declaration 'step_' definition 's'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/boyer_moore.h:75:47: note: Function 'BoyerMoore' argument 3 names different: declaration 'step_' definition 's'.
spaln-ver3.0.2/src/boyer_moore.cc:174:58: note: Function 'BoyerMoore' argument 3 names different: declaration 'step_' definition 's'.
spaln-ver3.0.2/src/clib.h:1109:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable val_t [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/calcserv.h:361:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable var_t [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/calcserv.h:384:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable var_t [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/calcserv.h:795:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable var_t [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer::optn_job' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:363:2: warning: Member variable 'CalcServer::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/clib.h:252:8: style:inconclusive: Technically the member function 'Dhash::undef' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:253:7: style:inconclusive: Technically the member function 'Dhash::write_binary' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:287:27: note: Technically the member function 'Dhash::write_binary' can be const.
spaln-ver3.0.2/src/clib.h:253:7: note: Technically the member function 'Dhash::write_binary' can be const.
spaln-ver3.0.2/src/clib.h:998:6: style:inconclusive: Technically the member function 'StrHash::size' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:1002:8: style:inconclusive: Technically the member function 'StrHash::undef' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:251:7: style:inconclusive: Technically the member function 'CalcServer::initvars' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:736:26: note: Technically the member function 'CalcServer::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:251:7: note: Technically the member function 'CalcServer::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:252:7: performance:inconclusive: Technically the member function 'CalcServer::common_usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:645:25: note: Technically the member function 'CalcServer::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:252:7: note: Technically the member function 'CalcServer::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:279:7: performance:inconclusive: Technically the member function 'CalcServer::alias_of' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:295:6: style:inconclusive: Technically the member function 'CalcServer::getgrp2' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:296:6: style:inconclusive: Technically the member function 'CalcServer::getgrp22' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:299:6: style:inconclusive: Technically the member function 'CalcServer::memsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:312:6: style:inconclusive: Technically the member function 'CalcServer::calcsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:323:6: style:inconclusive: Technically the member function 'CalcServer::calcnbr' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:433:7: style:inconclusive: Technically the member function 'VarLoader::active_file' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:280:2: warning: Class 'Dhash' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:280:2: warning: Class 'Dhash' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:1035:2: warning: Class 'StrHash' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:205:2: style: Class 'Dhash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:945:2: style: Class 'StrHash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/clib.h:949:2: style: Class 'StrHash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:341:2: style: Class 'CalcServer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:363:2: style: Class 'CalcServer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:417:2: style: Class 'VarLoader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:279:35: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/clib.cc:433:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:913:7: style:inconclusive: Technically the member function 'Strlist::write_binary' can be const. [functionConst]
spaln-ver3.0.2/src/clib.cc:548:15: note: Technically the member function 'Strlist::write_binary' can be const.
spaln-ver3.0.2/src/clib.h:913:7: note: Technically the member function 'Strlist::write_binary' can be const.
spaln-ver3.0.2/src/clib.h:1201:6: style:inconclusive: Technically the member function 'Dixon::dixon' can be const. [functionConst]
spaln-ver3.0.2/src/clib.cc:760:12: note: Technically the member function 'Dixon::dixon' can be const.
spaln-ver3.0.2/src/clib.h:1201:6: note: Technically the member function 'Dixon::dixon' can be const.
spaln-ver3.0.2/src/clib.cc:422:2: warning: Class 'Strlist' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.cc:611:2: warning: Class 'PutIntoBins' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.cc:797:2: warning: Class 'RandNumGen' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.cc:797:2: warning: Class 'RandNumGen' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.cc:577:2: warning: Class 'AddExt' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.cc:577:2: warning: Class 'AddExt' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.cc:178:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/clib.cc:186:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/clib.cc:437:50: style: Checking if unsigned expression 'fread(strbuf,sizeof(char),totallen,gzfd)' is less than zero. [unsignedLessThanZero]
spaln-ver3.0.2/src/clib.cc:642:47: style:inconclusive: Function 'normalize' argument 2 names different: declaration 'ps' definition 'psc'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:1183:40: note: Function 'normalize' argument 2 names different: declaration 'ps' definition 'psc'.
spaln-ver3.0.2/src/clib.cc:642:47: note: Function 'normalize' argument 2 names different: declaration 'ps' definition 'psc'.
spaln-ver3.0.2/src/clib.cc:760:66: style:inconclusive: Function 'dixon' argument 5 names different: declaration 'md' definition 'min_deno'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:1201:60: note: Function 'dixon' argument 5 names different: declaration 'md' definition 'min_deno'.
spaln-ver3.0.2/src/clib.cc:760:66: note: Function 'dixon' argument 5 names different: declaration 'md' definition 'min_deno'.
spaln-ver3.0.2/src/clib.cc:794:51: style:inconclusive: Function 'RandNumGen' argument 3 names different: declaration 'resol' definition 'rslv'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/clib.h:1210:40: note: Function 'RandNumGen' argument 3 names different: declaration 'resol' definition 'rslv'.
spaln-ver3.0.2/src/clib.cc:794:51: note: Function 'RandNumGen' argument 3 names different: declaration 'resol' definition 'rslv'.
spaln-ver3.0.2/src/clib.cc:92:24: style: Parameter 'str' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/clib.cc:753:14: style: Variable 'pval' can be declared as const array [constVariable]
spaln-ver3.0.2/src/clib.cc:794:32: style: Parameter 'pcmp' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/clib.cc:636:23: style: Variable 'dx' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/codepot.cc:127:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FQUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/codepot.cc:237:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FQUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/codepot.h:124:7: style:inconclusive: Technically the member function 'Exinon::intron53_c' can be const. [functionConst]
spaln-ver3.0.2/src/codepot.cc:435:14: note: Technically the member function 'Exinon::intron53_c' can be const.
spaln-ver3.0.2/src/codepot.h:124:7: note: Technically the member function 'Exinon::intron53_c' can be const.
spaln-ver3.0.2/src/codepot.h:201:8: style:inconclusive: Technically the member function 'SpJunc::spjscr' can be const. [functionConst]
spaln-ver3.0.2/src/codepot.cc:72:15: note: Technically the member function 'SpJunc::spjscr' can be const.
spaln-ver3.0.2/src/codepot.h:201:8: note: Technically the member function 'SpJunc::spjscr' can be const.
spaln-ver3.0.2/src/codepot.h:202:13: style:inconclusive: Technically the member function 'SpJunc::spjseq' can be const. [functionConst]
spaln-ver3.0.2/src/codepot.cc:77:21: note: Technically the member function 'SpJunc::spjseq' can be const.
spaln-ver3.0.2/src/codepot.h:202:13: note: Technically the member function 'SpJunc::spjseq' can be const.
spaln-ver3.0.2/src/codepot.cc:383:2: warning: Class 'Exinon' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/codepot.cc:383:2: warning: Class 'Exinon' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/codepot.cc:156:2: warning: Class 'IntronPenalty' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/codepot.cc:156:2: warning: Class 'IntronPenalty' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/codepot.cc:239:6: warning: Struct 'EijPat' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/codepot.cc:239:6: warning: Struct 'EijPat' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/codepot.cc:279:2: warning: Struct 'Sig53' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/codepot.cc:279:2: warning: Struct 'Sig53' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/codepot.cc:59:2: style: Struct 'Sig53' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/codepot.cc:359:16: warning: Either the condition 'pwd' is redundant or there is possible null pointer dereference: pwd. [nullPointerRedundantCheck]
spaln-ver3.0.2/src/codepot.cc:362:6: note: Assuming that condition 'pwd' is not redundant
spaln-ver3.0.2/src/codepot.cc:359:16: note: Null pointer dereference
spaln-ver3.0.2/src/codepot.cc:221:8: style: Variable 'z' is reassigned a value before the old one has been used. [redundantAssignment]
spaln-ver3.0.2/src/codepot.cc:218:24: note: z is assigned
spaln-ver3.0.2/src/codepot.cc:221:8: note: z is overwritten
spaln-ver3.0.2/src/codepot.cc:164:9: style: The scope of the variable 'ipen' can be reduced. [variableScope]
spaln-ver3.0.2/src/codepot.cc:125:43: style:inconclusive: Function 'IntronPenalty' argument 2 names different: declaration 'hh' definition 'dvsp'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/codepot.h:231:29: note: Function 'IntronPenalty' argument 2 names different: declaration 'hh' definition 'dvsp'.
spaln-ver3.0.2/src/codepot.cc:125:43: note: Function 'IntronPenalty' argument 2 names different: declaration 'hh' definition 'dvsp'.
spaln-ver3.0.2/src/codepot.cc:233:20: style:inconclusive: Function 'EijPat' argument 1 names different: declaration 'hh' definition 'dvsp'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/utilseq.h:178:13: note: Function 'EijPat' argument 1 names different: declaration 'hh' definition 'dvsp'.
spaln-ver3.0.2/src/codepot.cc:233:20: note: Function 'EijPat' argument 1 names different: declaration 'hh' definition 'dvsp'.
spaln-ver3.0.2/src/codepot.cc:125:74: style: Parameter 'exinpot' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/codepot.cc:332:9: style: Variable 't' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/codepot.cc:440:8: style: Variable 'redctab' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/codepot.cc:445:8: style: Variable 'ts' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/codepot.cc:494:9: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/codepot.cc:567:8: style: Variable 'posB' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/codepot.cc:568:9: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/codepot.cc:136:12: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
spaln-ver3.0.2/src/codepot.cc:137:17: style: float result is assigned to const double variable. If the variable is const double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
spaln-ver3.0.2/src/codepot.cc:142:18: style: float result is assigned to const double variable. If the variable is const double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
spaln-ver3.0.2/src/codepot.cc:173:13: style: float result is assigned to double variable. If the variable is double to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
spaln-ver3.0.2/src/codepot.cc:48:8: style: struct member 'ALSP::scr' is never used. [unusedStructMember]
spaln-ver3.0.2/src/codepot.cc:49:9: style: struct member 'ALSP::rng' is never used. [unusedStructMember]
spaln-ver3.0.2/src/codepot.cc:50:6: style: struct member 'ALSP::eij' is never used. [unusedStructMember]
spaln-ver3.0.2/src/codepot.cc:164:14: style: Variable 'ipen' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/compild.cc:35:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/ildpdf.h:165:2: warning: Member variable 'IldPrm::dparam' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:193:2: warning:inconclusive: Member variable 'Ild::nfact' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:193:2: warning:inconclusive: Member variable 'Ild::sid' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:193:2: warning:inconclusive: Member variable 'Ild::vrtl' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:193:2: warning:inconclusive: Member variable 'Ild::ntotal' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:193:2: warning:inconclusive: Member variable 'Ild::ftotal' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:193:2: warning:inconclusive: Member variable 'Ild::fname' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:193:2: warning:inconclusive: Member variable 'Ild::intlf' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:193:2: warning:inconclusive: Member variable 'Ild::k_th_qtil' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Ild >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Ild >::optn_job' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:363:2: warning: Member variable 'CalcServer < Ild >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Lild >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Lild >::optn_job' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:363:2: warning: Member variable 'CalcServer < Lild >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < IldPrm >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < IldPrm >::optn_job' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:363:2: warning: Member variable 'CalcServer < IldPrm >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/ildpdf.h:101:6: style:inconclusive: Technically the member function 'SpecList::size' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.h:123:11: style:inconclusive: Technically the member function 'IldPrm::statdist' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.h:161:9: style:inconclusive: Technically the member function 'IldPrm::aic' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.h:192:7: style:inconclusive: Technically the member function 'Ild::empty' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.h:226:6: style:inconclusive: Technically the member function 'Ild::n_samples' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.h:227:6: style:inconclusive: Technically the member function 'Ild::minx' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.h:228:6: style:inconclusive: Technically the member function 'Ild::maxx' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:251:7: style:inconclusive: Technically the member function 'CalcServer < Ild >::initvars' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:736:26: note: Technically the member function 'CalcServer < Ild >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:251:7: note: Technically the member function 'CalcServer < Ild >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:252:7: performance:inconclusive: Technically the member function 'CalcServer < Ild >::common_usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:645:25: note: Technically the member function 'CalcServer < Ild >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:252:7: note: Technically the member function 'CalcServer < Ild >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:279:7: performance:inconclusive: Technically the member function 'CalcServer < Ild >::alias_of' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:295:6: style:inconclusive: Technically the member function 'CalcServer < Ild >::getgrp2' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:296:6: style:inconclusive: Technically the member function 'CalcServer < Ild >::getgrp22' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:299:6: style:inconclusive: Technically the member function 'CalcServer < Ild >::memsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:312:6: style:inconclusive: Technically the member function 'CalcServer < Ild >::calcsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:323:6: style:inconclusive: Technically the member function 'CalcServer < Ild >::calcnbr' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:251:7: style:inconclusive: Technically the member function 'CalcServer < Lild >::initvars' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:736:26: note: Technically the member function 'CalcServer < Lild >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:251:7: note: Technically the member function 'CalcServer < Lild >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:252:7: performance:inconclusive: Technically the member function 'CalcServer < Lild >::common_usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:645:25: note: Technically the member function 'CalcServer < Lild >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:252:7: note: Technically the member function 'CalcServer < Lild >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:279:7: performance:inconclusive: Technically the member function 'CalcServer < Lild >::alias_of' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:295:6: style:inconclusive: Technically the member function 'CalcServer < Lild >::getgrp2' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:296:6: style:inconclusive: Technically the member function 'CalcServer < Lild >::getgrp22' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:299:6: style:inconclusive: Technically the member function 'CalcServer < Lild >::memsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:312:6: style:inconclusive: Technically the member function 'CalcServer < Lild >::calcsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:323:6: style:inconclusive: Technically the member function 'CalcServer < Lild >::calcnbr' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:251:7: style:inconclusive: Technically the member function 'CalcServer < IldPrm >::initvars' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:736:26: note: Technically the member function 'CalcServer < IldPrm >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:251:7: note: Technically the member function 'CalcServer < IldPrm >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:252:7: performance:inconclusive: Technically the member function 'CalcServer < IldPrm >::common_usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:645:25: note: Technically the member function 'CalcServer < IldPrm >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:252:7: note: Technically the member function 'CalcServer < IldPrm >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:279:7: performance:inconclusive: Technically the member function 'CalcServer < IldPrm >::alias_of' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:295:6: style:inconclusive: Technically the member function 'CalcServer < IldPrm >::getgrp2' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:296:6: style:inconclusive: Technically the member function 'CalcServer < IldPrm >::getgrp22' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:299:6: style:inconclusive: Technically the member function 'CalcServer < IldPrm >::memsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:312:6: style:inconclusive: Technically the member function 'CalcServer < IldPrm >::calcsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:323:6: style:inconclusive: Technically the member function 'CalcServer < IldPrm >::calcnbr' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:433:7: style:inconclusive: Technically the member function 'VarLoader < Ild >::active_file' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:433:7: style:inconclusive: Technically the member function 'VarLoader < Lild >::active_file' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:433:7: style:inconclusive: Technically the member function 'VarLoader < IldPrm >::active_file' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Ild >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Ild >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Lild >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Lild >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < IldPrm >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < IldPrm >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/ildpdf.h:101:6: warning: The class 'SpecList' defines member function with name 'size' also defined in its parent class 'StrHash < int >'. [duplInheritedMember]
spaln-ver3.0.2/src/clib.h:998:6: note: Parent function 'StrHash < int >::size'
spaln-ver3.0.2/src/ildpdf.h:101:6: note: Derived function 'SpecList::size'
spaln-ver3.0.2/src/ildpdf.h:172:2: style: Class 'IldPrm' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:194:2: style: Class 'Ild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:208:2: style: Class 'Ild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:272:2: style: Class 'Lild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:276:2: style: Class 'Lild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:277:2: style: Class 'Lild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:307:2: style: Class 'GnuPlotLild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:311:2: style: Class 'GnuPlotLild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:312:2: style: Class 'GnuPlotLild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.h:317:2: style: Class 'GnuPlotLild' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:341:2: style: Class 'CalcServer < Ild >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:363:2: style: Class 'CalcServer < Ild >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:341:2: style: Class 'CalcServer < Lild >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:363:2: style: Class 'CalcServer < Lild >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:341:2: style: Class 'CalcServer < IldPrm >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:363:2: style: Class 'CalcServer < IldPrm >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:417:2: style: Class 'VarLoader < Ild >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:417:2: style: Class 'VarLoader < Lild >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:417:2: style: Class 'VarLoader < IldPrm >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/compild.cc:121:20: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:137:20: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:154:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:169:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:186:23: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:201:23: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:212:23: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:232:20: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:246:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/compild.cc:291:4: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/dist2.h:54:47: style:inconclusive: Function 'prepare' argument 1 names different: declaration 'svr' definition 'csvr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/dist2.h:43:34: note: Function 'prepare' argument 1 names different: declaration 'svr' definition 'csvr'.
spaln-ver3.0.2/src/dist2.h:54:47: note: Function 'prepare' argument 1 names different: declaration 'svr' definition 'csvr'.
spaln-ver3.0.2/src/ildpdf.h:200:11: style: Parameter 'src' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/compild.cc:210:11: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/compild.cc:211:11: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/compild.cc:230:8: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/compild.cc:231:8: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/compild.cc:244:9: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/compild.cc:245:9: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/ildpdf.h:367:38: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:377:36: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:382:39: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:387:41: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:392:40: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:397:38: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:402:40: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:407:38: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:412:41: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:417:44: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:422:44: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:444:38: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:449:40: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:454:38: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:459:42: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:492:34: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:497:34: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:530:36: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:535:38: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:562:26: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.h:562:36: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/dbs.cc:265:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FormID [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:281:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeqLabel [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:299:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:319:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:326:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:354:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DbsGrp [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:384:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbsgrp [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:395:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbsseq [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:408:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable curdb [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:417:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbsseq [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:428:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbsseq [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:441:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable curdb [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:500:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable curdb [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:603:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fseq [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:613:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fseq [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:636:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:749:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numidx [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:764:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable recodr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:780:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBSID [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:825:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_DBS [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dbs.cc:378:11: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/dbs.cc:324:13: style: The scope of the variable 'frmmsg' can be reduced. [variableScope]
spaln-ver3.0.2/src/dbs.cc:587:46: style: Checking if unsigned expression 'fread(dbsseq,sizeof(unsigned char),rss,gzfd)' is less than zero. [unsignedLessThanZero]
spaln-ver3.0.2/src/dbs.cc:742:8: style: Variable 'rng' can be declared as const array [constVariable]
spaln-ver3.0.2/src/dbs.cc:772:9: style: Variable 'maxrng' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/dbs.cc:789:8: style: Variable 'term' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/dbs.cc:721:8: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/decompild.cc:33:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/decompild.cc:45:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/divseq.cc:145:6: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/divseq.cc:210:14: style: The scope of the variable 'frmt1' can be reduced. [variableScope]
spaln-ver3.0.2/src/divseq.cc:66:41: style:inconclusive: Function 'pairdvn' argument 2 names different: declaration 'g1' definition 'gi'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/divseq.h:52:48: note: Function 'pairdvn' argument 2 names different: declaration 'g1' definition 'gi'.
spaln-ver3.0.2/src/divseq.cc:66:41: note: Function 'pairdvn' argument 2 names different: declaration 'g1' definition 'gi'.
spaln-ver3.0.2/src/divseq.cc:66:56: style:inconclusive: Function 'pairdvn' argument 3 names different: declaration 'g2' definition 'gj'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/divseq.h:52:63: note: Function 'pairdvn' argument 3 names different: declaration 'g2' definition 'gj'.
spaln-ver3.0.2/src/divseq.cc:66:56: note: Function 'pairdvn' argument 3 names different: declaration 'g2' definition 'gj'.
spaln-ver3.0.2/src/divseq.cc:210:14: style: Variable 'frmt1' can be declared as const array [constVariable]
spaln-ver3.0.2/src/divseq.cc:211:14: style: Variable 'frmt2' can be declared as const array [constVariable]
spaln-ver3.0.2/src/dvn.cc:113:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dvn.cc:483:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:615:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in_face [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:1011:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size1 [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:1046:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hz [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:1057:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size1 [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:1085:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:1094:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:1110:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size1 [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:1130:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hz [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dvn.cc:96:2: warning: Member variable 'Member::pid' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/autocomp.h:69:2: warning: Member variable 'AlnServer < Seq >::tmpdir' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/autocomp.h:80:2: warning: Member variable 'AlnServer < Seq >::tmpdir' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Member >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Member >::optn_job' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:363:2: warning: Member variable 'CalcServer < Member >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Species >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:341:2: warning: Member variable 'CalcServer < Species >::optn_job' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/calcserv.h:363:2: warning: Member variable 'CalcServer < Species >::in_face' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/dvn.cc:68:9: style:inconclusive: Technically the member function 'Dvn::fracnid' can be const. [functionConst]
spaln-ver3.0.2/src/dvn.cc:215:13: note: Technically the member function 'Dvn::fracnid' can be const.
spaln-ver3.0.2/src/dvn.cc:68:9: note: Technically the member function 'Dvn::fracnid' can be const.
spaln-ver3.0.2/src/dvn.cc:69:9: style:inconclusive: Technically the member function 'Dvn::kimura2' can be const. [functionConst]
spaln-ver3.0.2/src/dvn.cc:228:13: note: Technically the member function 'Dvn::kimura2' can be const.
spaln-ver3.0.2/src/dvn.cc:69:9: note: Technically the member function 'Dvn::kimura2' can be const.
spaln-ver3.0.2/src/dvn.cc:88:9: style:inconclusive: Technically the member function 'Bitsqtab::frac_mismatch' can be const. [functionConst]
spaln-ver3.0.2/src/dvn.cc:319:18: note: Technically the member function 'Bitsqtab::frac_mismatch' can be const.
spaln-ver3.0.2/src/dvn.cc:88:9: note: Technically the member function 'Bitsqtab::frac_mismatch' can be const.
spaln-ver3.0.2/src/dvn.cc:98:6: performance:inconclusive: Technically the member function 'Member::fget' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/autocomp.h:153:8: performance:inconclusive: Technically the member function 'AlnServer < Seq >::restsq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/autocomp.h:848:25: note: Technically the member function 'AlnServer < Seq >::restsq' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:153:8: note: Technically the member function 'AlnServer < Seq >::restsq' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:156:6: performance:inconclusive: Technically the member function 'AlnServer < Seq >::localoption' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/dvn.cc:137:23: note: Technically the member function 'AlnServer < Seq >::localoption' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:156:6: note: Technically the member function 'AlnServer < Seq >::localoption' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:163:7: performance:inconclusive: Technically the member function 'AlnServer < Seq >::common_usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/autocomp.h:370:24: note: Technically the member function 'AlnServer < Seq >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:163:7: note: Technically the member function 'AlnServer < Seq >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:165:7: performance:inconclusive: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/dvn.cc:125:24: note: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:165:7: note: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:251:7: style:inconclusive: Technically the member function 'CalcServer < Member >::initvars' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:736:26: note: Technically the member function 'CalcServer < Member >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:251:7: note: Technically the member function 'CalcServer < Member >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:252:7: performance:inconclusive: Technically the member function 'CalcServer < Member >::common_usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:645:25: note: Technically the member function 'CalcServer < Member >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:252:7: note: Technically the member function 'CalcServer < Member >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:279:7: performance:inconclusive: Technically the member function 'CalcServer < Member >::alias_of' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:295:6: style:inconclusive: Technically the member function 'CalcServer < Member >::getgrp2' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:296:6: style:inconclusive: Technically the member function 'CalcServer < Member >::getgrp22' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:299:6: style:inconclusive: Technically the member function 'CalcServer < Member >::memsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:312:6: style:inconclusive: Technically the member function 'CalcServer < Member >::calcsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:323:6: style:inconclusive: Technically the member function 'CalcServer < Member >::calcnbr' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:251:7: style:inconclusive: Technically the member function 'CalcServer < Species >::initvars' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:736:26: note: Technically the member function 'CalcServer < Species >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:251:7: note: Technically the member function 'CalcServer < Species >::initvars' can be const.
spaln-ver3.0.2/src/calcserv.h:252:7: performance:inconclusive: Technically the member function 'CalcServer < Species >::common_usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:645:25: note: Technically the member function 'CalcServer < Species >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:252:7: note: Technically the member function 'CalcServer < Species >::common_usage' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/calcserv.h:279:7: performance:inconclusive: Technically the member function 'CalcServer < Species >::alias_of' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/calcserv.h:295:6: style:inconclusive: Technically the member function 'CalcServer < Species >::getgrp2' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:296:6: style:inconclusive: Technically the member function 'CalcServer < Species >::getgrp22' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:299:6: style:inconclusive: Technically the member function 'CalcServer < Species >::memsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:312:6: style:inconclusive: Technically the member function 'CalcServer < Species >::calcsize' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:323:6: style:inconclusive: Technically the member function 'CalcServer < Species >::calcnbr' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:433:7: style:inconclusive: Technically the member function 'VarLoader < Member >::active_file' can be const. [functionConst]
spaln-ver3.0.2/src/calcserv.h:433:7: style:inconclusive: Technically the member function 'VarLoader < Species >::active_file' can be const. [functionConst]
spaln-ver3.0.2/src/dvn.cc:295:18: warning: Class 'Bitsqtab' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/dvn.cc:295:18: warning: Class 'Bitsqtab' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/dvn.cc:154:2: warning: Struct 'Species' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/dvn.cc:154:2: warning: Struct 'Species' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/autocomp.h:147:6: warning: Class 'AlnServer < Seq >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/autocomp.h:147:6: warning: Class 'AlnServer < Seq >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Member >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Member >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Species >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/calcserv.h:383:6: warning: Class 'CalcServer < Species >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/autocomp.h:51:7: warning: The class 'AlnServer < Seq >' defines member function with name 'initialize' also defined in its parent class 'CalcServer < Seq >'. [duplInheritedMember]
spaln-ver3.0.2/src/calcserv.h:283:7: note: Parent function 'CalcServer < Seq >::initialize'
spaln-ver3.0.2/src/autocomp.h:51:7: note: Derived function 'AlnServer < Seq >::initialize'
spaln-ver3.0.2/src/autocomp.h:609:23: warning: The class 'AlnServer < Seq >' defines member function with name 'serialJob' also defined in its parent class 'CalcServer < Seq >'. [duplInheritedMember]
spaln-ver3.0.2/src/calcserv.h:767:24: note: Parent function 'CalcServer < Seq >::serialJob'
spaln-ver3.0.2/src/autocomp.h:609:23: note: Derived function 'AlnServer < Seq >::serialJob'
spaln-ver3.0.2/src/autocomp.h:397:24: warning: The class 'AlnServer < Seq >' defines member function with name 'getoptions' also defined in its parent class 'CalcServer < Seq >'. [duplInheritedMember]
spaln-ver3.0.2/src/calcserv.h:661:25: note: Parent function 'CalcServer < Seq >::getoptions'
spaln-ver3.0.2/src/autocomp.h:397:24: note: Derived function 'AlnServer < Seq >::getoptions'
spaln-ver3.0.2/src/autocomp.h:626:23: warning: The class 'AlnServer < Seq >' defines member function with name 'auto_comp' also defined in its parent class 'CalcServer < Seq >'. [duplInheritedMember]
spaln-ver3.0.2/src/calcserv.h:777:24: note: Parent function 'CalcServer < Seq >::auto_comp'
spaln-ver3.0.2/src/autocomp.h:626:23: note: Derived function 'AlnServer < Seq >::auto_comp'
spaln-ver3.0.2/src/autocomp.h:158:6: warning: The class 'AlnServer < Seq >' defines member function with name 'autocomp' also defined in its parent class 'CalcServer < Seq >'. [duplInheritedMember]
spaln-ver3.0.2/src/calcserv.h:276:6: note: Parent function 'CalcServer < Seq >::autocomp'
spaln-ver3.0.2/src/autocomp.h:158:6: note: Derived function 'AlnServer < Seq >::autocomp'
spaln-ver3.0.2/src/autocomp.h:370:24: warning: The class 'AlnServer < Seq >' defines member function with name 'common_usage' also defined in its parent class 'CalcServer < Seq >'. [duplInheritedMember]
spaln-ver3.0.2/src/calcserv.h:645:25: note: Parent function 'CalcServer < Seq >::common_usage'
spaln-ver3.0.2/src/autocomp.h:370:24: note: Derived function 'AlnServer < Seq >::common_usage'
spaln-ver3.0.2/src/autocomp.h:200:20: warning: The class 'SeqLoader < Seq >' defines member variable with name 'svr' also defined in its parent class 'VarLoader < Seq >'. [duplInheritedMember]
spaln-ver3.0.2/src/calcserv.h:396:21: note: Parent variable 'VarLoader < Seq >::svr'
spaln-ver3.0.2/src/autocomp.h:200:20: note: Derived variable 'SeqLoader < Seq >::svr'
spaln-ver3.0.2/src/autocomp.h:309:24: warning: The class 'SeqLoader < Seq >' defines member function with name 'at' also defined in its parent class 'VarLoader < Seq >'. [duplInheritedMember]
spaln-ver3.0.2/src/calcserv.h:629:24: note: Parent function 'VarLoader < Seq >::at'
spaln-ver3.0.2/src/autocomp.h:309:24: note: Derived function 'SeqLoader < Seq >::at'
spaln-ver3.0.2/src/dvn.cc:82:2: style: Class 'Bitsqtab' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/dvn.cc:96:2: style: Struct 'Member' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/autocomp.h:93:2: style: Class 'AlnServer < Seq >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/autocomp.h:124:2: style: Class 'AlnServer < Seq >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:341:2: style: Class 'CalcServer < Member >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:363:2: style: Class 'CalcServer < Member >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:341:2: style: Class 'CalcServer < Species >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:363:2: style: Class 'CalcServer < Species >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/autocomp.h:206:2: style: Class 'SeqLoader < Seq >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:417:2: style: Class 'VarLoader < Member >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/calcserv.h:417:2: style: Class 'VarLoader < Species >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/autocomp.h:149:3: style: The destructor '~AlnServer < Seq >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
spaln-ver3.0.2/src/calcserv.h:386:10: note: Virtual destructor in base class
spaln-ver3.0.2/src/autocomp.h:149:3: note: Destructor in derived class
spaln-ver3.0.2/src/autocomp.h:155:6: style: The function 'nextvars' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
spaln-ver3.0.2/src/calcserv.h:293:13: note: Virtual function in base class
spaln-ver3.0.2/src/autocomp.h:155:6: note: Function in derived class
spaln-ver3.0.2/src/dvn.cc:400:12: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/dvn.cc:418:12: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/dvn.cc:468:40: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/dvn.cc:480:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/dvn.cc:594:41: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/dvn.cc:125:37: style:inconclusive: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/autocomp.h:165:20: note: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'.
spaln-ver3.0.2/src/dvn.cc:125:37: note: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'.
spaln-ver3.0.2/src/dvn.cc:403:7: style: Variable 'i' can be declared as reference to const [constVariableReference]
spaln-ver3.0.2/src/dvn.cc:404:7: style: Variable 'j' can be declared as reference to const [constVariableReference]
spaln-ver3.0.2/src/dvn.cc:98:17: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/dvn.cc:291:25: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/dvn.cc:354:28: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/dvn.cc:376:28: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/dvn.cc:387:28: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/dvn.cc:400:7: style: Variable 'sd' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/dvn.cc:418:7: style: Variable 'sd' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/dvn.cc:419:11: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/dvn.cc:420:11: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/dvn.cc:480:7: style: Variable 'msd' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/dvn.cc:481:12: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/dvn.cc:482:12: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/dvn.cc:504:12: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/dvn.cc:505:12: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/dvp.cc:53:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable getseq [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/dvp.cc:38:15: style: Variable 'frmt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/eijunc.cc:156:2: warning: Class 'EiJuncSeq' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/eijunc.cc:156:2: warning: Class 'EiJuncSeq' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/eijunc.cc:120:65: style:inconclusive: Function 'EiJuncSeq' argument 3 names different: declaration 'genome' definition 'gnmdb'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/eijunc.h:60:15: note: Function 'EiJuncSeq' argument 3 names different: declaration 'genome' definition 'gnmdb'.
spaln-ver3.0.2/src/eijunc.cc:120:65: note: Function 'EiJuncSeq' argument 3 names different: declaration 'genome' definition 'gnmdb'.
spaln-ver3.0.2/src/eijunc.cc:169:8: style: Variable 'chr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/exinpot.cc:48:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/exinpot.cc:256:7: style: The scope of the variable 'str' can be reduced. [variableScope]
spaln-ver3.0.2/src/seq.h:907:6: style: Local variable 'eij' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/exinpot.cc:40:20: note: Shadowed declaration
spaln-ver3.0.2/src/seq.h:907:6: note: Shadow variable
spaln-ver3.0.2/src/exinpot.cc:89:25: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/extcds.cc:134:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/extcds.cc:217:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/extcds.cc:326:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/extcds.cc:327:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
spaln-ver3.0.2/src/extcds.cc:137:3: portability: %d in format string (no. 3) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/extcds.cc:211:7: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
spaln-ver3.0.2/src/extcds.cc:174:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/extcds.cc:348:6: style: The scope of the variable 'endtype' can be reduced. [variableScope]
spaln-ver3.0.2/src/seq.h:637:6: style: Local variable 'feature' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/extcds.cc:184:12: note: Shadowed declaration
spaln-ver3.0.2/src/seq.h:637:6: note: Shadow variable
spaln-ver3.0.2/src/extcds.cc:72:26: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/extcds.cc:112:42: style: Parameter 'ps' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/extcds.cc:167:23: style: Parameter 'x' can be declared as pointer to const. However it seems that 'cmpf' is a callback function, if 'x' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/extcds.cc:174:53: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/extcds.cc:167:23: note: Parameter 'x' can be declared as pointer to const
spaln-ver3.0.2/src/extcds.cc:167:32: style: Parameter 'y' can be declared as pointer to const. However it seems that 'cmpf' is a callback function, if 'y' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/extcds.cc:174:53: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/extcds.cc:167:32: note: Parameter 'y' can be declared as pointer to const
spaln-ver3.0.2/src/extcds.cc:293:29: style: Parameter 'ps' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/fitild.cc:95:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fitild.cc:152:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fitild.cc:232:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MAX [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fitild.cc:337:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GSL_CONTINUE [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fitild.cc:360:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GSL_CONTINUE [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fitild.cc:380:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gsl_multimin_fdfminimizer_conjugate_fr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fitild.cc:407:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GSL_SUCCESS [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fitild.cc:312:11: warning: Member variable 'GslOptim::fx' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/fitild.cc:312:11: warning: Member variable 'GslOptim::status' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/fitild.cc:312:11: warning: Member variable 'GslOptim::niter' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/fitild.cc:80:6: style:inconclusive: Technically the member function 'GslOptim::niteration' can be const. [functionConst]
spaln-ver3.0.2/src/fitild.cc:81:6: style:inconclusive: Technically the member function 'GslOptim::status_code' can be const. [functionConst]
spaln-ver3.0.2/src/fitild.cc:264:2: warning: Class 'IldPrm' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/fitild.cc:94:12: style: Condition 'verbs&pro_phase' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/fitild.cc:253:10: style: Condition 'given_n_modes' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/fitild.cc:129:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fitild.cc:254:36: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fitild.cc:136:13: style: The scope of the variable 'frq' can be reduced. [variableScope]
spaln-ver3.0.2/src/fitild.cc:276:39: style:inconclusive: Function 'gsl_f' argument 1 names different: declaration 'x' definition 'v'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fitild.cc:86:40: note: Function 'gsl_f' argument 1 names different: declaration 'x' definition 'v'.
spaln-ver3.0.2/src/fitild.cc:276:39: note: Function 'gsl_f' argument 1 names different: declaration 'x' definition 'v'.
spaln-ver3.0.2/src/fitild.cc:286:38: style:inconclusive: Function 'gsl_df' argument 1 names different: declaration 'x' definition 'vx'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fitild.cc:87:39: note: Function 'gsl_df' argument 1 names different: declaration 'x' definition 'vx'.
spaln-ver3.0.2/src/fitild.cc:286:38: note: Function 'gsl_df' argument 1 names different: declaration 'x' definition 'vx'.
spaln-ver3.0.2/src/fitild.cc:286:66: style:inconclusive: Function 'gsl_df' argument 3 names different: declaration 'g' definition 'df'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fitild.cc:87:68: note: Function 'gsl_df' argument 3 names different: declaration 'g' definition 'df'.
spaln-ver3.0.2/src/fitild.cc:286:66: note: Function 'gsl_df' argument 3 names different: declaration 'g' definition 'df'.
spaln-ver3.0.2/src/fitild.cc:299:39: style:inconclusive: Function 'gsl_fdf' argument 1 names different: declaration 'x' definition 'vx'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fitild.cc:88:40: note: Function 'gsl_fdf' argument 1 names different: declaration 'x' definition 'vx'.
spaln-ver3.0.2/src/fitild.cc:299:39: note: Function 'gsl_fdf' argument 1 names different: declaration 'x' definition 'vx'.
spaln-ver3.0.2/src/fitild.cc:299:79: style:inconclusive: Function 'gsl_fdf' argument 4 names different: declaration 'g' definition 'df'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fitild.cc:88:81: note: Function 'gsl_fdf' argument 4 names different: declaration 'g' definition 'df'.
spaln-ver3.0.2/src/fitild.cc:299:79: note: Function 'gsl_fdf' argument 4 names different: declaration 'g' definition 'df'.
spaln-ver3.0.2/src/fwd2b1.cc:196:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2b1.cc:512:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2b1.cc:767:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2b1.cc:1003:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2b1.cc:1654:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2b1.cc:62:7: style:inconclusive: Technically the member function 'Aln2b1::hinitB_ng' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2b1.cc:403:14: note: Technically the member function 'Aln2b1::hinitB_ng' can be const.
spaln-ver3.0.2/src/fwd2b1.cc:62:7: note: Technically the member function 'Aln2b1::hinitB_ng' can be const.
spaln-ver3.0.2/src/fwd2b1.cc:65:7: style:inconclusive: Technically the member function 'Aln2b1::sinitB_ng' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2b1.cc:917:14: note: Technically the member function 'Aln2b1::sinitB_ng' can be const.
spaln-ver3.0.2/src/fwd2b1.cc:65:7: note: Technically the member function 'Aln2b1::sinitB_ng' can be const.
spaln-ver3.0.2/src/fwd2b1.cc:70:7: style:inconclusive: Technically the member function 'Aln2b1::cinitB_ng' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2b1.cc:703:14: note: Technically the member function 'Aln2b1::cinitB_ng' can be const.
spaln-ver3.0.2/src/fwd2b1.cc:70:7: note: Technically the member function 'Aln2b1::cinitB_ng' can be const.
spaln-ver3.0.2/src/udh_intermediate.h:45:6: warning: Class 'UdhIntermediate' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/udh_intermediate.h:45:6: warning: Class 'UdhIntermediate' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/udh_intermediate.h:76:6: warning: Class 'Udh_Imds' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/udh_intermediate.h:76:6: warning: Class 'Udh_Imds' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/fwd2b1.cc:1183:18: style: Condition 'b->left<0' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/fwd2b1.cc:1181:26: note: Assuming that condition 'b->left<0' is not redundant
spaln-ver3.0.2/src/fwd2b1.cc:1183:18: note: Condition 'b->left<0' is always false
spaln-ver3.0.2/src/fwd2b1.cc:1309:34: style: Condition 'm==1' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/fwd2b1.cc:1096:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1099:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1152:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1186:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1224:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1286:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1289:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1389:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1393:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1443:12: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1489:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1530:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1561:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1566:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1574:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1587:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1620:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1642:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1647:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1652:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:1659:33: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2b1.cc:573:7: style: The scope of the variable 'hd' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2b1.cc:661:10: style: The scope of the variable 'c' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2b1.cc:1364:29: style:inconclusive: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2b1.cc:72:22: note: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'.
spaln-ver3.0.2/src/fwd2b1.cc:1364:29: note: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'.
spaln-ver3.0.2/src/fwd2b1.cc:1427:41: style:inconclusive: Function 'seededB_ng' argument 2 names different: declaration 'cmode' definition 'eimode'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2b1.cc:76:34: note: Function 'seededB_ng' argument 2 names different: declaration 'cmode' definition 'eimode'.
spaln-ver3.0.2/src/fwd2b1.cc:1427:41: note: Function 'seededB_ng' argument 2 names different: declaration 'cmode' definition 'eimode'.
spaln-ver3.0.2/src/fwd2b1.cc:481:13: style: Local variable 'black_vpwml' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/aln.h:197:20: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2b1.cc:481:13: note: Shadow variable
spaln-ver3.0.2/src/fwd2b1.cc:1308:12: style: Local variable 'cvol' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2b1.cc:1300:8: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2b1.cc:1308:12: note: Shadow variable
spaln-ver3.0.2/src/fwd2b1.cc:82:29: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2b1.cc:118:30: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2b1.cc:403:31: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2b1.cc:448:33: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2b1.cc:703:31: style: Parameter 'hhc' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2b1.cc:758:13: style: Variable 'hrb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2b1.cc:950:32: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2b1.cc:952:9: style: Variable 'h9' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2b1.cc:1455:9: style: Variable 'wlprm' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2b1.cc:1624:73: style: Parameter 'clny' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/fwd2b1.cc:1557:13: error: Uninitialized variable: &wsk [uninitvar]
spaln-ver3.0.2/src/fwd2b1.cc:144:15: style: Variable 'rf' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2b1.cc:764:9: style: Variable 'hl[k]' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2d1.cc:45:8: style:inconclusive: Technically the member function 'Fwd2d::lastD' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2d1.cc:98:14: note: Technically the member function 'Fwd2d::lastD' can be const.
spaln-ver3.0.2/src/fwd2d1.cc:45:8: note: Technically the member function 'Fwd2d::lastD' can be const.
spaln-ver3.0.2/src/fwd2d1.cc:200:8: style:inconclusive: Technically the member function 'Fwd2d_vd::lastD' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2d1.cc:252:17: note: Technically the member function 'Fwd2d_vd::lastD' can be const.
spaln-ver3.0.2/src/fwd2d1.cc:200:8: note: Technically the member function 'Fwd2d_vd::lastD' can be const.
spaln-ver3.0.2/src/fwd2d1.cc:66:2: warning: Class 'Fwd2d' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/fwd2d1.cc:66:2: warning: Class 'Fwd2d' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/fwd2d1.cc:220:2: warning: Class 'Fwd2d_vd' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/fwd2d1.cc:220:2: warning: Class 'Fwd2d_vd' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/fwd2d1.cc:75:12: style: Local variable 'ge' shadows outer function [shadowFunction]
spaln-ver3.0.2/src/cmn.h:86:13: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2d1.cc:75:12: note: Shadow variable
spaln-ver3.0.2/src/fwd2d1.cc:84:12: style: Local variable 'ge' shadows outer function [shadowFunction]
spaln-ver3.0.2/src/cmn.h:86:13: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2d1.cc:84:12: note: Shadow variable
spaln-ver3.0.2/src/fwd2d1.cc:228:8: style: Local variable 'ge' shadows outer function [shadowFunction]
spaln-ver3.0.2/src/cmn.h:86:13: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2d1.cc:228:8: note: Shadow variable
spaln-ver3.0.2/src/fwd2d1.cc:100:9: style: Variable 'h9' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2d1.cc:254:10: style: Variable 'h9' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2h1.cc:367:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2h1.cc:686:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable supTcodon [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2h1.cc:1161:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2h1.cc:1627:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2h1.cc:1815:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2h1.cc:139:9: warning: Member variable 'Aln2h1::ss' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/fwd2h1.cc:139:9: warning: Member variable 'Aln2h1::imd_intvl' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/fwd2h1.cc:139:9: warning: Member variable 'Aln2h1::backward' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/boyer_moore.h:62:6: style:inconclusive: Technically the member function 'BoyerMoore::size' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2h1.cc:98:7: style:inconclusive: Technically the member function 'Aln2h1::hinitH_ng' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2h1.cc:953:14: note: Technically the member function 'Aln2h1::hinitH_ng' can be const.
spaln-ver3.0.2/src/fwd2h1.cc:98:7: note: Technically the member function 'Aln2h1::hinitH_ng' can be const.
spaln-ver3.0.2/src/fwd2h1.cc:108:7: performance:inconclusive: Technically the member function 'Aln2h1::isEIJ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/clib.h:467:6: style:inconclusive: Technically the member function 'PrQueue < int >::find' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:551:21: note: Technically the member function 'PrQueue < int >::find' can be const.
spaln-ver3.0.2/src/clib.h:467:6: note: Technically the member function 'PrQueue < int >::find' can be const.
spaln-ver3.0.2/src/fwd2h1.cc:147:6: warning: Class 'Aln2h1' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/fwd2h1.cc:147:6: warning: Class 'Aln2h1' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/fwd2h1.cc:707:22: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
spaln-ver3.0.2/src/fwd2h1.cc:707:15: note: outer condition: m
spaln-ver3.0.2/src/fwd2h1.cc:707:22: note: identical inner condition: m
spaln-ver3.0.2/src/fwd2h1.cc:1882:21: style: Condition 'l' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/fwd2h1.cc:1878:11: note: Assuming that condition 'l' is not redundant
spaln-ver3.0.2/src/fwd2h1.cc:1882:21: note: Condition 'l' is always true
spaln-ver3.0.2/src/fwd2h1.cc:2082:18: style: Condition 'b->left<0' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/fwd2h1.cc:2080:26: note: Assuming that condition 'b->left<0' is not redundant
spaln-ver3.0.2/src/fwd2h1.cc:2082:18: note: Condition 'b->left<0' is always false
spaln-ver3.0.2/src/fwd2h1.cc:358:11: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:1152:11: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:1995:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:1998:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:2054:22: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:2085:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:2121:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:2183:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:2186:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:2330:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:2365:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:2369:29: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3085:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3089:24: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3101:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3193:33: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3293:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3303:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3323:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3344:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:3351:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2h1.cc:850:25: style: Redundant initialization for 'n3'. The initialized value is overwritten before it is read. [redundantInitialization]
spaln-ver3.0.2/src/fwd2h1.cc:835:14: note: n3 is initialized
spaln-ver3.0.2/src/fwd2h1.cc:850:25: note: n3 is overwritten
spaln-ver3.0.2/src/fwd2h1.cc:1540:5: style: Redundant initialization for 'rr'. The initialized value is overwritten before it is read. [redundantInitialization]
spaln-ver3.0.2/src/fwd2h1.cc:1532:9: note: rr is initialized
spaln-ver3.0.2/src/fwd2h1.cc:1540:5: note: rr is overwritten
spaln-ver3.0.2/src/fwd2h1.cc:1566:5: style: Redundant initialization for 'rr'. The initialized value is overwritten before it is read. [redundantInitialization]
spaln-ver3.0.2/src/fwd2h1.cc:1558:9: note: rr is initialized
spaln-ver3.0.2/src/fwd2h1.cc:1566:5: note: rr is overwritten
spaln-ver3.0.2/src/fwd2h1.cc:161:6: style: The scope of the variable 'jnc' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2h1.cc:225:6: style: The scope of the variable 'glen' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2h1.cc:234:9: style: The scope of the variable 'mxv' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2h1.cc:1030:6: style: The scope of the variable 'glen' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2h1.cc:1487:10: style: The scope of the variable 'c' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2h1.cc:1921:7: style: The scope of the variable 'phs' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2h1.cc:155:29: style:inconclusive: Function 'initH_ng' argument 1 names different: declaration 'hf' definition 'hh'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:93:22: note: Function 'initH_ng' argument 1 names different: declaration 'hf' definition 'hh'.
spaln-ver3.0.2/src/fwd2h1.cc:155:29: note: Function 'initH_ng' argument 1 names different: declaration 'hf' definition 'hh'.
spaln-ver3.0.2/src/fwd2h1.cc:222:30: style:inconclusive: Function 'lastH_ng' argument 1 names different: declaration 'hhb' definition 'hh'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:94:23: note: Function 'lastH_ng' argument 1 names different: declaration 'hhb' definition 'hh'.
spaln-ver3.0.2/src/fwd2h1.cc:222:30: note: Function 'lastH_ng' argument 1 names different: declaration 'hhb' definition 'hh'.
spaln-ver3.0.2/src/fwd2h1.cc:953:32: style:inconclusive: Function 'hinitH_ng' argument 1 names different: declaration 'hhf' definition 'hhg'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:98:25: note: Function 'hinitH_ng' argument 1 names different: declaration 'hhf' definition 'hhg'.
spaln-ver3.0.2/src/fwd2h1.cc:953:32: note: Function 'hinitH_ng' argument 1 names different: declaration 'hhf' definition 'hhg'.
spaln-ver3.0.2/src/fwd2h1.cc:1028:35: style:inconclusive: Function 'hlastH_ng' argument 1 names different: declaration 'hhf' definition 'hhg'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:99:28: note: Function 'hlastH_ng' argument 1 names different: declaration 'hhf' definition 'hhg'.
spaln-ver3.0.2/src/fwd2h1.cc:1028:35: note: Function 'hlastH_ng' argument 1 names different: declaration 'hhf' definition 'hhg'.
spaln-ver3.0.2/src/fwd2h1.cc:2002:72: style:inconclusive: Function 'trcbkalignH_ng' argument 3 names different: declaration 'cutrng' definition 'mc'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:112:16: note: Function 'trcbkalignH_ng' argument 3 names different: declaration 'cutrng' definition 'mc'.
spaln-ver3.0.2/src/fwd2h1.cc:2002:72: note: Function 'trcbkalignH_ng' argument 3 names different: declaration 'cutrng' definition 'mc'.
spaln-ver3.0.2/src/fwd2h1.cc:2276:44: style:inconclusive: Function 'shortcutH_ng' argument 2 names different: declaration 'lub' definition 'bab'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:97:37: note: Function 'shortcutH_ng' argument 2 names different: declaration 'lub' definition 'bab'.
spaln-ver3.0.2/src/fwd2h1.cc:2276:44: note: Function 'shortcutH_ng' argument 2 names different: declaration 'lub' definition 'bab'.
spaln-ver3.0.2/src/fwd2h1.cc:2337:29: style:inconclusive: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:110:22: note: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'.
spaln-ver3.0.2/src/fwd2h1.cc:2337:29: note: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'.
spaln-ver3.0.2/src/fwd2h1.cc:2491:45: style:inconclusive: Function 'indelfreespjH' argument 2 names different: declaration 'scr' definition 'iscr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:107:38: note: Function 'indelfreespjH' argument 2 names different: declaration 'scr' definition 'iscr'.
spaln-ver3.0.2/src/fwd2h1.cc:2491:45: note: Function 'indelfreespjH' argument 2 names different: declaration 'scr' definition 'iscr'.
spaln-ver3.0.2/src/fwd2h1.cc:2753:43: style:inconclusive: Function 'first_exon_wmm' argument 2 names different: declaration 'maxscr' definition 'retscr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:118:36: note: Function 'first_exon_wmm' argument 2 names different: declaration 'maxscr' definition 'retscr'.
spaln-ver3.0.2/src/fwd2h1.cc:2753:43: note: Function 'first_exon_wmm' argument 2 names different: declaration 'maxscr' definition 'retscr'.
spaln-ver3.0.2/src/fwd2h1.cc:2901:31: style:inconclusive: Function 'last_exon_wmm' argument 1 names different: declaration 'd3' definition 'd5'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:120:24: note: Function 'last_exon_wmm' argument 1 names different: declaration 'd3' definition 'd5'.
spaln-ver3.0.2/src/fwd2h1.cc:2901:31: note: Function 'last_exon_wmm' argument 1 names different: declaration 'd3' definition 'd5'.
spaln-ver3.0.2/src/fwd2h1.cc:2901:42: style:inconclusive: Function 'last_exon_wmm' argument 2 names different: declaration 'maxscr' definition 'retscr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:120:35: note: Function 'last_exon_wmm' argument 2 names different: declaration 'maxscr' definition 'retscr'.
spaln-ver3.0.2/src/fwd2h1.cc:2901:42: note: Function 'last_exon_wmm' argument 2 names different: declaration 'maxscr' definition 'retscr'.
spaln-ver3.0.2/src/fwd2h1.cc:3222:41: style:inconclusive: Function 'seededH_ng' argument 2 names different: declaration 'cmode' definition 'eimode'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2h1.cc:127:34: note: Function 'seededH_ng' argument 2 names different: declaration 'cmode' definition 'eimode'.
spaln-ver3.0.2/src/fwd2h1.cc:3222:41: note: Function 'seededH_ng' argument 2 names different: declaration 'cmode' definition 'eimode'.
spaln-ver3.0.2/src/fwd2h1.cc:547:16: style: Local variable 'k' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:353:11: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:547:16: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:1113:9: style: Local variable 'black_vdwml' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/aln.h:199:21: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:1113:9: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:1303:16: style: Local variable 'k' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:1147:11: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:1303:16: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:1373:16: style: Local variable 'k' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:1147:11: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:1373:16: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:1437:16: style: Local variable 'k' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:1147:11: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:1437:16: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:1446:12: style: Local variable 'k' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:1147:11: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:1446:12: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:1506:11: style: Local variable 'd' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:1485:6: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:1506:11: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:2696:13: style: Local variable 'ss' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:74:6: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:2696:13: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:2761:13: style: Local variable 'ss' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:74:6: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:2761:13: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:2910:13: style: Local variable 'ss' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2h1.cc:74:6: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2h1.cc:2910:13: note: Shadow variable
spaln-ver3.0.2/src/fwd2h1.cc:2337:41: style: Parameter 'lub' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/fwd2h1.cc:2455:53: style: Parameter 'lub' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/fwd2h1.cc:2471:54: style: Parameter 'lub' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/fwd2h1.cc:2568:31: style: Parameter 'bab' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/fwd2h1.cc:2615:31: style: Parameter 'bab' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/fwd2h1.cc:3222:56: style: Parameter 'lub' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/fwd2h1.cc:155:29: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2h1.cc:953:32: style: Parameter 'hhg' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2h1.cc:1529:31: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2h1.cc:1555:31: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2h1.cc:1621:12: style: Variable 'mxd' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2h1.cc:1811:12: style: Variable 'mxd' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2h1.cc:2860:12: style: Variable 'bbi' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2h1.cc:2947:42: style: Parameter 'pskl' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/fwd2h1.cc:3025:12: style: Variable 'bb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2h1.cc:1485:8: style: Variable 'd' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2h1.cc:2357:5: style: Variable 'bb' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2h1.cc:3040:39: style: Variable 'd5' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2h1.cc:3145:11: style: Variable 'agap' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2h1.cc:3235:14: style: Variable 'wlu' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2s1.cc:278:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2s1.cc:825:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2s1.cc:1213:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2s1.cc:1434:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2s1.cc:1557:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable debug [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/fwd2s1.cc:135:9: warning: Member variable 'Aln2s1::imd_intvl' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/fwd2s1.cc:135:9: warning: Member variable 'Aln2s1::backward' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/fwd2s1.cc:95:7: style:inconclusive: Technically the member function 'Aln2s1::hinitS_ng' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2s1.cc:708:14: note: Technically the member function 'Aln2s1::hinitS_ng' can be const.
spaln-ver3.0.2/src/fwd2s1.cc:95:7: note: Technically the member function 'Aln2s1::hinitS_ng' can be const.
spaln-ver3.0.2/src/fwd2s1.cc:98:7: style:inconclusive: Technically the member function 'Aln2s1::sinitS_ng' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2s1.cc:1119:14: note: Technically the member function 'Aln2s1::sinitS_ng' can be const.
spaln-ver3.0.2/src/fwd2s1.cc:98:7: note: Technically the member function 'Aln2s1::sinitS_ng' can be const.
spaln-ver3.0.2/src/fwd2s1.cc:117:8: style:inconclusive: Technically the member function 'Aln2s1::failed' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2s1.cc:121:6: style:inconclusive: Technically the member function 'Aln2s1::first_exon_wmm' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2s1.cc:2283:13: note: Technically the member function 'Aln2s1::first_exon_wmm' can be const.
spaln-ver3.0.2/src/fwd2s1.cc:121:6: note: Technically the member function 'Aln2s1::first_exon_wmm' can be const.
spaln-ver3.0.2/src/fwd2s1.cc:123:6: style:inconclusive: Technically the member function 'Aln2s1::last_exon_wmm' can be const. [functionConst]
spaln-ver3.0.2/src/fwd2s1.cc:2372:13: note: Technically the member function 'Aln2s1::last_exon_wmm' can be const.
spaln-ver3.0.2/src/fwd2s1.cc:123:6: note: Technically the member function 'Aln2s1::last_exon_wmm' can be const.
spaln-ver3.0.2/src/fwd2s1.cc:143:6: warning: Class 'Aln2s1' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/fwd2s1.cc:143:6: warning: Class 'Aln2s1' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/fwd2s1.cc:2472:18: style: Condition 'wjxt' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/fwd2s1.cc:2586:12: style: Condition 'Local' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/fwd2s1.cc:2568:10: note: Assuming that condition 'Local' is not redundant
spaln-ver3.0.2/src/fwd2s1.cc:2586:12: note: Condition 'Local' is always false
spaln-ver3.0.2/src/fwd2s1.cc:274:11: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1666:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1669:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1726:22: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1754:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1790:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1852:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1855:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1999:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2031:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2035:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2467:24: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2473:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2479:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2483:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2487:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2503:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2513:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2517:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2571:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2709:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2719:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2739:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2760:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2767:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2811:34: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2814:34: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2846:15: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2848:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:2855:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/fwd2s1.cc:1356:5: style: Redundant initialization for 'rr'. The initialized value is overwritten before it is read. [redundantInitialization]
spaln-ver3.0.2/src/fwd2s1.cc:1348:9: note: rr is initialized
spaln-ver3.0.2/src/fwd2s1.cc:1356:5: note: rr is overwritten
spaln-ver3.0.2/src/fwd2s1.cc:1378:5: style: Redundant initialization for 'rr'. The initialized value is overwritten before it is read. [redundantInitialization]
spaln-ver3.0.2/src/fwd2s1.cc:1370:9: note: rr is initialized
spaln-ver3.0.2/src/fwd2s1.cc:1378:5: note: rr is overwritten
spaln-ver3.0.2/src/fwd2s1.cc:1072:10: style: The scope of the variable 'c' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2s1.cc:2839:8: style: The scope of the variable 'b' can be reduced. [variableScope]
spaln-ver3.0.2/src/fwd2s1.cc:1636:33: style:inconclusive: Function 'diagonalS_ng' argument 1 names different: declaration 'r_justt' definition 'r_just'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2s1.cc:107:26: note: Function 'diagonalS_ng' argument 1 names different: declaration 'r_justt' definition 'r_just'.
spaln-ver3.0.2/src/fwd2s1.cc:1636:33: note: Function 'diagonalS_ng' argument 1 names different: declaration 'r_justt' definition 'r_just'.
spaln-ver3.0.2/src/fwd2s1.cc:1674:72: style:inconclusive: Function 'trcbkalignS_ng' argument 3 names different: declaration 'cutrng' definition 'mc'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2s1.cc:109:16: note: Function 'trcbkalignS_ng' argument 3 names different: declaration 'cutrng' definition 'mc'.
spaln-ver3.0.2/src/fwd2s1.cc:1674:72: note: Function 'trcbkalignS_ng' argument 3 names different: declaration 'cutrng' definition 'mc'.
spaln-ver3.0.2/src/fwd2s1.cc:2006:29: style:inconclusive: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2s1.cc:111:22: note: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'.
spaln-ver3.0.2/src/fwd2s1.cc:2006:29: note: Function 'backforth' argument 1 names different: declaration 'n' definition 'ovr'.
spaln-ver3.0.2/src/fwd2s1.cc:2638:41: style:inconclusive: Function 'seededS_ng' argument 2 names different: declaration 'cmode' definition 'eimode'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/fwd2s1.cc:128:34: note: Function 'seededS_ng' argument 2 names different: declaration 'cmode' definition 'eimode'.
spaln-ver3.0.2/src/fwd2s1.cc:2638:41: note: Function 'seededS_ng' argument 2 names different: declaration 'cmode' definition 'eimode'.
spaln-ver3.0.2/src/fwd2s1.cc:212:16: style: Local variable 'h' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2s1.cc:202:7: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2s1.cc:212:16: note: Shadow variable
spaln-ver3.0.2/src/fwd2s1.cc:352:16: style: Local variable 'k' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2s1.cc:266:10: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2s1.cc:352:16: note: Shadow variable
spaln-ver3.0.2/src/fwd2s1.cc:389:16: style: Local variable 'k' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2s1.cc:266:10: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2s1.cc:389:16: note: Shadow variable
spaln-ver3.0.2/src/fwd2s1.cc:510:9: style: Local variable 'xi' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2s1.cc:464:8: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2s1.cc:510:9: note: Shadow variable
spaln-ver3.0.2/src/fwd2s1.cc:788:13: style: Local variable 'black_vpwml' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/aln.h:197:20: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2s1.cc:788:13: note: Shadow variable
spaln-ver3.0.2/src/fwd2s1.cc:2072:8: style: Local variable 'n' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/fwd2s1.cc:2056:6: note: Shadowed declaration
spaln-ver3.0.2/src/fwd2s1.cc:2072:8: note: Shadow variable
spaln-ver3.0.2/src/fwd2s1.cc:1448:21: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
spaln-ver3.0.2/src/fwd2s1.cc:149:28: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2s1.cc:196:28: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2s1.cc:708:31: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2s1.cc:751:33: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2s1.cc:1152:32: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2s1.cc:1154:9: style: Variable 'h9' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/fwd2s1.cc:1345:30: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2s1.cc:1367:30: style: Parameter 'hh' can be declared as const array [constParameter]
spaln-ver3.0.2/src/fwd2s1.cc:1485:10: style: Variable 'nr' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2s1.cc:1607:10: style: Variable 'nr' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/fwd2s1.cc:2651:14: style: Variable 'wlu' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/gaps.cc:262:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable exgl [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/gaps.cc:198:24: style: Condition 'df>0' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/gaps.cc:198:15: note: Assuming that condition 'df' is not redundant
spaln-ver3.0.2/src/gaps.cc:198:24: note: Condition 'df>0' is always true
spaln-ver3.0.2/src/gaps.cc:206:10: style: Condition 'df<0' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/gaps.cc:202:16: note: Assuming that condition 'df' is not redundant
spaln-ver3.0.2/src/gaps.cc:206:10: note: Condition 'df<0' is always false
spaln-ver3.0.2/src/gaps.cc:210:10: style: Condition 'df>0' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/gaps.cc:202:16: note: Assuming that condition 'df' is not redundant
spaln-ver3.0.2/src/gaps.cc:210:10: note: Condition 'df>0' is always true
spaln-ver3.0.2/src/gaps.cc:149:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/gaps.cc:185:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/gaps.cc:225:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/gaps.cc:275:26: style:inconclusive: Function 'gap2skl' argument 1 names different: declaration 'ga' definition 'gga'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gaps.h:44:33: note: Function 'gap2skl' argument 1 names different: declaration 'ga' definition 'gga'.
spaln-ver3.0.2/src/gaps.cc:275:26: note: Function 'gap2skl' argument 1 names different: declaration 'ga' definition 'gga'.
spaln-ver3.0.2/src/gaps.cc:275:43: style:inconclusive: Function 'gap2skl' argument 2 names different: declaration 'gb' definition 'ggb'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gaps.h:44:49: note: Function 'gap2skl' argument 2 names different: declaration 'gb' definition 'ggb'.
spaln-ver3.0.2/src/gaps.cc:275:43: note: Function 'gap2skl' argument 2 names different: declaration 'gb' definition 'ggb'.
spaln-ver3.0.2/src/gaps.cc:150:7: style: Variable 'prv' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gaps.cc:188:7: style: Variable 'prv' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gaps.cc:239:6: style: Variable 'step' can be declared as const array [constVariable]
spaln-ver3.0.2/src/gaps.cc:281:6: style: Variable 'mn' can be declared as const array [constVariable]
spaln-ver3.0.2/src/gsinfo.cc:531:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable deflbl [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/gsinfo.h:58:7: style:inconclusive: Technically the member function 'SigII::swaplst' can be const. [functionConst]
spaln-ver3.0.2/src/gsinfo.cc:265:13: note: Technically the member function 'SigII::swaplst' can be const.
spaln-ver3.0.2/src/gsinfo.h:58:7: note: Technically the member function 'SigII::swaplst' can be const.
spaln-ver3.0.2/src/gsinfo.h:66:7: style:inconclusive: Technically the member function 'SigII::locate' can be const. [functionConst]
spaln-ver3.0.2/src/gsinfo.cc:256:13: note: Technically the member function 'SigII::locate' can be const.
spaln-ver3.0.2/src/gsinfo.h:66:7: note: Technically the member function 'SigII::locate' can be const.
spaln-ver3.0.2/src/gsinfo.h:358:7: style:inconclusive: Technically the member function 'Eijnc::store' can be const. [functionConst]
spaln-ver3.0.2/src/gsinfo.cc:1237:13: note: Technically the member function 'Eijnc::store' can be const.
spaln-ver3.0.2/src/gsinfo.h:358:7: note: Technically the member function 'Eijnc::store' can be const.
spaln-ver3.0.2/src/clib.h:721:6: style:inconclusive: Technically the member function 'PrQueue_idx < int >::gettop_idx' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:724:7: style:inconclusive: Technically the member function 'PrQueue_idx < int >::empty' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:725:6: style:inconclusive: Technically the member function 'PrQueue_idx < int >::size' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:726:7: style:inconclusive: Technically the member function 'PrQueue_idx < int >::lt' can be const. [functionConst]
spaln-ver3.0.2/src/gsinfo.cc:124:6: warning: Struct 'SigII' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/gsinfo.cc:69:6: warning: Class 'Cip_score' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/gsinfo.cc:69:6: warning: Class 'Cip_score' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/gsinfo.cc:84:2: warning: Struct 'Iiinfo' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/gsinfo.cc:84:2: warning: Struct 'Iiinfo' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/gsinfo.cc:1230:2: warning: Class 'Eijnc' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/gsinfo.cc:1230:2: warning: Class 'Eijnc' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:736:2: warning: Class 'PrQueue_idx < int >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:736:2: warning: Class 'PrQueue_idx < int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/gsinfo.cc:1109:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/gsinfo.cc:120:35: style:inconclusive: Function 'SigII' argument 2 names different: declaration 'num' definition 'nn'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:54:29: note: Function 'SigII' argument 2 names different: declaration 'num' definition 'nn'.
spaln-ver3.0.2/src/gsinfo.cc:120:35: note: Function 'SigII' argument 2 names different: declaration 'num' definition 'nn'.
spaln-ver3.0.2/src/gsinfo.cc:120:43: style:inconclusive: Function 'SigII' argument 3 names different: declaration 'step' definition 's'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:54:38: note: Function 'SigII' argument 3 names different: declaration 'step' definition 's'.
spaln-ver3.0.2/src/gsinfo.cc:120:43: note: Function 'SigII' argument 3 names different: declaration 'step' definition 's'.
spaln-ver3.0.2/src/gsinfo.cc:137:26: style:inconclusive: Function 'SigII' argument 1 names different: declaration 'sq' definition 'slist'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:51:20: note: Function 'SigII' argument 1 names different: declaration 'sq' definition 'slist'.
spaln-ver3.0.2/src/gsinfo.cc:137:26: note: Function 'SigII' argument 1 names different: declaration 'sq' definition 'slist'.
spaln-ver3.0.2/src/gsinfo.cc:913:20: style:inconclusive: Function 'cutSigII' argument 1 names different: declaration 'dstseq' definition 'dest'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:442:27: note: Function 'cutSigII' argument 1 names different: declaration 'dstseq' definition 'dest'.
spaln-ver3.0.2/src/gsinfo.cc:913:20: note: Function 'cutSigII' argument 1 names different: declaration 'dstseq' definition 'dest'.
spaln-ver3.0.2/src/gsinfo.cc:913:37: style:inconclusive: Function 'cutSigII' argument 2 names different: declaration 'srcseq' definition 'sorc'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:442:46: note: Function 'cutSigII' argument 2 names different: declaration 'srcseq' definition 'sorc'.
spaln-ver3.0.2/src/gsinfo.cc:913:37: note: Function 'cutSigII' argument 2 names different: declaration 'srcseq' definition 'sorc'.
spaln-ver3.0.2/src/gsinfo.cc:974:20: style:inconclusive: Function 'catSigII' argument 1 names different: declaration 'dstseq' definition 'dest'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:443:27: note: Function 'catSigII' argument 1 names different: declaration 'dstseq' definition 'dest'.
spaln-ver3.0.2/src/gsinfo.cc:974:20: note: Function 'catSigII' argument 1 names different: declaration 'dstseq' definition 'dest'.
spaln-ver3.0.2/src/gsinfo.cc:974:37: style:inconclusive: Function 'catSigII' argument 2 names different: declaration 'srcseq' definition 'sorc'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:443:46: note: Function 'catSigII' argument 2 names different: declaration 'srcseq' definition 'sorc'.
spaln-ver3.0.2/src/gsinfo.cc:974:37: note: Function 'catSigII' argument 2 names different: declaration 'srcseq' definition 'sorc'.
spaln-ver3.0.2/src/gsinfo.cc:1117:34: style:inconclusive: Function 'rmGapPfq' argument 1 names different: declaration 'gg' definition 'gp'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:56:28: note: Function 'rmGapPfq' argument 1 names different: declaration 'gg' definition 'gp'.
spaln-ver3.0.2/src/gsinfo.cc:1117:34: note: Function 'rmGapPfq' argument 1 names different: declaration 'gg' definition 'gp'.
spaln-ver3.0.2/src/gsinfo.cc:909:9: style: Local variable 'scr' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/gsinfo.h:396:8: note: Shadowed declaration
spaln-ver3.0.2/src/gsinfo.cc:909:9: note: Shadow variable
spaln-ver3.0.2/src/gsinfo.cc:882:10: style: Local variable 'scr' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/gsinfo.h:396:8: note: Shadowed declaration
spaln-ver3.0.2/src/gsinfo.cc:882:10: note: Shadow variable
spaln-ver3.0.2/src/gsinfo.cc:897:10: style: Local variable 'scr' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/gsinfo.h:396:8: note: Shadowed declaration
spaln-ver3.0.2/src/gsinfo.cc:897:10: note: Shadow variable
spaln-ver3.0.2/src/gsinfo.cc:1022:11: style: Local variable 'tmp' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/gsinfo.cc:1008:7: note: Shadowed declaration
spaln-ver3.0.2/src/gsinfo.cc:1022:11: note: Shadow variable
spaln-ver3.0.2/src/gsinfo.cc:1237:39: style: Parameter 'now' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/gsinfo.cc:1237:51: style: Parameter 'prv' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/gsinfo.cc:1255:39: style: Parameter 'now' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/gsinfo.cc:267:7: style: Variable 'tst' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.cc:287:7: style: Variable 'tst' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.cc:462:9: style: Variable 'sgi' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.cc:800:8: style: Variable 'decode' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.cc:1125:7: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.cc:1198:7: style: Variable 'tfq' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.cc:1208:10: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/gsinfo.cc:165:20: error: Memory is allocated but not initialized: pfqs[j] [uninitdata]
spaln-ver3.0.2/src/ildpdf.cc:322:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gsl_root_fdfsolver_newton [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/ildpdf.cc:351:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gsl_root_fdfsolver_newton [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/ildpdf.cc:424:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/ildpdf.cc:955:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/ildpdf.h:124:9: style:inconclusive: Technically the member function 'IldPrm::pdf_function' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:200:16: note: Technically the member function 'IldPrm::pdf_function' can be const.
spaln-ver3.0.2/src/ildpdf.h:124:9: note: Technically the member function 'IldPrm::pdf_function' can be const.
spaln-ver3.0.2/src/ildpdf.h:125:9: style:inconclusive: Technically the member function 'IldPrm::cumulative' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:247:16: note: Technically the member function 'IldPrm::cumulative' can be const.
spaln-ver3.0.2/src/ildpdf.h:125:9: note: Technically the member function 'IldPrm::cumulative' can be const.
spaln-ver3.0.2/src/ildpdf.h:129:7: style:inconclusive: Technically the member function 'IldPrm::proper' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:369:14: note: Technically the member function 'IldPrm::proper' can be const.
spaln-ver3.0.2/src/ildpdf.h:129:7: note: Technically the member function 'IldPrm::proper' can be const.
spaln-ver3.0.2/src/ildpdf.h:215:7: style:inconclusive: Technically the member function 'Ild::print_lf' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:952:11: note: Technically the member function 'Ild::print_lf' can be const.
spaln-ver3.0.2/src/ildpdf.h:215:7: note: Technically the member function 'Ild::print_lf' can be const.
spaln-ver3.0.2/src/ildpdf.h:217:9: style:inconclusive: Technically the member function 'Ild::mean' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:840:13: note: Technically the member function 'Ild::mean' can be const.
spaln-ver3.0.2/src/ildpdf.h:217:9: note: Technically the member function 'Ild::mean' can be const.
spaln-ver3.0.2/src/ildpdf.h:218:9: style:inconclusive: Technically the member function 'Ild::logmean' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:858:13: note: Technically the member function 'Ild::logmean' can be const.
spaln-ver3.0.2/src/ildpdf.h:218:9: note: Technically the member function 'Ild::logmean' can be const.
spaln-ver3.0.2/src/ildpdf.h:219:9: style:inconclusive: Technically the member function 'Ild::quantile' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:880:13: note: Technically the member function 'Ild::quantile' can be const.
spaln-ver3.0.2/src/ildpdf.h:219:9: note: Technically the member function 'Ild::quantile' can be const.
spaln-ver3.0.2/src/ildpdf.h:221:9: style:inconclusive: Technically the member function 'Ild::kolmo_smir' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:921:13: note: Technically the member function 'Ild::kolmo_smir' can be const.
spaln-ver3.0.2/src/ildpdf.h:221:9: note: Technically the member function 'Ild::kolmo_smir' can be const.
spaln-ver3.0.2/src/ildpdf.h:222:9: style:inconclusive: Technically the member function 'Ild::kolmo_smir' can be const. [functionConst]
spaln-ver3.0.2/src/ildpdf.cc:904:13: note: Technically the member function 'Ild::kolmo_smir' can be const.
spaln-ver3.0.2/src/ildpdf.h:222:9: note: Technically the member function 'Ild::kolmo_smir' can be const.
spaln-ver3.0.2/src/clib.h:252:8: style:inconclusive: Technically the member function 'Dhash < int , double >::undef' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:253:7: style:inconclusive: Technically the member function 'Dhash < int , double >::write_binary' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:287:27: note: Technically the member function 'Dhash < int , double >::write_binary' can be const.
spaln-ver3.0.2/src/clib.h:253:7: note: Technically the member function 'Dhash < int , double >::write_binary' can be const.
spaln-ver3.0.2/src/ildpdf.cc:193:6: warning: Class 'IldPrm' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/ildpdf.cc:778:2: warning: Class 'Ild' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:263:6: warning: Class 'Dhash < int , double >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:263:6: warning: Class 'Dhash < int , double >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:205:2: style: Class 'Dhash < int , double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/ildpdf.cc:1703:17: warning: Either the condition 'lild' is redundant or there is possible null pointer dereference: lild. [nullPointerRedundantCheck]
spaln-ver3.0.2/src/ildpdf.cc:1707:6: note: Assuming that condition 'lild' is not redundant
spaln-ver3.0.2/src/ildpdf.cc:1703:17: note: Null pointer dereference
spaln-ver3.0.2/src/ildpdf.cc:320:15: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:349:15: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:514:15: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:523:19: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:677:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:690:22: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:691:22: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:721:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:745:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:746:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:774:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:815:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:820:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1031:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1037:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1043:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1050:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1057:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1066:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1085:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1094:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1102:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1111:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1118:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1127:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1140:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1158:15: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:1179:15: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/ildpdf.cc:330:13: style: Variable 'status' is reassigned a value before the old one has been used. [redundantAssignment]
spaln-ver3.0.2/src/ildpdf.cc:327:13: note: status is assigned
spaln-ver3.0.2/src/ildpdf.cc:330:13: note: status is overwritten
spaln-ver3.0.2/src/ildpdf.cc:359:13: style: Variable 'status' is reassigned a value before the old one has been used. [redundantAssignment]
spaln-ver3.0.2/src/ildpdf.cc:356:13: note: status is assigned
spaln-ver3.0.2/src/ildpdf.cc:359:13: note: status is overwritten
spaln-ver3.0.2/src/ildpdf.cc:910:9: style: The scope of the variable 'f' can be reduced. [variableScope]
spaln-ver3.0.2/src/ildpdf.cc:140:30: style:inconclusive: Function 'get_IldPrm' argument 1 names different: declaration 'str' definition 'ps'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:156:23: note: Function 'get_IldPrm' argument 1 names different: declaration 'str' definition 'ps'.
spaln-ver3.0.2/src/ildpdf.cc:140:30: note: Function 'get_IldPrm' argument 1 names different: declaration 'str' definition 'ps'.
spaln-ver3.0.2/src/ildpdf.cc:311:42: style:inconclusive: Function 'quantile' argument 2 names different: declaration 'iv' definition 'x'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:127:35: note: Function 'quantile' argument 2 names different: declaration 'iv' definition 'x'.
spaln-ver3.0.2/src/ildpdf.cc:311:42: note: Function 'quantile' argument 2 names different: declaration 'iv' definition 'x'.
spaln-ver3.0.2/src/ildpdf.cc:482:31: style:inconclusive: Function 'convert' argument 1 names different: declaration 'topdf' definition 'tipdf'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:157:24: note: Function 'convert' argument 1 names different: declaration 'topdf' definition 'tipdf'.
spaln-ver3.0.2/src/ildpdf.cc:482:31: note: Function 'convert' argument 1 names different: declaration 'topdf' definition 'tipdf'.
spaln-ver3.0.2/src/ildpdf.cc:705:30: style:inconclusive: Function 'Ild' argument 2 names different: declaration 'nsample' definition 'n_sample'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:209:26: note: Function 'Ild' argument 2 names different: declaration 'nsample' definition 'n_sample'.
spaln-ver3.0.2/src/ildpdf.cc:705:30: note: Function 'Ild' argument 2 names different: declaration 'nsample' definition 'n_sample'.
spaln-ver3.0.2/src/ildpdf.cc:921:29: style:inconclusive: Function 'kolmo_smir' argument 1 names different: declaration 'ild2' definition 'b'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:221:25: note: Function 'kolmo_smir' argument 1 names different: declaration 'ild2' definition 'b'.
spaln-ver3.0.2/src/ildpdf.cc:921:29: note: Function 'kolmo_smir' argument 1 names different: declaration 'ild2' definition 'b'.
spaln-ver3.0.2/src/ildpdf.cc:1683:28: style:inconclusive: Function 'add' argument 1 names different: declaration 'lild' definition 'ild'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:301:16: note: Function 'add' argument 1 names different: declaration 'lild' definition 'ild'.
spaln-ver3.0.2/src/ildpdf.cc:1683:28: note: Function 'add' argument 1 names different: declaration 'lild' definition 'ild'.
spaln-ver3.0.2/src/ildpdf.cc:1719:44: style:inconclusive: Function 'GnuPlotLild' argument 2 names different: declaration 'nprm' definition 'np'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:313:32: note: Function 'GnuPlotLild' argument 2 names different: declaration 'nprm' definition 'np'.
spaln-ver3.0.2/src/ildpdf.cc:1719:44: note: Function 'GnuPlotLild' argument 2 names different: declaration 'nprm' definition 'np'.
spaln-ver3.0.2/src/ildpdf.cc:1719:65: style:inconclusive: Function 'GnuPlotLild' argument 4 names different: declaration 'nild' definition 'ni'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:313:55: note: Function 'GnuPlotLild' argument 4 names different: declaration 'nild' definition 'ni'.
spaln-ver3.0.2/src/ildpdf.cc:1719:65: note: Function 'GnuPlotLild' argument 4 names different: declaration 'nild' definition 'ni'.
spaln-ver3.0.2/src/ildpdf.cc:1719:74: style:inconclusive: Function 'GnuPlotLild' argument 5 names different: declaration 'compo' definition 'ildents'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:313:70: note: Function 'GnuPlotLild' argument 5 names different: declaration 'compo' definition 'ildents'.
spaln-ver3.0.2/src/ildpdf.cc:1719:74: note: Function 'GnuPlotLild' argument 5 names different: declaration 'compo' definition 'ildents'.
spaln-ver3.0.2/src/ildpdf.cc:1734:44: style:inconclusive: Function 'GnuPlotLild' argument 2 names different: declaration 'nprm' definition 'np'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:314:32: note: Function 'GnuPlotLild' argument 2 names different: declaration 'nprm' definition 'np'.
spaln-ver3.0.2/src/ildpdf.cc:1734:44: note: Function 'GnuPlotLild' argument 2 names different: declaration 'nprm' definition 'np'.
spaln-ver3.0.2/src/ildpdf.cc:1734:64: style:inconclusive: Function 'GnuPlotLild' argument 4 names different: declaration 'nild' definition 'ni'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:314:54: note: Function 'GnuPlotLild' argument 4 names different: declaration 'nild' definition 'ni'.
spaln-ver3.0.2/src/ildpdf.cc:1734:64: note: Function 'GnuPlotLild' argument 4 names different: declaration 'nild' definition 'ni'.
spaln-ver3.0.2/src/ildpdf.cc:1734:73: style:inconclusive: Function 'GnuPlotLild' argument 5 names different: declaration 'compo' definition 'ildents'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:314:69: note: Function 'GnuPlotLild' argument 5 names different: declaration 'compo' definition 'ildents'.
spaln-ver3.0.2/src/ildpdf.cc:1734:73: note: Function 'GnuPlotLild' argument 5 names different: declaration 'compo' definition 'ildents'.
spaln-ver3.0.2/src/ildpdf.cc:1770:35: style:inconclusive: Function 'GnuPlotLild' argument 1 names different: declaration 'lilds' definition 'dprms'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/ildpdf.h:317:23: note: Function 'GnuPlotLild' argument 1 names different: declaration 'lilds' definition 'dprms'.
spaln-ver3.0.2/src/ildpdf.cc:1770:35: note: Function 'GnuPlotLild' argument 1 names different: declaration 'lilds' definition 'dprms'.
spaln-ver3.0.2/src/ildpdf.cc:671:7: style: Local variable 'frq' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/ildpdf.cc:658:9: note: Shadowed declaration
spaln-ver3.0.2/src/ildpdf.cc:671:7: note: Shadow variable
spaln-ver3.0.2/src/ildpdf.cc:1654:14: style: Local variable 'y' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/ildpdf.cc:1649:10: note: Shadowed declaration
spaln-ver3.0.2/src/ildpdf.cc:1654:14: note: Shadow variable
spaln-ver3.0.2/src/ildpdf.cc:1805:15: style: Local variable 'c' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/ildpdf.cc:1788:6: note: Shadowed declaration
spaln-ver3.0.2/src/ildpdf.cc:1805:15: note: Shadow variable
spaln-ver3.0.2/src/ildpdf.cc:153:12: style: Variable 'tm' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:338:32: style: Parameter 'q123_4' can be declared as const array [constParameter]
spaln-ver3.0.2/src/ildpdf.cc:421:10: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:777:10: style: Variable 'tlf' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:891:10: style: Variable 'prv' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:926:10: style: Variable 'tfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:927:10: style: Variable 'tfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:958:10: style: Variable 'tf' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1000:10: style: Variable 'tlf' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1050:10: style: Variable 'mlogq' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1057:10: style: Variable 'mlogq' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1066:10: style: Variable 'mlogq' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1238:10: style: Variable 'tfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1239:10: style: Variable 'tfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1259:10: style: Variable 'tfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1260:10: style: Variable 'tfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1280:10: style: Variable 'tfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1281:10: style: Variable 'tfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1312:10: style: Variable 'tfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1313:10: style: Variable 'tfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1343:10: style: Variable 'tfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1344:10: style: Variable 'tfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1382:10: style: Variable 'tfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1383:10: style: Variable 'tfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1424:10: style: Variable 'tfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1425:10: style: Variable 'tfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1476:10: style: Variable 'lfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1477:10: style: Variable 'lfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1487:10: style: Variable 'lfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1488:10: style: Variable 'lfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1498:10: style: Variable 'lfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1499:10: style: Variable 'lfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1512:10: style: Variable 'lfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1513:10: style: Variable 'lfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1523:10: style: Variable 'lfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1524:10: style: Variable 'lfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1543:10: style: Variable 'lfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1544:10: style: Variable 'lfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1562:10: style: Variable 'lfa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1563:10: style: Variable 'lfb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1779:52: style: Parameter 'iname' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/ildpdf.cc:1832:25: style: Variable 'kv' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/ildpdf.cc:1852:21: style: Variable 'kv' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/clib.h:91:10: warning: Uninitialized variable: head [uninitvar]
spaln-ver3.0.2/src/ildpdf.cc:488:8: note: Calling function 'vcopy', 1st argument 'tparam' value is <Uninit>
spaln-ver3.0.2/src/clib.h:89:12: note: Assignment 'head=dst', assigned value is <Uninit>
spaln-ver3.0.2/src/clib.h:90:13: note: Assuming condition is false
spaln-ver3.0.2/src/clib.h:91:10: note: Uninitialized variable: head
spaln-ver3.0.2/src/iolib.cc:230:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:276:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:298:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:309:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:323:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_tabpath [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:344:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_tabpath [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:388:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tabpath [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:553:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:609:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:621:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:635:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:657:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:741:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:765:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:774:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fd [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:795:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fd [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:802:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fd [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:814:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fd [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:829:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable domphy [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:907:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:945:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n_tabpath [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/iolib.cc:89:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/iolib.cc:749:45: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/iolib.cc:518:7: style: The scope of the variable 'csv' can be reduced. [variableScope]
spaln-ver3.0.2/src/iolib.cc:519:7: style: The scope of the variable 'psv' can be reduced. [variableScope]
spaln-ver3.0.2/src/iolib.cc:523:8: style: The scope of the variable 'ptr' can be reduced. [variableScope]
spaln-ver3.0.2/src/iolib.cc:541:7: style: The scope of the variable 'c' can be reduced. [variableScope]
spaln-ver3.0.2/src/iolib.cc:605:10: style: The scope of the variable 'args' can be reduced. [variableScope]
spaln-ver3.0.2/src/iolib.cc:617:10: style: The scope of the variable 'args' can be reduced. [variableScope]
spaln-ver3.0.2/src/iolib.cc:631:10: style: The scope of the variable 'ap' can be reduced. [variableScope]
spaln-ver3.0.2/src/iolib.cc:731:6: style: The scope of the variable 'num' can be reduced. [variableScope]
spaln-ver3.0.2/src/iolib.cc:194:8: style: Variable 'dot' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/iolib.cc:542:8: style: Variable 'c_ptr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/iolib.cc:543:7: style: Variable 'i_ptr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/iolib.cc:544:7: style: Variable 'u_ptr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/iolib.cc:545:8: style: Variable 'l_ptr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/iolib.cc:546:10: style: Variable 'd_ptr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/iolib.cc:914:8: style: Variable 'tq' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/iolib.cc:348:14: error: Uninitialized variable: str [uninitvar]
spaln-ver3.0.2/src/iolib.cc:206:11: style: Variable 'fd' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/iolib.cc:322:11: style: Variable 'fd' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/iolib.cc:693:9: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/iolib.cc:883:12: style: Variable 'fd' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/iolib.cc:943:12: style: Variable 'fd' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/kmers.cc:45:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/kmers.cc:188:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/kmers.cc:208:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/kmers.cc:343:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/kmers.cc:90:8: warning: Member variable 'Kmers::words' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/kmers.cc:95:2: warning: Class 'Kmers' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/kmers.cc:95:2: warning: Class 'Kmers' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/kmers.cc:237:18: style: Condition 'no_amb' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/kmers.cc:251:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/kmers.cc:263:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/kmers.cc:90:25: style:inconclusive: Function 'Kmers' argument 2 names different: declaration 'k' definition 'kk'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/kmers.cc:71:19: note: Function 'Kmers' argument 2 names different: declaration 'k' definition 'kk'.
spaln-ver3.0.2/src/kmers.cc:90:25: note: Function 'Kmers' argument 2 names different: declaration 'k' definition 'kk'.
spaln-ver3.0.2/src/kmers.cc:242:31: style:inconclusive: Function 'outputCount' argument 1 names different: declaration 'decode' definition 'decoder'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/kmers.cc:85:25: note: Function 'outputCount' argument 1 names different: declaration 'decode' definition 'decoder'.
spaln-ver3.0.2/src/kmers.cc:242:31: note: Function 'outputCount' argument 1 names different: declaration 'decode' definition 'decoder'.
spaln-ver3.0.2/src/kmers.cc:93:6: style: Local variable 'words' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/kmers.cc:63:6: note: Shadowed declaration
spaln-ver3.0.2/src/kmers.cc:93:6: note: Shadow variable
spaln-ver3.0.2/src/kmers.cc:141:38: style: Parameter 'encoder' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/kmers.cc:144:15: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/kmers.cc:162:26: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/kmers.cc:166:8: style: Variable 'ts' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/kmers.cc:167:8: style: Variable 'encode' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/kmers.cc:180:12: style: Variable 'nc16to4' can be declared as const array [constVariable]
spaln-ver3.0.2/src/kmers.cc:242:31: style: Parameter 'decoder' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/kmers.cc:63:6: style: class member 'Kmers::words' is never used. [unusedStructMember]
spaln-ver3.0.2/src/makdbs.cc:43:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.cc:98:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQ_DELIM [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.cc:120:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQ_DELIM [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.cc:143:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DbsRec [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.cc:165:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.cc:193:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magicver21 [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.cc:202:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable entptr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.cc:215:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DbsRec [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.cc:286:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SGZ_EXT [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makdbs.h:48:6: style:inconclusive: Technically the member function 'Makdbs::encode' can be const. [functionConst]
spaln-ver3.0.2/src/makdbs.cc:150:13: note: Technically the member function 'Makdbs::encode' can be const.
spaln-ver3.0.2/src/makdbs.h:48:6: note: Technically the member function 'Makdbs::encode' can be const.
spaln-ver3.0.2/src/makdbs.h:58:7: performance:inconclusive: Technically the member function 'Makdbs::skip_till_nl' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/makdbs.cc:75:14: note: Technically the member function 'Makdbs::skip_till_nl' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/makdbs.h:58:7: note: Technically the member function 'Makdbs::skip_till_nl' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/makdbs.h:64:2: style: Class 'Makdbs' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/makdbs.cc:219:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/makdbs.cc:228:33: style:inconclusive: Function 'makdbs' argument 1 names different: declaration 'fn' definition 'av'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/makdbs.h:66:26: note: Function 'makdbs' argument 1 names different: declaration 'fn' definition 'av'.
spaln-ver3.0.2/src/makdbs.cc:228:33: note: Function 'makdbs' argument 1 names different: declaration 'fn' definition 'av'.
spaln-ver3.0.2/src/makdbs.cc:248:20: style:inconclusive: Function 'Makdbs' argument 1 names different: declaration 'ac' definition 'argc'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/makdbs.h:63:13: note: Function 'Makdbs' argument 1 names different: declaration 'ac' definition 'argc'.
spaln-ver3.0.2/src/makdbs.cc:248:20: note: Function 'Makdbs' argument 1 names different: declaration 'ac' definition 'argc'.
spaln-ver3.0.2/src/makdbs.cc:248:39: style:inconclusive: Function 'Makdbs' argument 2 names different: declaration 'av' definition 'argv'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/makdbs.h:63:30: note: Function 'Makdbs' argument 2 names different: declaration 'av' definition 'argv'.
spaln-ver3.0.2/src/makdbs.cc:248:39: note: Function 'Makdbs' argument 2 names different: declaration 'av' definition 'argv'.
spaln-ver3.0.2/src/makdbs.cc:134:9: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/makdbs.cc:200:24: style: Parameter 'a' can be declared as pointer to const. However it seems that 'cmpkey' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/makdbs.cc:219:50: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/makdbs.cc:200:24: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/makdbs.cc:200:32: style: Parameter 'b' can be declared as pointer to const. However it seems that 'cmpkey' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/makdbs.cc:219:50: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/makdbs.cc:200:32: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/makmdm.cc:68:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makmdm.cc:122:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/makmdm.cc:365:44: style: Parameter 'a' can be declared as const array [constParameter]
spaln-ver3.0.2/src/makmdm.cc:365:62: style: Parameter 'comp' can be declared as const array [constParameter]
spaln-ver3.0.2/src/makmdm.cc:376:69: style: Parameter 'comp' can be declared as const array [constParameter]
spaln-ver3.0.2/src/makmdm.cc:895:15: style: Variable 'd' can be declared as const array [constVariable]
spaln-ver3.0.2/src/mfile.cc:84:15: warning: 'operator=' should check for assignment to self to avoid problems with dynamic memory. [operatorEqToSelf]
spaln-ver3.0.2/src/mfile.cc:54:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/montseq.cc:40:16: style: The scope of the variable 'v2' can be reduced. [variableScope]
spaln-ver3.0.2/src/npssm.cc:47:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/npssm.cc:105:10: warning: Member variable 'TriFreq::sumi' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/npssm.cc:159:10: warning: Member variable 'TriFreq::sumi' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/npssm.cc:96:7: style:inconclusive: Technically the member function 'TriFreq::rel_frequency' can be const. [functionConst]
spaln-ver3.0.2/src/npssm.cc:335:15: note: Technically the member function 'TriFreq::rel_frequency' can be const.
spaln-ver3.0.2/src/npssm.cc:96:7: note: Technically the member function 'TriFreq::rel_frequency' can be const.
spaln-ver3.0.2/src/npssm.cc:98:7: style:inconclusive: Technically the member function 'TriFreq::setrange' can be const. [functionConst]
spaln-ver3.0.2/src/npssm.cc:473:15: note: Technically the member function 'TriFreq::setrange' can be const.
spaln-ver3.0.2/src/npssm.cc:98:7: note: Technically the member function 'TriFreq::setrange' can be const.
spaln-ver3.0.2/src/npssm.cc:115:7: warning: Class 'TriFreq' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/npssm.cc:115:7: warning: Class 'TriFreq' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/npssm.cc:90:2: style: Class 'TriFreq' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/npssm.cc:321:3: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
spaln-ver3.0.2/src/npssm.cc:546:19: style: Local variable 'write_error' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/adddef.h:172:20: note: Shadowed declaration
spaln-ver3.0.2/src/npssm.cc:546:19: note: Shadow variable
spaln-ver3.0.2/src/npssm.cc:236:33: style: Parameter 'sd' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/npssm.cc:492:34: style: Parameter 'sd' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/npssm.cc:284:13: style: Variable 'w' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/npssm.cc:295:9: style: Variable 'w' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/npssm.cc:536:9: style: Variable 'lod' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/pattern.cc:100:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/pattern.cc:175:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/pattern.cc:208:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/pattern.cc:299:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/pattern.cc:348:12: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
spaln-ver3.0.2/src/pattern.cc:109:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/pattern.cc:114:42: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/pattern.cc:115:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/pattern.cc:116:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/pattern.cc:353:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/pattern.cc:62:63: style: Parameter 'defcode' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/pattern.cc:74:38: style: Parameter 'pat' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/pattern.cc:90:47: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/pattern.cc:97:8: style: Variable 'sr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/pattern.cc:152:63: style: Parameter 'defcode' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/pattern.cc:171:38: style: Parameter 'mb' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/pattern.cc:281:8: style: Variable 'sr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/pattern.cc:327:23: style: Parameter 'a' can be declared as pointer to const. However it seems that 'icmpf' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/pattern.cc:353:51: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/pattern.cc:327:23: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/pattern.cc:327:31: style: Parameter 'b' can be declared as pointer to const. However it seems that 'icmpf' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/pattern.cc:353:51: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/pattern.cc:327:31: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/pattern.cc:332:51: style: Parameter 'pat' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/pattern.cc:334:13: style: Variable 'cmppat' can be declared as const array [constVariable]
spaln-ver3.0.2/src/pattern.cc:357:28: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/plotild.cc:41:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/plotild.cc:143:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:67:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:187:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:230:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:243:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:316:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out_file [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:372:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable trimendgap [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:548:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SILENT [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:88:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/rdn.cc:36:7: style:inconclusive: Technically the member function 'Submembers::check' can be const. [functionConst]
spaln-ver3.0.2/src/rdn.cc:155:18: note: Technically the member function 'Submembers::check' can be const.
spaln-ver3.0.2/src/rdn.cc:36:7: note: Technically the member function 'Submembers::check' can be const.
spaln-ver3.0.2/src/autocomp.h:156:6: performance:inconclusive: Technically the member function 'AlnServer < Seq >::localoption' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/rdn.cc:460:23: note: Technically the member function 'AlnServer < Seq >::localoption' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:156:6: note: Technically the member function 'AlnServer < Seq >::localoption' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:165:7: performance:inconclusive: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/rdn.cc:85:24: note: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:165:7: note: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/rdn.cc:217:2: warning: Struct 'Submembers' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/rdn.cc:217:2: warning: Struct 'Submembers' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/rdn.cc:135:40: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/rdn.cc:143:40: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/rdn.cc:146:40: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/rdn.cc:246:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/rdn.cc:85:37: style:inconclusive: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/autocomp.h:165:20: note: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'.
spaln-ver3.0.2/src/rdn.cc:85:37: note: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'.
spaln-ver3.0.2/src/rdn.cc:125:51: style: Parameter 'sseq' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/rdn.cc:125:64: style: Parameter 'wt' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/rdn.cc:30:25: style: struct member 'STAT3::amc' is never used. [unusedStructMember]
spaln-ver3.0.2/src/rdn.cc:30:30: style: struct member 'STAT3::tmc' is never used. [unusedStructMember]
spaln-ver3.0.2/src/rdn.cc:30:35: style: struct member 'STAT3::mmc' is never used. [unusedStructMember]
spaln-ver3.0.2/src/rdn.cc:30:40: style: struct member 'STAT3::gap' is never used. [unusedStructMember]
spaln-ver3.0.2/src/rdn.cc:30:45: style: struct member 'STAT3::unp' is never used. [unusedStructMember]
spaln-ver3.0.2/src/rdn.cc:31:21: style: struct member 'HOMSET::sib' is never used. [unusedStructMember]
spaln-ver3.0.2/src/rdn.cc:31:31: style: struct member 'HOMSET::last' is never used. [unusedStructMember]
spaln-ver3.0.2/src/resite.cc:49:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/resite.cc:137:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/resite.cc:78:2: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
spaln-ver3.0.2/src/resite.cc:70:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/resite.cc:80:11: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/resite.cc:83:10: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/resite.cc:107:56: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/resite.cc:120:31: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/resite.cc:145:31: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/resite.cc:130:10: style: The scope of the variable 'res' can be reduced. [variableScope]
spaln-ver3.0.2/src/resite.cc:68:14: style: Local variable 'complcod' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/seq.h:1416:13: note: Shadowed declaration
spaln-ver3.0.2/src/resite.cc:68:14: note: Shadow variable
spaln-ver3.0.2/src/resite.cc:57:34: style: Parameter 'str' can be declared as pointer to const. However it seems that 'cmpf' is a callback function, if 'str' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/resite.cc:107:63: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/resite.cc:57:34: note: Parameter 'str' can be declared as pointer to const
spaln-ver3.0.2/src/resite.cc:66:38: style: Parameter 'src' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/resite.cc:112:23: style: Parameter 'a' can be declared as pointer to const. However it seems that 'icmpf' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/resite.cc:145:38: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/resite.cc:112:23: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/resite.cc:112:31: style: Parameter 'b' can be declared as pointer to const. However it seems that 'icmpf' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/resite.cc:145:38: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/resite.cc:112:31: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/resite.cc:145:8: warning: Uninitialized variable: loc [uninitvar]
spaln-ver3.0.2/src/resite.cc:132:9: note: Assuming condition is false
spaln-ver3.0.2/src/resite.cc:145:8: note: Uninitialized variable: loc
spaln-ver3.0.2/src/seq.cc:161:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbs_dt [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:221:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBSID [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1329:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1342:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1601:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1625:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1708:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1745:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1780:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1791:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/seq.cc:1698:3: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
spaln-ver3.0.2/src/seq.cc:569:6: warning: Member variable 'Seq::jscr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/seq.cc:828:17: debug: CheckClass::isMemberVar found used member variable 'right' with varid 0 [varid0]
spaln-ver3.0.2/src/seq.h:247:8: performance:inconclusive: Technically the member function 'Seq::onecds' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/seq.cc:1288:12: note: Technically the member function 'Seq::onecds' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/seq.h:247:8: note: Technically the member function 'Seq::onecds' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/seq.h:298:13: performance:inconclusive: Technically the member function 'Seq::path2fn' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/seq.cc:618:18: note: Technically the member function 'Seq::path2fn' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/seq.h:298:13: note: Technically the member function 'Seq::path2fn' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/seq.cc:1444:2: warning: Class 'StrPhrases' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/seq.cc:1444:2: warning: Class 'StrPhrases' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/seq.cc:1940:6: style: Condition '!wt' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/seq.cc:1935:14: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/seq.cc:1940:6: note: Condition '!wt' is always true
spaln-ver3.0.2/src/seq.cc:1358:6: error: Mismatching allocation and deallocation: gzfd [mismatchAllocDealloc]
spaln-ver3.0.2/src/seq.cc:1354:20: note: Mismatching allocation and deallocation: gzfd
spaln-ver3.0.2/src/seq.cc:1358:6: note: Mismatching allocation and deallocation: gzfd
spaln-ver3.0.2/src/seq.cc:412:9: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/seq.cc:1258:19: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/seq.cc:1465:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/seq.cc:2015:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/seq.cc:1495:7: style: The scope of the variable 'str' can be reduced. [variableScope]
spaln-ver3.0.2/src/seq.cc:1689:8: style: The scope of the variable 'res' can be reduced. [variableScope]
spaln-ver3.0.2/src/seq.cc:407:42: style:inconclusive: Function 'aliaseq' argument 2 names different: declaration 'thisisalias' definition 'this_is_alias'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:346:38: note: Function 'aliaseq' argument 2 names different: declaration 'thisisalias' definition 'this_is_alias'.
spaln-ver3.0.2/src/seq.cc:407:42: note: Function 'aliaseq' argument 2 names different: declaration 'thisisalias' definition 'this_is_alias'.
spaln-ver3.0.2/src/seq.cc:569:37: style:inconclusive: Function 'Seq' argument 2 names different: declaration 'lenth' definition 'length'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:428:37: note: Function 'Seq' argument 2 names different: declaration 'lenth' definition 'length'.
spaln-ver3.0.2/src/seq.cc:569:37: note: Function 'Seq' argument 2 names different: declaration 'lenth' definition 'length'.
spaln-ver3.0.2/src/seq.cc:702:24: style:inconclusive: Function 'comrev' argument 1 names different: declaration 'sqs' definition 'dest'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:336:20: note: Function 'comrev' argument 1 names different: declaration 'sqs' definition 'dest'.
spaln-ver3.0.2/src/seq.cc:702:24: note: Function 'comrev' argument 1 names different: declaration 'sqs' definition 'dest'.
spaln-ver3.0.2/src/seq.cc:774:32: style:inconclusive: Function 'tron2nuc' argument 1 names different: declaration 'rev' definition 'cmpl'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:356:28: note: Function 'tron2nuc' argument 1 names different: declaration 'rev' definition 'cmpl'.
spaln-ver3.0.2/src/seq.cc:774:32: note: Function 'tron2nuc' argument 1 names different: declaration 'rev' definition 'cmpl'.
spaln-ver3.0.2/src/seq.cc:791:34: style:inconclusive: Function 'setrange' argument 1 names different: declaration 'pa' definition 'attr'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:237:30: note: Function 'setrange' argument 1 names different: declaration 'pa' definition 'attr'.
spaln-ver3.0.2/src/seq.cc:791:34: note: Function 'setrange' argument 1 names different: declaration 'pa' definition 'attr'.
spaln-ver3.0.2/src/seq.cc:1199:51: style:inconclusive: Function 'splice' argument 3 names different: declaration 'edit' definition 'bias'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:307:47: note: Function 'splice' argument 3 names different: declaration 'edit' definition 'bias'.
spaln-ver3.0.2/src/seq.cc:1199:51: note: Function 'splice' argument 3 names different: declaration 'edit' definition 'bias'.
spaln-ver3.0.2/src/seq.cc:1430:36: style:inconclusive: Function 'StrPhrases' argument 1 names different: declaration 'aname' definition 'fname'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:1207:25: note: Function 'StrPhrases' argument 1 names different: declaration 'aname' definition 'fname'.
spaln-ver3.0.2/src/seq.cc:1430:36: note: Function 'StrPhrases' argument 1 names different: declaration 'aname' definition 'fname'.
spaln-ver3.0.2/src/seq.cc:1472:31: style:inconclusive: Function 'setstrand' argument 1 names different: declaration 'id_or_com' definition 'idorcom'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:415:27: note: Function 'setstrand' argument 1 names different: declaration 'id_or_com' definition 'idorcom'.
spaln-ver3.0.2/src/seq.cc:1472:31: note: Function 'setstrand' argument 1 names different: declaration 'id_or_com' definition 'idorcom'.
spaln-ver3.0.2/src/seq.cc:1591:31: style:inconclusive: Function 'estimate_len' argument 1 names different: declaration 'fd' definition 'gzfd'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:242:27: note: Function 'estimate_len' argument 1 names different: declaration 'fd' definition 'gzfd'.
spaln-ver3.0.2/src/seq.cc:1591:31: note: Function 'estimate_len' argument 1 names different: declaration 'fd' definition 'gzfd'.
spaln-ver3.0.2/src/seq.cc:1839:32: style:inconclusive: Function 'composition' argument 1 names different: declaration 'cmps' definition 'cmp'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:394:28: note: Function 'composition' argument 1 names different: declaration 'cmps' definition 'cmp'.
spaln-ver3.0.2/src/seq.cc:1839:32: note: Function 'composition' argument 1 names different: declaration 'cmps' definition 'cmp'.
spaln-ver3.0.2/src/seq.cc:237:9: style: Variable 'qs' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:257:9: style: Variable 'qs' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:482:12: style: Variable 'sd' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/seq.cc:664:12: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:722:17: style: Variable 'lst' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:760:8: style: Variable 'trm' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:935:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:982:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1123:8: style: Variable 's' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1229:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1383:8: style: Variable 'maxa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1384:8: style: Variable 'maxt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1389:8: style: Variable 't' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1448:19: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1500:12: style: Variable 'pl' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1540:40: style: Parameter 'lastseq' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/seq.cc:1557:8: style: Variable 'tab' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1689:8: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1820:8: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1821:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1844:8: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1845:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1935:9: style: Variable 'wt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/seq.cc:1946:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sets.cc:102:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sets.cc:74:24: style:inconclusive: Function 'Subset' argument 1 names different: declaration 'ss' definition 'src'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/sets.h:32:17: note: Function 'Subset' argument 1 names different: declaration 'ss' definition 'src'.
spaln-ver3.0.2/src/sets.cc:74:24: note: Function 'Subset' argument 1 names different: declaration 'ss' definition 'src'.
spaln-ver3.0.2/src/sets.cc:90:20: style:inconclusive: Function 'Subset' argument 1 names different: declaration 'n' definition 'nn'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/sets.h:41:13: note: Function 'Subset' argument 1 names different: declaration 'n' definition 'nn'.
spaln-ver3.0.2/src/sets.cc:90:20: note: Function 'Subset' argument 1 names different: declaration 'n' definition 'nn'.
spaln-ver3.0.2/src/sets.cc:90:36: style:inconclusive: Function 'Subset' argument 2 names different: declaration 'str' definition 'ps'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/sets.h:41:28: note: Function 'Subset' argument 2 names different: declaration 'str' definition 'ps'.
spaln-ver3.0.2/src/sets.cc:90:36: note: Function 'Subset' argument 2 names different: declaration 'str' definition 'ps'.
spaln-ver3.0.2/src/sets.cc:74:24: style: Parameter 'src' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/sets.cc:82:7: style: Variable 'sp' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/simmtx.cc:578:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FPOPUP [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/simmtx.cc:587:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable POPUP [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/simmtx.cc:616:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/simmtx.cc:724:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FQUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/simmtx.cc:101:9: warning: Member variable 'Simmtx::cols' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/simmtx.cc:118:9: warning: Member variable 'Simmtx::cols' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/simmtx.cc:625:61: style: Condition 'opt=='r'' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/simmtx.cc:158:47: style: Same expression on both sides of '&'. [duplicateExpression]
spaln-ver3.0.2/src/simmtx.cc:625:54: style: Same expression 'opt=='r'' found multiple times in chain of '||' operators. [duplicateExpression]
spaln-ver3.0.2/src/simmtx.cc:629:14: style: The scope of the variable 'ps' can be reduced. [variableScope]
spaln-ver3.0.2/src/simmtx.cc:553:26: style:inconclusive: Function 'setpam' argument 2 names different: declaration 'scnd' definition 'mtxno'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/simmtx.h:93:33: note: Function 'setpam' argument 2 names different: declaration 'scnd' definition 'mtxno'.
spaln-ver3.0.2/src/simmtx.cc:553:26: note: Function 'setpam' argument 2 names different: declaration 'scnd' definition 'mtxno'.
spaln-ver3.0.2/src/simmtx.cc:558:16: style:inconclusive: Function 'getpam' argument 1 names different: declaration 'scnd' definition 'mtxno'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/simmtx.h:96:23: note: Function 'getpam' argument 1 names different: declaration 'scnd' definition 'mtxno'.
spaln-ver3.0.2/src/simmtx.cc:558:16: note: Function 'getpam' argument 1 names different: declaration 'scnd' definition 'mtxno'.
spaln-ver3.0.2/src/simmtx.cc:483:30: style: Parameter 'ConvTab' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/simmtx.cc:504:10: style: Variable 'comp' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:71:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sortgrcd.cc:1239:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out_file [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sortgrcd.cc:1013:11: warning: Member variable 'Sortgrcd::nchr' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/sortgrcd.cc:1013:11: warning: Member variable 'Sortgrcd::grcd' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/sortgrcd.cc:1013:11: warning: Member variable 'Sortgrcd::ercd' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/sortgrcd.cc:1013:11: warning: Member variable 'Sortgrcd::chrlist' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/sortgrcd.h:158:6: style:inconclusive: Technically the member function 'Sortgrcd::read_chr_rec' can be const. [functionConst]
spaln-ver3.0.2/src/sortgrcd.cc:844:15: note: Technically the member function 'Sortgrcd::read_chr_rec' can be const.
spaln-ver3.0.2/src/sortgrcd.h:158:6: note: Technically the member function 'Sortgrcd::read_chr_rec' can be const.
spaln-ver3.0.2/src/sortgrcd.h:161:7: style:inconclusive: Technically the member function 'Sortgrcd::printGrcd' can be const. [functionConst]
spaln-ver3.0.2/src/sortgrcd.cc:1119:16: note: Technically the member function 'Sortgrcd::printGrcd' can be const.
spaln-ver3.0.2/src/sortgrcd.h:161:7: note: Technically the member function 'Sortgrcd::printGrcd' can be const.
spaln-ver3.0.2/src/sortgrcd.h:165:7: performance:inconclusive: Technically the member function 'Sortgrcd::print_cds' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/sortgrcd.cc:308:16: note: Technically the member function 'Sortgrcd::print_cds' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/sortgrcd.h:165:7: note: Technically the member function 'Sortgrcd::print_cds' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/sortgrcd.h:166:7: performance:inconclusive: Technically the member function 'Sortgrcd::print_bed' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/sortgrcd.cc:368:16: note: Technically the member function 'Sortgrcd::print_bed' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/sortgrcd.h:166:7: note: Technically the member function 'Sortgrcd::print_bed' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/sortgrcd.h:167:7: style:inconclusive: Technically the member function 'Sortgrcd::Exonform' can be const. [functionConst]
spaln-ver3.0.2/src/sortgrcd.cc:215:16: note: Technically the member function 'Sortgrcd::Exonform' can be const.
spaln-ver3.0.2/src/sortgrcd.h:167:7: note: Technically the member function 'Sortgrcd::Exonform' can be const.
spaln-ver3.0.2/src/sortgrcd.h:168:7: style:inconclusive: Technically the member function 'Sortgrcd::Intronform' can be const. [functionConst]
spaln-ver3.0.2/src/sortgrcd.cc:577:16: note: Technically the member function 'Sortgrcd::Intronform' can be const.
spaln-ver3.0.2/src/sortgrcd.h:168:7: note: Technically the member function 'Sortgrcd::Intronform' can be const.
spaln-ver3.0.2/src/sortgrcd.h:169:7: style:inconclusive: Technically the member function 'Sortgrcd::Gff3form' can be const. [functionConst]
spaln-ver3.0.2/src/sortgrcd.cc:709:16: note: Technically the member function 'Sortgrcd::Gff3form' can be const.
spaln-ver3.0.2/src/sortgrcd.h:169:7: note: Technically the member function 'Sortgrcd::Gff3form' can be const.
spaln-ver3.0.2/src/sortgrcd.h:172:6: style:inconclusive: Technically the member function 'Sortgrcd::nGrcd' can be const. [functionConst]
spaln-ver3.0.2/src/sortgrcd.h:173:6: style:inconclusive: Technically the member function 'Sortgrcd::nErcd' can be const. [functionConst]
spaln-ver3.0.2/src/sortgrcd.cc:107:2: warning: Struct 'Chash' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/sortgrcd.cc:107:2: warning: Struct 'Chash' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/sortgrcd.cc:166:2: warning: Class 'Ehash' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/sortgrcd.cc:166:2: warning: Class 'Ehash' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/sortgrcd.cc:503:2: warning: Class 'Ihash' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/sortgrcd.cc:503:2: warning: Class 'Ihash' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/sortgrcd.h:74:2: style: Struct 'Chash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/sortgrcd.h:93:2: style: Class 'Ehash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/sortgrcd.h:120:2: style: Class 'Ihash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/sortgrcd.cc:242:28: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sortgrcd.cc:283:27: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sortgrcd.cc:611:28: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sortgrcd.cc:674:7: portability: %d in format string (no. 5) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sortgrcd.cc:685:27: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sortgrcd.cc:812:2: warning: Possible leak in public function. The pointer 'ercd' is not deallocated before it is allocated. [publicAllocationError]
spaln-ver3.0.2/src/sortgrcd.cc:573:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sortgrcd.cc:972:9: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sortgrcd.cc:973:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sortgrcd.cc:1045:9: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sortgrcd.cc:1114:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sortgrcd.cc:314:6: style: The scope of the variable 'Glen' can be reduced. [variableScope]
spaln-ver3.0.2/src/sortgrcd.cc:412:20: style: The scope of the variable 'BedHeader' can be reduced. [variableScope]
spaln-ver3.0.2/src/sortgrcd.cc:428:7: style: The scope of the variable 'n_cds' can be reduced. [variableScope]
spaln-ver3.0.2/src/sortgrcd.cc:980:13: style: The scope of the variable 'errmsg' can be reduced. [variableScope]
spaln-ver3.0.2/src/sortgrcd.cc:831:56: style: Checking if unsigned expression 'fread(ewrk,sizeof(ExonRecord),nwrk->ern,gzfe)' is less than zero. [unsignedLessThanZero]
spaln-ver3.0.2/src/sortgrcd.cc:852:55: style: Checking if unsigned expression 'fread(ewrk,sizeof(ExonRecord),gwrk->nexn,fe)' is less than zero. [unsignedLessThanZero]
spaln-ver3.0.2/src/sortgrcd.cc:308:69: style:inconclusive: Function 'print_cds' argument 3 names different: declaration 'rname' definition 'Rname'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/sortgrcd.h:165:60: note: Function 'print_cds' argument 3 names different: declaration 'rname' definition 'Rname'.
spaln-ver3.0.2/src/sortgrcd.cc:308:69: note: Function 'print_cds' argument 3 names different: declaration 'rname' definition 'Rname'.
spaln-ver3.0.2/src/sortgrcd.cc:376:7: style: Variable 'n_exon' can be declared as reference to const [constVariableReference]
spaln-ver3.0.2/src/sortgrcd.cc:42:31: style: Parameter 'a' can be declared as pointer to const. However it seems that 'cmpcif_hit' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/sortgrcd.cc:1112:29: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/sortgrcd.cc:42:31: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/sortgrcd.cc:42:42: style: Parameter 'b' can be declared as pointer to const. However it seems that 'cmpcif_hit' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/sortgrcd.cc:1112:29: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/sortgrcd.cc:42:42: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/sortgrcd.cc:43:31: style: Parameter 'a' can be declared as pointer to const. However it seems that 'cmpcif_did' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/sortgrcd.cc:1110:29: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/sortgrcd.cc:43:31: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/sortgrcd.cc:43:42: style: Parameter 'b' can be declared as pointer to const. However it seems that 'cmpcif_did' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/sortgrcd.cc:1110:29: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/sortgrcd.cc:43:42: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/sortgrcd.cc:115:10: style: Variable 'ht' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:157:10: style: Variable 'hz' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:195:10: style: Variable 'ht' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:286:38: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/sortgrcd.cc:357:27: style: Parameter 'gene' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/sortgrcd.cc:357:40: style: Parameter 'exon' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/sortgrcd.cc:390:9: style: Variable 'txn' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:507:59: style: Parameter 'ewrk' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/sortgrcd.cc:508:13: style: Parameter 'fwrk' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/sortgrcd.cc:508:52: style: Parameter 'intends' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/sortgrcd.cc:543:13: style: Variable 'ht' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:559:30: style: Parameter 'a' can be declared as pointer to const. However it seems that 'icompf' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/sortgrcd.cc:573:50: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/sortgrcd.cc:559:30: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/sortgrcd.cc:559:44: style: Parameter 'b' can be declared as pointer to const. However it seems that 'icompf' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/sortgrcd.cc:573:50: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/sortgrcd.cc:559:44: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/sortgrcd.cc:689:58: style: Parameter 'llocus' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/sortgrcd.cc:692:14: style: Variable 'pwrk' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:776:11: style: Variable 'eif' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:846:8: style: Variable 'ftrm' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:950:11: style: Variable 'hv' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sortgrcd.cc:1309:14: style: Variable 'hz' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/spaln.cc:163:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/spaln.cc:251:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbs_dt [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/spaln.cc:762:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dbs_dt [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/spaln.cc:865:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable supself [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/spaln.cc:1047:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BKA_EXT [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/spaln.cc:1188:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DbsDt [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/spaln.cc:1461:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/spaln.cc:1513:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SC_NPROCESSORS_CONF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/clib.h:467:6: style:inconclusive: Technically the member function 'PrQueue < BlkScr >::find' can be const. [functionConst]
spaln-ver3.0.2/src/clib.h:551:21: note: Technically the member function 'PrQueue < BlkScr >::find' can be const.
spaln-ver3.0.2/src/clib.h:467:6: note: Technically the member function 'PrQueue < BlkScr >::find' can be const.
spaln-ver3.0.2/src/spaln.cc:1200:2: warning: Class 'ThQueue' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/spaln.cc:1200:2: warning: Class 'ThQueue' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/clib.h:602:2: warning: Class 'PrQueue_wh < BlkScr >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/clib.h:602:2: warning: Class 'PrQueue_wh < BlkScr >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/spaln.cc:85:2: style: Class 'ThQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/spaln.cc:379:17: warning: Either the condition 'val=getarg(argc,argv,true)' is redundant or there is possible null pointer dereference: val. [nullPointerRedundantCheck]
spaln-ver3.0.2/src/spaln.cc:377:16: note: Assuming that condition 'val=getarg(argc,argv,true)' is not redundant
spaln-ver3.0.2/src/spaln.cc:379:17: note: Null pointer dereference
spaln-ver3.0.2/src/spaln.cc:580:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:589:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:604:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:609:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:621:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:667:37: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:672:37: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:681:27: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:684:28: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:685:32: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:727:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:728:24: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1043:29: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1134:14: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1141:38: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1161:12: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1277:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1315:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1322:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1340:23: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1341:30: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1373:38: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1390:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1393:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1402:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1408:42: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1410:49: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1417:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1421:45: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1423:50: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1435:18: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1494:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1560:44: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1562:27: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1582:44: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:1584:27: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/spaln.cc:342:8: style: Statements following 'break' will never be executed. [unreachableCode]
spaln-ver3.0.2/src/spaln.cc:258:10: style: The scope of the variable 'k' can be reduced. [variableScope]
spaln-ver3.0.2/src/spaln.cc:1210:29: style:inconclusive: Function 'enqueue' argument 1 names different: declaration 'fsd' definition 'sqs'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/spaln.cc:87:21: note: Function 'enqueue' argument 1 names different: declaration 'fsd' definition 'sqs'.
spaln-ver3.0.2/src/spaln.cc:1210:29: note: Function 'enqueue' argument 1 names different: declaration 'fsd' definition 'sqs'.
spaln-ver3.0.2/src/spaln.cc:1230:29: style:inconclusive: Function 'dequeue' argument 1 names different: declaration 'fsd' definition 'sqs'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/spaln.cc:88:21: note: Function 'dequeue' argument 1 names different: declaration 'fsd' definition 'sqs'.
spaln-ver3.0.2/src/spaln.cc:1230:29: note: Function 'dequeue' argument 1 names different: declaration 'fsd' definition 'sqs'.
spaln-ver3.0.2/src/spaln.cc:1275:32: style:inconclusive: Function 'master_func' argument 1 names different: declaration 'targ' definition 'arg'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/spaln.cc:111:32: note: Function 'master_func' argument 1 names different: declaration 'targ' definition 'arg'.
spaln-ver3.0.2/src/spaln.cc:1275:32: note: Function 'master_func' argument 1 names different: declaration 'targ' definition 'arg'.
spaln-ver3.0.2/src/spaln.cc:1338:32: style:inconclusive: Function 'worker_func' argument 1 names different: declaration 'targ' definition 'arg'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/spaln.cc:113:32: note: Function 'worker_func' argument 1 names different: declaration 'targ' definition 'arg'.
spaln-ver3.0.2/src/spaln.cc:1338:32: note: Function 'worker_func' argument 1 names different: declaration 'targ' definition 'arg'.
spaln-ver3.0.2/src/spaln.cc:798:14: style: Local variable 'gsinf' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/spaln.cc:765:10: note: Shadowed declaration
spaln-ver3.0.2/src/spaln.cc:798:14: note: Shadow variable
spaln-ver3.0.2/src/spaln.cc:954:14: style: Local variable 'gsinf' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/spaln.cc:859:10: note: Shadowed declaration
spaln-ver3.0.2/src/spaln.cc:954:14: note: Shadow variable
spaln-ver3.0.2/src/spaln.cc:1114:41: style: Parameter 'pwd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/spaln.cc:1299:27: style: Parameter 'a' can be declared as pointer to const. However it seems that 'hcmp' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/spaln.cc:1322:62: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/spaln.cc:1299:27: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/spaln.cc:1299:40: style: Parameter 'b' can be declared as pointer to const. However it seems that 'hcmp' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/spaln.cc:1322:62: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/spaln.cc:1299:40: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/spaln.cc:1319:12: style: Variable 'thf' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:80:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:88:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:98:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:122:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:138:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ColorEij [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:464:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EMBL [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:862:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gzipped [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1148:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1237:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1354:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out_file [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1498:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1613:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BlkSz [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1663:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fastanno [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1906:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable taxoncode [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1944:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ColorEij [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:1991:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BlkSz [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:2017:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:2098:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:2179:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:2325:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:2333:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:2413:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable noseqline [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/sqpr.cc:851:2: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
spaln-ver3.0.2/src/sqpr.cc:1940:11: warning: Member variable 'PrintAln::htl' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/sqpr.cc:1940:11: warning: Member variable 'PrintAln::pro' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/sqpr.cc:1940:11: warning: Member variable 'PrintAln::gene' is not initialized in the constructor. [uninitMemberVar]
spaln-ver3.0.2/src/seq.h:246:6: style:inconclusive: Technically the member function 'Seq::calcResNum' can be const. [functionConst]
spaln-ver3.0.2/src/sqpr.cc:1845:10: note: Technically the member function 'Seq::calcResNum' can be const.
spaln-ver3.0.2/src/seq.h:246:6: note: Technically the member function 'Seq::calcResNum' can be const.
spaln-ver3.0.2/src/seq.h:402:6: style:inconclusive: Technically the member function 'Seq::calcnbr' can be const. [functionConst]
spaln-ver3.0.2/src/sqpr.cc:1695:10: note: Technically the member function 'Seq::calcnbr' can be const.
spaln-ver3.0.2/src/seq.h:402:6: note: Technically the member function 'Seq::calcnbr' can be const.
spaln-ver3.0.2/src/seq.h:407:7: style:inconclusive: Technically the member function 'Seq::findGate' can be const. [functionConst]
spaln-ver3.0.2/src/sqpr.cc:1813:11: note: Technically the member function 'Seq::findGate' can be const.
spaln-ver3.0.2/src/seq.h:407:7: note: Technically the member function 'Seq::findGate' can be const.
spaln-ver3.0.2/src/sqpr.cc:1967:2: warning: Class 'PrintAln' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/sqpr.cc:1967:2: warning: Class 'PrintAln' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/sqpr.cc:988:6: portability: %d in format string (no. 18) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sqpr.cc:1381:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sqpr.cc:1909:3: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sqpr.cc:1914:3: portability: %d in format string (no. 1) requires 'int' but the argument type is 'INT {aka unsigned int}'. [invalidPrintfArgType_sint]
spaln-ver3.0.2/src/sqpr.cc:254:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sqpr.cc:1180:26: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sqpr.cc:1603:34: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sqpr.cc:2428:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/sqpr.cc:350:13: style: The scope of the variable 'gftcds' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:351:13: style: The scope of the variable 'eftcds' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:751:20: style: The scope of the variable 'BedHeader' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:1236:6: style: The scope of the variable 'width' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:1353:6: style: The scope of the variable 'slen' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:1484:14: style: The scope of the variable 'msg1' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:1486:14: style: The scope of the variable 'msg2' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:1489:14: style: The scope of the variable 'msg4' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:1707:7: style: The scope of the variable 'str' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:2068:8: style: The scope of the variable 'decode' can be reduced. [variableScope]
spaln-ver3.0.2/src/sqpr.cc:458:55: style:inconclusive: Function 'GBcdsForm' argument 3 names different: declaration 'fd' definition '_fd'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:1456:62: note: Function 'GBcdsForm' argument 3 names different: declaration 'fd' definition '_fd'.
spaln-ver3.0.2/src/sqpr.cc:458:55: note: Function 'GBcdsForm' argument 3 names different: declaration 'fd' definition '_fd'.
spaln-ver3.0.2/src/sqpr.cc:1058:35: style:inconclusive: Function 'CigarForm' argument 1 names different: declaration 'gene' definition 'gen'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:391:28: note: Function 'CigarForm' argument 1 names different: declaration 'gene' definition 'gen'.
spaln-ver3.0.2/src/sqpr.cc:1058:35: note: Function 'CigarForm' argument 1 names different: declaration 'gene' definition 'gen'.
spaln-ver3.0.2/src/sqpr.cc:1078:36: style:inconclusive: Function 'VulgarForm' argument 1 names different: declaration 'gene' definition 'gen'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:392:29: note: Function 'VulgarForm' argument 1 names different: declaration 'gene' definition 'gen'.
spaln-ver3.0.2/src/sqpr.cc:1078:36: note: Function 'VulgarForm' argument 1 names different: declaration 'gene' definition 'gen'.
spaln-ver3.0.2/src/sqpr.cc:1098:33: style:inconclusive: Function 'SamForm' argument 1 names different: declaration 'gene' definition 'gen'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:393:26: note: Function 'SamForm' argument 1 names different: declaration 'gene' definition 'gen'.
spaln-ver3.0.2/src/sqpr.cc:1098:33: note: Function 'SamForm' argument 1 names different: declaration 'gene' definition 'gen'.
spaln-ver3.0.2/src/sqpr.cc:1124:53: style:inconclusive: Function 'repalninf' argument 3 names different: declaration 'fd' definition '_fd'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/gsinfo.h:432:46: note: Function 'repalninf' argument 3 names different: declaration 'fd' definition '_fd'.
spaln-ver3.0.2/src/sqpr.cc:1124:53: note: Function 'repalninf' argument 3 names different: declaration 'fd' definition '_fd'.
spaln-ver3.0.2/src/sqpr.cc:1331:38: style:inconclusive: Function 'getopt' argument 1 names different: declaration 'arg' definition 'val'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/aln.h:312:26: note: Function 'getopt' argument 1 names different: declaration 'arg' definition 'val'.
spaln-ver3.0.2/src/sqpr.cc:1331:38: note: Function 'getopt' argument 1 names different: declaration 'arg' definition 'val'.
spaln-ver3.0.2/src/sqpr.cc:1345:36: style:inconclusive: Function 'setup' argument 1 names different: declaration 'prefix' definition 'spath'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/aln.h:313:24: note: Function 'setup' argument 1 names different: declaration 'prefix' definition 'spath'.
spaln-ver3.0.2/src/sqpr.cc:1345:36: note: Function 'setup' argument 1 names different: declaration 'prefix' definition 'spath'.
spaln-ver3.0.2/src/sqpr.cc:2062:52: style:inconclusive: Function 'prnt_aln' argument 2 names different: declaration 'rght' definition 'right'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/seq.h:1380:46: note: Function 'prnt_aln' argument 2 names different: declaration 'rght' definition 'right'.
spaln-ver3.0.2/src/sqpr.cc:2062:52: note: Function 'prnt_aln' argument 2 names different: declaration 'rght' definition 'right'.
spaln-ver3.0.2/src/sqpr.cc:160:9: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:161:9: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:179:9: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:180:9: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:220:9: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:221:9: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:277:9: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:278:9: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:299:9: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:312:9: style: Variable 'a' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:313:9: style: Variable 'b' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:350:13: style: Variable 'gftcds' can be declared as const array [constVariable]
spaln-ver3.0.2/src/sqpr.cc:351:13: style: Variable 'eftcds' can be declared as const array [constVariable]
spaln-ver3.0.2/src/sqpr.cc:354:13: style: Variable 'emblxx' can be declared as const array [constVariable]
spaln-ver3.0.2/src/sqpr.cc:1150:10: style: Variable 'sm' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:1492:9: style: Variable 'sdb' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:1771:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:1796:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:1824:12: style: Variable 't' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:1837:17: style: Variable 't' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:1849:8: style: Variable 't' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:2031:10: style: Variable 'sm' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:2065:8: style: Variable 'prv' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:2066:8: style: Variable 'brc' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:2075:10: style: Variable 'sd' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:2254:13: style: Variable 'sd' can be declared as pointer to const [constVariableReference]
spaln-ver3.0.2/src/sqpr.cc:2407:12: style: Variable 't' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/sqpr.cc:565:17: style: Variable 'prv' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/sqpr.cc:766:6: style: Variable 'prv' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/sqpr.cc:780:7: style: Variable 'prv' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/sqpr.cc:955:6: style: Variable 'cds' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/supprime.cc:385:20: style: Array index 'm' is used before limits check. [arrayIndexThenCheck]
spaln-ver3.0.2/src/clib.h:300:6: style: Local variable 'u' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/supprime.cc:373:18: note: Shadowed declaration
spaln-ver3.0.2/src/clib.h:300:6: note: Shadow variable
spaln-ver3.0.2/src/clib.h:1058:6: style: Local variable 'u' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/supprime.cc:373:18: note: Shadowed declaration
spaln-ver3.0.2/src/clib.h:1058:6: note: Shadow variable
spaln-ver3.0.2/src/utilseq.cc:134:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utilseq.cc:491:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utilseq.cc:563:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GenBank [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utilseq.cc:597:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeqDBs [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utilseq.cc:694:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utilseq.cc:762:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utilseq.cc:1059:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utilseq.cc:806:9: warning:inconclusive: Member variable 'PatMat::transvers' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
spaln-ver3.0.2/src/utilseq.cc:806:9: warning:inconclusive: Member variable 'PatMat::skip' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
spaln-ver3.0.2/src/utilseq.cc:791:17: warning: Member variable 'PatMat::min_elem' is not assigned a value in 'PatMat::operator='. [operatorEqVarError]
spaln-ver3.0.2/src/utilseq.cc:791:17: warning: Member variable 'PatMat::transvers' is not assigned a value in 'PatMat::operator='. [operatorEqVarError]
spaln-ver3.0.2/src/utilseq.cc:791:17: warning: Member variable 'PatMat::skip' is not assigned a value in 'PatMat::operator='. [operatorEqVarError]
spaln-ver3.0.2/src/utilseq.cc:791:17: warning: Member variable 'PatMat::morder' is not assigned a value in 'PatMat::operator='. [operatorEqVarError]
spaln-ver3.0.2/src/utilseq.cc:791:17: warning: 'operator=' should check for assignment to self to avoid problems with dynamic memory. [operatorEqToSelf]
spaln-ver3.0.2/src/utilseq.h:86:7: style:inconclusive: Technically the member function 'PatMat::increment' can be const. [functionConst]
spaln-ver3.0.2/src/utilseq.cc:882:14: note: Technically the member function 'PatMat::increment' can be const.
spaln-ver3.0.2/src/utilseq.h:86:7: note: Technically the member function 'PatMat::increment' can be const.
spaln-ver3.0.2/src/utilseq.h:105:7: style:inconclusive: Technically the member function 'ExinPot::count_kmers_1' can be const. [functionConst]
spaln-ver3.0.2/src/utilseq.cc:1169:15: note: Technically the member function 'ExinPot::count_kmers_1' can be const.
spaln-ver3.0.2/src/utilseq.h:105:7: note: Technically the member function 'ExinPot::count_kmers_1' can be const.
spaln-ver3.0.2/src/utilseq.h:106:7: style:inconclusive: Technically the member function 'ExinPot::count_kmers_3' can be const. [functionConst]
spaln-ver3.0.2/src/utilseq.cc:1191:15: note: Technically the member function 'ExinPot::count_kmers_3' can be const.
spaln-ver3.0.2/src/utilseq.h:106:7: note: Technically the member function 'ExinPot::count_kmers_3' can be const.
spaln-ver3.0.2/src/utilseq.h:107:7: style:inconclusive: Technically the member function 'ExinPot::reform_1' can be const. [functionConst]
spaln-ver3.0.2/src/utilseq.cc:1254:15: note: Technically the member function 'ExinPot::reform_1' can be const.
spaln-ver3.0.2/src/utilseq.h:107:7: note: Technically the member function 'ExinPot::reform_1' can be const.
spaln-ver3.0.2/src/utilseq.h:108:7: style:inconclusive: Technically the member function 'ExinPot::reform_3' can be const. [functionConst]
spaln-ver3.0.2/src/utilseq.cc:1277:15: note: Technically the member function 'ExinPot::reform_3' can be const.
spaln-ver3.0.2/src/utilseq.h:108:7: note: Technically the member function 'ExinPot::reform_3' can be const.
spaln-ver3.0.2/src/utilseq.cc:1158:10: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
spaln-ver3.0.2/src/utilseq.cc:1370:6: error: Resource leak: fd [resourceLeak]
spaln-ver3.0.2/src/utilseq.cc:1375:6: error: Resource leak: fd [resourceLeak]
spaln-ver3.0.2/src/utilseq.cc:475:9: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utilseq.cc:480:34: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utilseq.cc:896:23: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utilseq.cc:673:8: style: The scope of the variable 'ps' can be reduced. [variableScope]
spaln-ver3.0.2/src/utilseq.cc:914:8: style: The scope of the variable 'minval' can be reduced. [variableScope]
spaln-ver3.0.2/src/utilseq.cc:142:33: style:inconclusive: Function 'codon_id' argument 2 names different: declaration 'byte' definition 'many'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/utilseq.h:184:40: note: Function 'codon_id' argument 2 names different: declaration 'byte' definition 'many'.
spaln-ver3.0.2/src/utilseq.cc:142:33: note: Function 'codon_id' argument 2 names different: declaration 'byte' definition 'many'.
spaln-ver3.0.2/src/utilseq.cc:1302:29: style:inconclusive: Function 'reform' argument 1 names different: declaration 'background' definition 'bkg'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/utilseq.h:149:21: note: Function 'reform' argument 1 names different: declaration 'background' definition 'bkg'.
spaln-ver3.0.2/src/utilseq.cc:1302:29: note: Function 'reform' argument 1 names different: declaration 'background' definition 'bkg'.
spaln-ver3.0.2/src/utilseq.cc:1312:40: style:inconclusive: Function 'makeExinPot' argument 1 names different: declaration 'gfq' definition 'bkg'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/utilseq.h:150:32: note: Function 'makeExinPot' argument 1 names different: declaration 'gfq' definition 'bkg'.
spaln-ver3.0.2/src/utilseq.cc:1312:40: note: Function 'makeExinPot' argument 1 names different: declaration 'gfq' definition 'bkg'.
spaln-ver3.0.2/src/utilseq.cc:740:6: style: Local variable 'skip' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/utilseq.h:68:21: note: Shadowed declaration
spaln-ver3.0.2/src/utilseq.cc:740:6: note: Shadow variable
spaln-ver3.0.2/src/utilseq.cc:502:36: style: Parameter 'orf' can be declared as reference to const [constParameterReference]
spaln-ver3.0.2/src/utilseq.cc:345:23: style: Parameter 'a' can be declared as pointer to const. However it seems that 'lcomp' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/utilseq.cc:480:41: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/utilseq.cc:345:23: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/utilseq.cc:345:31: style: Parameter 'b' can be declared as pointer to const. However it seems that 'lcomp' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/utilseq.cc:480:41: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/utilseq.cc:345:31: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/utilseq.cc:530:52: style: Parameter 'form' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utilseq.cc:675:13: style: Variable 'errmsg' can be declared as const array [constVariable]
spaln-ver3.0.2/src/utilseq.cc:817:62: style: Parameter 'm' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utilseq.cc:913:9: style: Variable 'last' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1091:8: style: Variable 'dot' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1127:12: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1228:11: style: Variable 'sd' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1259:9: style: Variable 'fre' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1283:9: style: Variable 'fre' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1316:9: style: Variable 'frq' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1317:9: style: Variable 'fed' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1372:9: style: Variable 'pot' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utilseq.cc:1425:10: style: Variable 'redctab' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:106:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:224:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:292:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lpw [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:407:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:421:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:1412:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:1491:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SILENT [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:139:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable jobcode [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:209:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable QUERY [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/utn.cc:1447:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in_face [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/autocomp.h:165:7: performance:inconclusive: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/utn.cc:206:24: note: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/autocomp.h:165:7: note: Technically the member function 'AlnServer < Seq >::setparam' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/utn.cc:47:2: style: Class 'Composit' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
spaln-ver3.0.2/src/utn.cc:1400:42: warning: Logical conjunction always evaluates to false: svr->jobcode == 'o' && svr->jobcode == 'O'. [incorrectLogicOperator]
spaln-ver3.0.2/src/utn.cc:674:11: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:667:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:674:11: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:748:8: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:739:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:748:8: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:750:18: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:739:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:750:18: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:796:8: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:784:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:796:8: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:798:18: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:784:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:798:18: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:923:8: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:914:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:920:18: note: Assignment 'w=wt', assigned value is 0
spaln-ver3.0.2/src/utn.cc:920:16: note: w is assigned 'wt' here.
spaln-ver3.0.2/src/utn.cc:923:8: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:925:18: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:914:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:920:18: note: Assignment 'w=wt', assigned value is 0
spaln-ver3.0.2/src/utn.cc:920:16: note: w is assigned 'wt' here.
spaln-ver3.0.2/src/utn.cc:925:18: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:981:8: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:970:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:981:8: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:983:18: style: Condition 'wt' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:970:18: note: Assignment 'wt=0', assigned value is 0
spaln-ver3.0.2/src/utn.cc:983:18: note: Condition 'wt' is always false
spaln-ver3.0.2/src/utn.cc:1400:20: style: Condition '!(svr->jobcode=='o'&&svr->jobcode=='O')' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/utn.cc:1400:35: note: Assuming that condition 'svr->jobcode=='o'' is not redundant
spaln-ver3.0.2/src/utn.cc:1400:20: note: Condition '!(svr->jobcode=='o'&&svr->jobcode=='O')' is always true
spaln-ver3.0.2/src/utn.cc:1269:11: error: Memory leak: nbr [memleak]
spaln-ver3.0.2/src/utn.cc:227:28: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utn.cc:379:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utn.cc:425:12: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utn.cc:1381:17: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utn.cc:1387:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utn.cc:1396:21: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/utn.cc:524:7: style: Redundant initialization for 'orfn'. The initialized value is overwritten before it is read. [redundantInitialization]
spaln-ver3.0.2/src/utn.cc:517:11: note: orfn is initialized
spaln-ver3.0.2/src/utn.cc:524:7: note: orfn is overwritten
spaln-ver3.0.2/src/utn.cc:804:9: style: The scope of the variable 'denom' can be reduced. [variableScope]
spaln-ver3.0.2/src/utn.cc:206:37: style:inconclusive: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/autocomp.h:165:20: note: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'.
spaln-ver3.0.2/src/utn.cc:206:37: note: Function 'setparam' argument 1 names different: declaration 'level' definition 'lvl'.
spaln-ver3.0.2/src/utn.cc:390:12: style: Local variable 'm' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/utn.cc:354:6: note: Shadowed declaration
spaln-ver3.0.2/src/utn.cc:390:12: note: Shadow variable
spaln-ver3.0.2/src/utn.cc:707:10: style: Local variable 'ff' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/utn.cc:682:9: note: Shadowed declaration
spaln-ver3.0.2/src/utn.cc:707:10: note: Shadow variable
spaln-ver3.0.2/src/utn.cc:225:12: style: Variable 'ps' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:232:25: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utn.cc:242:8: style: Variable 'maxa' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:243:8: style: Variable 'maxt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:245:8: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:246:8: style: Variable 't' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:299:36: style: Parameter 'sub' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utn.cc:332:23: style: Parameter 'a' can be declared as pointer to const. However it seems that 'icmpf' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/utn.cc:425:57: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/utn.cc:332:23: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/utn.cc:332:31: style: Parameter 'b' can be declared as pointer to const. However it seems that 'icmpf' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/utn.cc:425:57: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/utn.cc:332:31: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/utn.cc:340:26: style: Parameter 'a' can be declared as pointer to const. However it seems that 'ildcmpf' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/utn.cc:379:55: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/utn.cc:340:26: note: Parameter 'a' can be declared as pointer to const
spaln-ver3.0.2/src/utn.cc:340:35: style: Parameter 'b' can be declared as pointer to const. However it seems that 'ildcmpf' is a callback function, if 'b' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
spaln-ver3.0.2/src/utn.cc:379:55: note: You might need to cast the function pointer here
spaln-ver3.0.2/src/utn.cc:340:35: note: Parameter 'b' can be declared as pointer to const
spaln-ver3.0.2/src/utn.cc:396:12: style: Variable 'u' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:593:30: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utn.cc:664:12: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:665:12: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:672:10: style: Variable 'w' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:737:12: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:781:12: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:858:12: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:901:31: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utn.cc:911:12: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:912:12: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:946:32: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utn.cc:965:12: style: Variable 'ss' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:966:12: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:1045:33: style: Parameter 'sd' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utn.cc:1060:12: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:1109:8: style: Variable 'tt' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:1119:13: style: Variable 'w' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:1266:8: style: Variable 'ts' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/utn.cc:1294:45: style: Parameter 'pat' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utn.cc:1350:36: style: Parameter 'ns' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/utn.cc:385:15: error: Uninitialized struct member: idl.pos [uninitStructMember]
spaln-ver3.0.2/src/utn.cc:879:20: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/utn.cc:925:23: style: Variable 'w' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/utn.cc:1022:32: style: Variable 'RefFreq' is assigned a value that is never used. [unreadVariable]
spaln-ver3.0.2/src/vmf.h:57:7: performance:inconclusive: Technically the member function 'Vmf::vmferror' can be static (but you may consider moving to unnamed namespace). [functionStatic]
spaln-ver3.0.2/src/vmf.cc:118:11: note: Technically the member function 'Vmf::vmferror' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/vmf.h:57:7: note: Technically the member function 'Vmf::vmferror' can be static (but you may consider moving to unnamed namespace).
spaln-ver3.0.2/src/vmf.cc:120:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/vmf.cc:137:13: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/vmf.cc:129:12: error: Uninitialized variable: &sv [uninitvar]
spaln-ver3.0.2/src/wln.cc:1061:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MaxOut [valueFlowBailoutIncompleteVar]
spaln-ver3.0.2/src/wln.h:86:7: style:inconclusive: Technically the member function 'Wilip::shift_y' can be const. [functionConst]
spaln-ver3.0.2/src/wln.cc:995:13: note: Technically the member function 'Wilip::shift_y' can be const.
spaln-ver3.0.2/src/wln.h:86:7: note: Technically the member function 'Wilip::shift_y' can be const.
spaln-ver3.0.2/src/wln.h:192:8: style:inconclusive: Technically the member function 'Wlp::LinkHspScr' can be const. [functionConst]
spaln-ver3.0.2/src/wln.cc:680:12: note: Technically the member function 'Wlp::LinkHspScr' can be const.
spaln-ver3.0.2/src/wln.h:192:8: note: Technically the member function 'Wlp::LinkHspScr' can be const.
spaln-ver3.0.2/src/wln.h:219:7: style:inconclusive: Technically the member function 'Wlprms::initilize' can be const. [functionConst]
spaln-ver3.0.2/src/wln.cc:119:14: note: Technically the member function 'Wlprms::initilize' can be const.
spaln-ver3.0.2/src/wln.h:219:7: note: Technically the member function 'Wlprms::initilize' can be const.
spaln-ver3.0.2/src/wln.cc:229:2: warning: Class 'Wlp' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
spaln-ver3.0.2/src/wln.cc:229:2: warning: Class 'Wlp' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
spaln-ver3.0.2/src/wln.h:182:14: style: Virtual function 'foldseq' is called from constructor 'Wlp(const Seq*seqs[],const PwdB*_pwd,const int level)' at line 230. Dynamic binding is not used. [virtualCallInConstructor]
spaln-ver3.0.2/src/wln.cc:230:13: note: Calling foldseq
spaln-ver3.0.2/src/wln.h:182:14: note: foldseq is a virtual function
spaln-ver3.0.2/src/wln.h:182:14: style: Virtual function 'foldseq' is called from constructor 'Wlp(Seq*seqs[])' at line 239. Dynamic binding is not used. [virtualCallInConstructor]
spaln-ver3.0.2/src/wln.cc:239:13: note: Calling foldseq
spaln-ver3.0.2/src/wln.h:182:14: note: foldseq is a virtual function
spaln-ver3.0.2/src/wln.cc:242:6: style: Condition 'masked' is always false [knownConditionTrueFalse]
spaln-ver3.0.2/src/wln.cc:241:23: note: Calling function 'lowic' returns 0
spaln-ver3.0.2/src/wln.cc:241:23: note: Assignment 'masked=lowic(cnt)', assigned value is 0
spaln-ver3.0.2/src/wln.cc:242:6: note: Condition 'masked' is always false
spaln-ver3.0.2/src/wln.cc:294:9: style: Condition 'nk<=0' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/wln.cc:293:19: note: Assignment 'nk=mm-awspan', assigned value is 0
spaln-ver3.0.2/src/wln.cc:294:9: note: Condition 'nk<=0' is always true
spaln-ver3.0.2/src/wln.cc:378:10: style: Condition 'scr<=0' is always true [knownConditionTrueFalse]
spaln-ver3.0.2/src/wln.cc:360:14: note: Assignment 'scr=0', assigned value is 0
spaln-ver3.0.2/src/wln.cc:378:10: note: Condition 'scr<=0' is always true
spaln-ver3.0.2/src/wln.cc:373:9: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:528:28: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:529:28: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:530:28: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:533:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:813:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:862:16: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:870:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:921:8: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:947:12: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:1016:12: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:1029:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:1032:25: style: C-style pointer casting [cstyleCast]
spaln-ver3.0.2/src/wln.cc:221:9: style: The comparison 'mm <= awspan' is always true because 'mm' and 'awspan' represent the same value. [knownConditionTrueFalse]
spaln-ver3.0.2/src/wln.h:164:16: note: 'mm' is assigned value '0' here.
spaln-ver3.0.2/src/wln.h:170:20: note: 'awspan' is assigned value '0' here.
spaln-ver3.0.2/src/wln.cc:221:9: note: The comparison 'mm <= awspan' is always true because 'mm' and 'awspan' represent the same value.
spaln-ver3.0.2/src/wln.cc:274:9: style: The comparison 'mm <= awspan' is always true because 'mm' and 'awspan' represent the same value. [knownConditionTrueFalse]
spaln-ver3.0.2/src/wln.h:164:16: note: 'mm' is assigned value '0' here.
spaln-ver3.0.2/src/wln.h:170:20: note: 'awspan' is assigned value '0' here.
spaln-ver3.0.2/src/wln.cc:274:9: note: The comparison 'mm <= awspan' is always true because 'mm' and 'awspan' represent the same value.
spaln-ver3.0.2/src/wln.cc:324:23: style: The comparison 'mm <= awspan' is always true because 'mm' and 'awspan' represent the same value. [knownConditionTrueFalse]
spaln-ver3.0.2/src/wln.h:164:16: note: 'mm' is assigned value '0' here.
spaln-ver3.0.2/src/wln.h:170:20: note: 'awspan' is assigned value '0' here.
spaln-ver3.0.2/src/wln.cc:324:23: note: The comparison 'mm <= awspan' is always true because 'mm' and 'awspan' represent the same value.
spaln-ver3.0.2/src/wln.cc:332:6: style: Same expression used in consecutive assignments of 'ml' and 'mr'. [duplicateAssignExpression]
spaln-ver3.0.2/src/wln.cc:333:6: note: Same expression used in consecutive assignments of 'ml' and 'mr'.
spaln-ver3.0.2/src/wln.cc:332:6: note: Same expression used in consecutive assignments of 'ml' and 'mr'.
spaln-ver3.0.2/src/wln.cc:333:6: style: Same expression used in consecutive assignments of 'mr' and 'ms'. [duplicateAssignExpression]
spaln-ver3.0.2/src/wln.cc:334:6: note: Same expression used in consecutive assignments of 'mr' and 'ms'.
spaln-ver3.0.2/src/wln.cc:333:6: note: Same expression used in consecutive assignments of 'mr' and 'ms'.
spaln-ver3.0.2/src/wln.cc:475:33: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:542:34: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:544:45: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:558:39: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:609:28: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:621:35: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:656:28: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:668:39: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:689:5: error: Division by zero. [zerodiv]
spaln-ver3.0.2/src/wln.cc:773:39: style:inconclusive: Function 'jxtcore' argument 2 names different: declaration 'ptop' definition 'jxt'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/wln.h:194:35: note: Function 'jxtcore' argument 2 names different: declaration 'ptop' definition 'jxt'.
spaln-ver3.0.2/src/wln.cc:773:39: note: Function 'jxtcore' argument 2 names different: declaration 'ptop' definition 'jxt'.
spaln-ver3.0.2/src/wln.cc:995:35: style:inconclusive: Function 'shift_y' argument 2 names different: declaration 'rbias' definition 'ylen'. [funcArgNamesDifferent]
spaln-ver3.0.2/src/wln.h:86:29: note: Function 'shift_y' argument 2 names different: declaration 'rbias' definition 'ylen'.
spaln-ver3.0.2/src/wln.cc:995:35: note: Function 'shift_y' argument 2 names different: declaration 'rbias' definition 'ylen'.
spaln-ver3.0.2/src/wln.cc:913:15: style: Local variable 'wlul' shadows outer variable [shadowVariable]
spaln-ver3.0.2/src/wln.cc:863:10: note: Shadowed declaration
spaln-ver3.0.2/src/wln.cc:913:15: note: Shadow variable
spaln-ver3.0.2/src/wln.cc:680:28: style: Parameter 'mcl' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/wln.cc:680:38: style: Parameter 'ncl' can be declared as pointer to const [constParameterPointer]
spaln-ver3.0.2/src/wln.cc:724:11: style: Variable 'mcl' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/wln.cc:779:7: style: Variable 'lcl' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/wln.cc:866:12: style: Variable 'jxtr' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/wln.cc:998:10: style: Variable 'tlu' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/wln.cc:1030:14: style: Variable 'wlu0' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/wln.cc:1033:14: style: Variable 'wlu1' can be declared as pointer to const [constVariablePointer]
spaln-ver3.0.2/src/blksrc.h:230:1: error: The one definition rule is violated, different classes/structs have the same name 'Chash' [ctuOneDefinitionRuleViolation]
spaln-ver3.0.2/src/sortgrcd.h:70:1: note: The one definition rule is violated, different classes/structs have the same name 'Chash'
spaln-ver3.0.2/src/blksrc.h:230:1: note: The one definition rule is violated, different classes/structs have the same name 'Chash'
diff:


DONE