2026-09-01 19:48 ftp://ftp.de.debian.org/debian/pool/main/i/ivar/ivar_1.4.4+dfsg.orig.tar.xz cppcheck-options: --library=posix --library=gnu --library=bsd --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j96 platform: Linux-6.8.0-137-generic-x86_64-with-glibc2.39 python: 3.12.3 client-version: 1.4.0 compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0 cppcheck: head 2.21.0 head-info: 8357500 (2026-08-31 12:14:55 +0200) count: 471 468 elapsed-time: 2.0 0.9 head-timing-info: old-timing-info: head results: ivar-1.4.4/src/get_common_variants.cpp:94:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/interval_tree.cpp:73:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_consensus_min_depth.cpp:45:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_allele_depth.cpp:16:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_consensus_seq_id.cpp:42:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/primer_bed.h:14:3: warning: Member variable 'primer::start' is not initialized. [uninitMemberVarPrivate] ivar-1.4.4/src/primer_bed.h:15:3: warning: Member variable 'primer::end' is not initialized. [uninitMemberVarPrivate] ivar-1.4.4/src/primer_bed.h:18:3: warning: Member variable 'primer::strand' is not initialized. [uninitMemberVarPrivate] ivar-1.4.4/src/primer_bed.h:19:3: warning: Member variable 'primer::pair_indice' is not initialized. [uninitMemberVarPrivate] ivar-1.4.4/src/primer_bed.h:20:3: warning: Member variable 'primer::indice' is not initialized. [uninitMemberVarPrivate] ivar-1.4.4/tests/test_primer_trim_pairs.cpp:81:44: error: Unmatched '{'. Configuration: '__GNUC__=1'. [syntaxError] ivar-1.4.4/src/interval_tree.cpp:51:20: style: The member function 'IntervalTree::envelopSearch' can be static. [functionStatic] ivar-1.4.4/src/interval_tree.h:47:8: note: The member function 'IntervalTree::envelopSearch' can be static. ivar-1.4.4/src/interval_tree.cpp:51:20: note: The member function 'IntervalTree::envelopSearch' can be static. ivar-1.4.4/src/interval_tree.cpp:70:20: style: The member function 'IntervalTree::inOrder' can be static. [functionStatic] ivar-1.4.4/src/interval_tree.h:48:8: note: The member function 'IntervalTree::inOrder' can be static. ivar-1.4.4/src/interval_tree.cpp:70:20: note: The member function 'IntervalTree::inOrder' can be static. ivar-1.4.4/tests/test_interval_tree.cpp:12:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/interval_tree.h:32:9: warning: Class 'ITNode' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] ivar-1.4.4/tests/test_interval_tree.cpp:32:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/interval_tree.h:32:9: warning: Class 'ITNode' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] ivar-1.4.4/src/interval_tree.h:31:3: style: Class 'ITNode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] ivar-1.4.4/tests/test_amplicon_search.cpp:14:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_primer_bed.cpp:23:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/allele_functions.h:11:12: warning: Member variable 'allele::depth' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/allele_functions.h:12:12: warning: Member variable 'allele::reverse' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/allele_functions.h:13:11: warning: Member variable 'allele::mean_qual' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/tests/test_consensus_threshold.cpp:24:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/allele_functions.h:14:12: warning: Member variable 'allele::beg' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/allele_functions.h:15:12: warning: Member variable 'allele::end' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/allele_functions.h:16:9: warning: Member variable 'allele::tmp_mean_qual' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/tests/test_consensus_min_insert_threshold.cpp:21:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/vcf_writer.cpp:55:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/vcf_writer.cpp:79:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/interval_tree.cpp:82:7: style: The scope of the variable 'amplicon_start' can be reduced. [variableScope] ivar-1.4.4/src/interval_tree.cpp:83:7: style: The scope of the variable 'amplicon_end' can be reduced. [variableScope] ivar-1.4.4/src/interval_tree.cpp:51:57: style:inconclusive: Function 'envelopSearch' argument 2 names different: declaration 'data' definition 'i'. [funcArgNamesDifferent] ivar-1.4.4/src/interval_tree.h:47:45: note: Function 'envelopSearch' argument 2 names different: declaration 'data' definition 'i'. ivar-1.4.4/src/interval_tree.cpp:51:57: note: Function 'envelopSearch' argument 2 names different: declaration 'data' definition 'i'. ivar-1.4.4/src/parse_gff.cpp:40:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/interval_tree.cpp:80:45: performance: Function parameter 'pair_info_file' should be passed by const reference. [passedByValue] ivar-1.4.4/src/parse_gff.cpp:45:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/parse_gff.cpp:134:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_consensus_min_depth.cpp:8:40: performance: Function parameter 'input_id' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_consensus_min_depth.cpp:8:62: performance: Function parameter 'prefix' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_consensus_min_depth.cpp:9:40: performance: Function parameter 'cns' should be passed by const reference. [passedByValue] ivar-1.4.4/src/interval_tree.cpp:82:22: style: Variable 'amplicon_start' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/interval_tree.cpp:83:20: style: Variable 'amplicon_end' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/tests/test_ref_seq.cpp:5:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_ref_seq.cpp:39:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/alignment.cpp:67:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/alignment.cpp:109:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_variants_reverse_strand.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_quality_trim.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_variants_reverse_strand.cpp:41:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_quality_trim_unpaired.cpp:24:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/remove_reads_from_amplicon.cpp:11:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_isize_trim.cpp:40:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_variants.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_variants.cpp:66:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_common_variants.cpp:35:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_removereads.cpp:27:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_consensus_seq_id.cpp:24:3: error: Memory leak: o [memleak] ivar-1.4.4/tests/test_allele_depth.cpp:12:12: style: Local variable 'i' shadows outer variable [shadowVariable] ivar-1.4.4/tests/test_allele_depth.cpp:8:30: note: Shadowed variable ivar-1.4.4/tests/test_allele_depth.cpp:12:12: note: Shadow local variable ivar-1.4.4/src/primer_bed.cpp:44:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/primer_bed.cpp:96:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_consensus_seq_id.cpp:21:16: style: Redundant initialization for 'expctd_hdr'. The initialized value is overwritten before it is read. [redundantInitialization] ivar-1.4.4/tests/test_consensus_seq_id.cpp:11:26: note: expctd_hdr is initialized ivar-1.4.4/tests/test_consensus_seq_id.cpp:21:16: note: expctd_hdr is overwritten ivar-1.4.4/src/primer_bed.cpp:172:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_primer_trim_edge_cases.cpp:18:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/primer_bed.cpp:269:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/primer_bed.cpp:306:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/primer_bed.cpp:315:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_consensus_seq_id.cpp:8:40: performance: Function parameter 'seq_id' should be passed by const reference. [passedByValue] ivar-1.4.4/src/vcf_writer.h:10:1: style: The class 'vcf_writer' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor] ivar-1.4.4/src/vcf_writer.h:11:12: warning: Member variable 'vcf_writer::file' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/vcf_writer.h:13:14: warning: Member variable 'vcf_writer::hdr' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/vcf_writer.cpp:65:17: style: Unused private function: 'vcf_writer::write_record' [unusedPrivateFunction] ivar-1.4.4/src/vcf_writer.h:16:7: note: Unused private function: 'vcf_writer::write_record' ivar-1.4.4/src/vcf_writer.cpp:65:17: note: Unused private function: 'vcf_writer::write_record' ivar-1.4.4/tests/test_interval_tree.cpp:8:7: style: The scope of the variable 'result' can be reduced. [variableScope] ivar-1.4.4/src/parse_gff.h:42:3: style: Class 'gff3_feature' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] ivar-1.4.4/src/parse_gff.h:78:3: style: Class 'gff3' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] ivar-1.4.4/src/ref_seq.h:18:3: style: Class 'ref_antd' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] ivar-1.4.4/tests/test_interval_tree.cpp:7:29: style: Parameter 'expected' can be declared as const array [constParameter] ivar-1.4.4/tests/test_trim.cpp:39:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/vcf_writer.cpp:71:3: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn] ivar-1.4.4/tests/test_consensus_seq_id.cpp:33:18: style: Variable 'c_' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/tests/test_ref_seq.cpp:17:3: error: Memory leak: codon [memleak] ivar-1.4.4/src/get_masked_amplicons.cpp:46:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_interval_tree.cpp:8:14: style: Variable 'result' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/tests/test_ref_seq.cpp:20:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:18:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:20:15: note: num_success is overwritten ivar-1.4.4/tests/test_ref_seq.cpp:22:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:20:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:22:15: note: num_success is overwritten ivar-1.4.4/tests/test_ref_seq.cpp:25:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:22:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:25:15: note: num_success is overwritten ivar-1.4.4/tests/test_ref_seq.cpp:27:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:25:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:27:15: note: num_success is overwritten ivar-1.4.4/tests/test_ref_seq.cpp:29:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:27:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:29:15: note: num_success is overwritten ivar-1.4.4/tests/test_ref_seq.cpp:31:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:29:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:31:15: note: num_success is overwritten ivar-1.4.4/tests/test_ref_seq.cpp:34:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:31:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:34:15: note: num_success is overwritten ivar-1.4.4/tests/test_ref_seq.cpp:36:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:34:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:36:15: note: num_success is overwritten ivar-1.4.4/tests/test_ref_seq.cpp:38:15: style: Variable 'num_success' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/tests/test_ref_seq.cpp:36:15: note: num_success is assigned ivar-1.4.4/tests/test_ref_seq.cpp:38:15: note: num_success is overwritten ivar-1.4.4/tests/test_variants.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations] ivar-1.4.4/src/call_consensus.cpp:97:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/vcf_writer.cpp:98:3: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] ivar-1.4.4/src/vcf_writer.cpp:97:33: note: Assuming allocation function fails ivar-1.4.4/src/vcf_writer.cpp:97:20: note: Assignment 'tmpia=(int*)malloc(bcf_hdr_nsamples(h)*2*sizeof(int))', assigned value is 0 ivar-1.4.4/src/vcf_writer.cpp:98:3: note: Null pointer dereference ivar-1.4.4/src/vcf_writer.cpp:99:3: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] ivar-1.4.4/src/vcf_writer.cpp:97:33: note: Assuming allocation function fails ivar-1.4.4/src/vcf_writer.cpp:97:20: note: Assignment 'tmpia=(int*)malloc(bcf_hdr_nsamples(h)*2*sizeof(int))', assigned value is 0 ivar-1.4.4/src/vcf_writer.cpp:99:3: note: Null pointer dereference ivar-1.4.4/tests/test_ref_seq.cpp:3:52: style: Parameter 'codon' can be declared as pointer to const [constParameterPointer] ivar-1.4.4/src/vcf_writer.cpp:101:3: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] ivar-1.4.4/src/vcf_writer.cpp:97:33: note: Assuming allocation function fails ivar-1.4.4/src/vcf_writer.cpp:97:20: note: Assignment 'tmpia=(int*)malloc(bcf_hdr_nsamples(h)*2*sizeof(int))', assigned value is 0 ivar-1.4.4/src/vcf_writer.cpp:101:3: note: Null pointer dereference ivar-1.4.4/src/vcf_writer.cpp:102:3: warning: If memory allocation fails, then there is a possible null pointer dereference: tmpia [nullPointerOutOfMemory] ivar-1.4.4/src/vcf_writer.cpp:97:33: note: Assuming allocation function fails ivar-1.4.4/src/vcf_writer.cpp:97:20: note: Assignment 'tmpia=(int*)malloc(bcf_hdr_nsamples(h)*2*sizeof(int))', assigned value is 0 ivar-1.4.4/src/vcf_writer.cpp:102:3: note: Null pointer dereference ivar-1.4.4/src/vcf_writer.cpp:97:20: style: C-style pointer casting [cstyleCast] ivar-1.4.4/tests/test_variants_reverse_strand.cpp:8:40: performance: Function parameter 'prefix' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_variants_reverse_strand.cpp:10:40: style: Parameter 'out' can be declared as const array [constParameter] ivar-1.4.4/src/vcf_writer.cpp:9:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:6:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:9:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:12:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:9:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:12:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:16:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:12:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:16:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:20:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:16:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:20:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:24:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:20:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:24:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:29:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:24:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:29:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:31:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:29:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:31:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:33:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:31:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:33:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:36:7: style: Variable 'res' is reassigned a value before the old one has been used. [redundantAssignment] ivar-1.4.4/src/vcf_writer.cpp:33:7: note: res is assigned ivar-1.4.4/src/vcf_writer.cpp:36:7: note: res is overwritten ivar-1.4.4/src/vcf_writer.cpp:45:65: style: Argument 'region' shadows outer member [shadowMember] ivar-1.4.4/src/vcf_writer.h:14:15: note: Shadowed member ivar-1.4.4/src/vcf_writer.cpp:45:65: note: Shadow argument ivar-1.4.4/src/vcf_writer.cpp:46:34: style: Argument 'sample_name' shadows outer member [shadowMember] ivar-1.4.4/src/vcf_writer.h:15:15: note: Shadowed member ivar-1.4.4/src/vcf_writer.cpp:46:34: note: Shadow argument ivar-1.4.4/src/vcf_writer.cpp:66:35: style: Argument 'ref' shadows outer member [shadowMember] ivar-1.4.4/src/vcf_writer.h:12:13: note: Shadowed member ivar-1.4.4/src/vcf_writer.cpp:66:35: note: Shadow argument ivar-1.4.4/src/vcf_writer.cpp:45:46: performance: Function parameter 'fname' should be passed by const reference. [passedByValue] ivar-1.4.4/src/vcf_writer.cpp:45:65: performance: Function parameter 'region' should be passed by const reference. [passedByValue] ivar-1.4.4/src/vcf_writer.cpp:46:34: performance: Function parameter 'sample_name' should be passed by const reference. [passedByValue] ivar-1.4.4/src/vcf_writer.cpp:46:59: performance: Function parameter 'ref_path' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_primer_bed.cpp:11:15: style: Variable 'primer_names' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_bed.cpp:15:7: style: Variable 'primer_indices' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_bed.cpp:16:16: style: Variable 'primer_start' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_bed.cpp:17:16: style: Variable 'primer_end' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_bed.cpp:36:7: style: Variable 'pair_indices' can be declared as const array [constVariable] ivar-1.4.4/src/vcf_writer.cpp:79:7: error: Uninitialized variable: res [uninitvar] ivar-1.4.4/src/vcf_writer.cpp:106:7: error: Uninitialized variable: res [legacyUninitvar] ivar-1.4.4/tests/test_variants.cpp:8:40: performance: Function parameter 'prefix' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_variants.cpp:10:40: style: Parameter 'out' can be declared as const array [constParameter] ivar-1.4.4/tests/test_amplicon_search.cpp:20:7: style: The scope of the variable 'res' can be reduced. [variableScope] ivar-1.4.4/tests/test_quality_trim.cpp:18:10: style: The scope of the variable 't' can be reduced. [variableScope] ivar-1.4.4/tests/test_quality_trim_unpaired.cpp:18:10: style: The scope of the variable 't' can be reduced. [variableScope] ivar-1.4.4/tests/test_amplicon_search.cpp:8:38: performance: Function parameter 'bam_file' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_amplicon_search.cpp:8:60: performance: Function parameter 'bed_file' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_amplicon_search.cpp:9:38: performance: Function parameter 'pair_info_file' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_amplicon_search.cpp:10:31: style: Parameter 'expected' can be declared as const array [constParameter] ivar-1.4.4/tests/test_quality_trim.cpp:19:7: style: Variable 'lengths' can be declared as const array [constVariable] ivar-1.4.4/tests/test_quality_trim.cpp:20:7: style: Variable 'start_pos_rev' can be declared as const array [constVariable] ivar-1.4.4/tests/test_quality_trim_unpaired.cpp:19:7: style: Variable 'lengths' can be declared as const array [constVariable] ivar-1.4.4/tests/test_quality_trim_unpaired.cpp:20:7: style: Variable 'start_pos_rev' can be declared as const array [constVariable] ivar-1.4.4/tests/test_quality_trim_unpaired.cpp:21:7: style: Variable 'qual_thresholds' can be declared as const array [constVariable] ivar-1.4.4/src/call_variants.cpp:61:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ref_seq.cpp:180:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ref_seq.cpp:207:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_call_consensus_from_plup.cpp:41:9: style: Unused variable: del_s [unusedVariable] ivar-1.4.4/tests/test_amplicon_search.cpp:20:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/tests/test_amplicon_search.cpp:42:22: style: Variable 'prefix' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/tests/test_amplicon_search.cpp:43:23: style: Variable 'bam_out' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/tests/test_quality_trim.cpp:14:19: style: Variable 'temp' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/tests/test_quality_trim_unpaired.cpp:14:19: style: Variable 'temp' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/get_common_variants.cpp:18:27: style: The scope of the variable 'tab_delimited_key' can be reduced. [variableScope] ivar-1.4.4/src/get_common_variants.cpp:81:66: style: Parameter 'files' can be declared as const array [constParameter] ivar-1.4.4/src/get_common_variants.cpp:132:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/get_common_variants.cpp:20:15: style: Unused variable: region [unusedVariable] ivar-1.4.4/src/get_common_variants.cpp:20:23: style: Unused variable: ref [unusedVariable] ivar-1.4.4/src/get_common_variants.cpp:20:28: style: Unused variable: alt [unusedVariable] ivar-1.4.4/tests/test_removereads.cpp:45:7: warning: Uninitialized variable: w [uninitvar] ivar-1.4.4/tests/test_removereads.cpp:34:38: note: Assuming condition is false ivar-1.4.4/tests/test_removereads.cpp:45:7: note: Uninitialized variable: w ivar-1.4.4/src/parse_gff.cpp:86:27: style:inconclusive: Technically the member function 'gff3_feature::get_type' can be const. [functionConst] ivar-1.4.4/src/parse_gff.h:47:15: note: Technically the member function 'gff3_feature::get_type' can be const. ivar-1.4.4/src/parse_gff.cpp:86:27: note: Technically the member function 'gff3_feature::get_type' can be const. ivar-1.4.4/src/parse_gff.cpp:80:24: style:inconclusive: Technically the member function 'gff3_feature::get_start' can be const. [functionConst] ivar-1.4.4/src/parse_gff.h:48:12: note: Technically the member function 'gff3_feature::get_start' can be const. ivar-1.4.4/src/parse_gff.cpp:80:24: note: Technically the member function 'gff3_feature::get_start' can be const. ivar-1.4.4/src/parse_gff.cpp:82:24: style:inconclusive: Technically the member function 'gff3_feature::get_end' can be const. [functionConst] ivar-1.4.4/src/parse_gff.h:49:12: note: Technically the member function 'gff3_feature::get_end' can be const. ivar-1.4.4/src/parse_gff.cpp:82:24: note: Technically the member function 'gff3_feature::get_end' can be const. ivar-1.4.4/src/parse_gff.cpp:88:20: style:inconclusive: Technically the member function 'gff3_feature::get_strand' can be const. [functionConst] ivar-1.4.4/src/parse_gff.h:50:8: note: Technically the member function 'gff3_feature::get_strand' can be const. ivar-1.4.4/src/parse_gff.cpp:88:20: note: Technically the member function 'gff3_feature::get_strand' can be const. ivar-1.4.4/src/parse_gff.cpp:84:19: style:inconclusive: Technically the member function 'gff3_feature::get_phase' can be const. [functionConst] ivar-1.4.4/src/parse_gff.h:51:7: note: Technically the member function 'gff3_feature::get_phase' can be const. ivar-1.4.4/src/parse_gff.cpp:84:19: note: Technically the member function 'gff3_feature::get_phase' can be const. ivar-1.4.4/src/parse_gff.cpp:122:33: style:inconclusive: Technically the member function 'gff3::get_features' can be const. [functionConst] ivar-1.4.4/src/parse_gff.h:79:29: note: Technically the member function 'gff3::get_features' can be const. ivar-1.4.4/src/parse_gff.cpp:122:33: note: Technically the member function 'gff3::get_features' can be const. ivar-1.4.4/src/parse_gff.cpp:165:11: style:inconclusive: Technically the member function 'gff3::get_count' can be const. [functionConst] ivar-1.4.4/src/parse_gff.h:83:7: note: Technically the member function 'gff3::get_count' can be const. ivar-1.4.4/src/parse_gff.cpp:165:11: note: Technically the member function 'gff3::get_count' can be const. ivar-1.4.4/src/parse_gff.cpp:167:12: style:inconclusive: Technically the member function 'gff3::empty' can be const. [functionConst] ivar-1.4.4/src/parse_gff.h:84:8: note: Technically the member function 'gff3::empty' can be const. ivar-1.4.4/src/parse_gff.cpp:167:12: note: Technically the member function 'gff3::empty' can be const. ivar-1.4.4/src/parse_gff.h:47:15: performance: Function 'get_type()' should return member 'type' by const reference. [returnByReference] ivar-1.4.4/src/parse_gff.h:79:29: performance: Function 'get_features()' should return member 'features' by const reference. [returnByReference] ivar-1.4.4/src/parse_gff.cpp:64:15: style: The scope of the variable 'key' can be reduced. [variableScope] ivar-1.4.4/src/parse_gff.cpp:3:40: performance: Function parameter 'line' should be passed by const reference. [passedByValue] ivar-1.4.4/src/parse_gff.cpp:126:24: performance: Function parameter 'path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/parse_gff.cpp:153:74: performance: Function parameter 'type' should be passed by const reference. [passedByValue] ivar-1.4.4/src/parse_gff.cpp:48:57: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/parse_gff.cpp:93:57: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/parse_gff.cpp:105:57: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/call_consensus_pileup.cpp:172:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/parse_gff.cpp:116:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/parse_gff.cpp:156:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/parse_gff.cpp:139:13: warning: Either the condition 'line.empty()' is redundant or expression 'line[0]' causes access out of bounds. [containerOutOfBounds] ivar-1.4.4/src/parse_gff.cpp:141:19: note: Assuming that condition 'line.empty()' is not redundant ivar-1.4.4/src/parse_gff.cpp:139:13: note: Access out of bounds ivar-1.4.4/src/parse_gff.cpp:94:48: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] ivar-1.4.4/src/parse_gff.cpp:106:48: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] ivar-1.4.4/src/ivar.cpp:51:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:70:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:102:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:127:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:142:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:195:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:212:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:228:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:240:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/ivar.cpp:307:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/allele_functions.cpp:11:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_primer_trim.cpp:19:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/remove_reads_from_amplicon.cpp:56:20: warning:inconclusive: Either the condition 'header==NULL' is redundant or there is possible null pointer dereference: header. [nullPointerRedundantCheck] ivar-1.4.4/src/remove_reads_from_amplicon.cpp:67:14: note: Assuming that condition 'header==NULL' is not redundant ivar-1.4.4/src/remove_reads_from_amplicon.cpp:56:20: note: Null pointer dereference ivar-1.4.4/tests/test_isize_trim.cpp:19:13: style: The scope of the variable 'cigar' can be reduced. [variableScope] ivar-1.4.4/tests/test_unpaired_trim.cpp:19:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/remove_reads_from_amplicon.cpp:75:8: style: The scope of the variable 'w' can be reduced. [variableScope] ivar-1.4.4/tests/test_isize_trim.cpp:15:49: performance: Function parameter 'testname' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_isize_trim.cpp:16:29: style: Parameter 'cigar_flag' can be declared as const array [constParameter] ivar-1.4.4/tests/test_isize_trim.cpp:16:57: style: Parameter 'cigar_len' can be declared as const array [constParameter] ivar-1.4.4/tests/test_isize_trim.cpp:19:13: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] ivar-1.4.4/src/remove_reads_from_amplicon.cpp:3:41: performance: Function parameter 'bam' should be passed by const reference. [passedByValue] ivar-1.4.4/src/remove_reads_from_amplicon.cpp:4:75: performance: Function parameter 'amp' should be passed by const reference. [passedByValue] ivar-1.4.4/src/remove_reads_from_amplicon.cpp:5:41: performance: Function parameter 'bed' should be passed by const reference. [passedByValue] ivar-1.4.4/src/remove_reads_from_amplicon.cpp:58:7: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind] ivar-1.4.4/tests/test_isize_trim.cpp:30:23: style: Variable 'region_' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/primer_bed.cpp:3:21: style:inconclusive: Technically the member function 'primer::get_name' can be const. [functionConst] ivar-1.4.4/src/primer_bed.h:24:15: note: Technically the member function 'primer::get_name' can be const. ivar-1.4.4/src/primer_bed.cpp:3:21: note: Technically the member function 'primer::get_name' can be const. ivar-1.4.4/src/primer_bed.cpp:5:21: style:inconclusive: Technically the member function 'primer::get_region' can be const. [functionConst] ivar-1.4.4/src/primer_bed.h:25:15: note: Technically the member function 'primer::get_region' can be const. ivar-1.4.4/src/primer_bed.cpp:5:21: note: Technically the member function 'primer::get_region' can be const. ivar-1.4.4/src/primer_bed.cpp:7:13: style:inconclusive: Technically the member function 'primer::get_score' can be const. [functionConst] ivar-1.4.4/src/primer_bed.h:26:7: note: Technically the member function 'primer::get_score' can be const. ivar-1.4.4/src/primer_bed.cpp:7:13: note: Technically the member function 'primer::get_score' can be const. ivar-1.4.4/src/primer_bed.cpp:13:14: style:inconclusive: Technically the member function 'primer::get_strand' can be const. [functionConst] ivar-1.4.4/src/primer_bed.h:29:8: note: Technically the member function 'primer::get_strand' can be const. ivar-1.4.4/src/primer_bed.cpp:13:14: note: Technically the member function 'primer::get_strand' can be const. ivar-1.4.4/src/primer_bed.cpp:15:13: style:inconclusive: Technically the member function 'primer::get_length' can be const. [functionConst] ivar-1.4.4/src/primer_bed.h:30:7: note: Technically the member function 'primer::get_length' can be const. ivar-1.4.4/src/primer_bed.cpp:15:13: note: Technically the member function 'primer::get_length' can be const. ivar-1.4.4/src/primer_bed.cpp:17:17: style:inconclusive: Technically the member function 'primer::get_pair_indice' can be const. [functionConst] ivar-1.4.4/src/primer_bed.h:31:11: note: Technically the member function 'primer::get_pair_indice' can be const. ivar-1.4.4/src/primer_bed.cpp:17:17: note: Technically the member function 'primer::get_pair_indice' can be const. ivar-1.4.4/src/primer_bed.h:24:15: performance: Function 'get_name()' should return member 'name' by const reference. [returnByReference] ivar-1.4.4/src/primer_bed.h:25:15: performance: Function 'get_region()' should return member 'region' by const reference. [returnByReference] ivar-1.4.4/src/primer_bed.cpp:257:8: style: Redundant assignment of 'p1' to itself. [selfAssignment] ivar-1.4.4/src/primer_bed.cpp:258:8: style: Redundant assignment of 'p2' to itself. [selfAssignment] ivar-1.4.4/src/primer_bed.cpp:243:27: style: The scope of the variable 'p1' can be reduced. [variableScope] ivar-1.4.4/src/primer_bed.cpp:243:31: style: The scope of the variable 'p2' can be reduced. [variableScope] ivar-1.4.4/src/primer_bed.cpp:314:31: style:inconclusive: Function 'print_primer_info' argument 1 names different: declaration 'primers' definition 'primer'. [funcArgNamesDifferent] ivar-1.4.4/src/primer_bed.h:54:31: note: Function 'print_primer_info' argument 1 names different: declaration 'primers' definition 'primer'. ivar-1.4.4/src/primer_bed.cpp:314:31: note: Function 'print_primer_info' argument 1 names different: declaration 'primers' definition 'primer'. ivar-1.4.4/src/primer_bed.cpp:29:37: performance: Function parameter 'r' should be passed by const reference. [passedByValue] ivar-1.4.4/src/primer_bed.cpp:31:35: performance: Function parameter 'n' should be passed by const reference. [passedByValue] ivar-1.4.4/src/primer_bed.cpp:52:52: performance: Function parameter 'path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/primer_bed.cpp:129:52: performance: Function parameter 'path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/primer_bed.cpp:235:69: performance: Function parameter 'path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/primer_bed.cpp:292:17: performance: Function parameter 'lhs' should be passed by const reference. [passedByValue] ivar-1.4.4/src/primer_bed.cpp:292:29: performance: Function parameter 'rhs' should be passed by const reference. [passedByValue] ivar-1.4.4/src/primer_bed.cpp:299:17: performance: Function parameter 'lhs' should be passed by const reference. [passedByValue] ivar-1.4.4/src/primer_bed.cpp:299:29: performance: Function parameter 'rhs' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:62:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/suffix_tree.cpp:107:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/suffix_tree.cpp:282:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/primer_bed.cpp:289:33: style: Unused variable: it [unusedVariable] ivar-1.4.4/src/alignment.cpp:156:11: error: Array 'h[500][60]' accessed at index h[-1][-1], which is out of bounds. [negativeIndex] ivar-1.4.4/src/alignment.cpp:124:72: note: Assignment 'max_j=0', assigned value is 0 ivar-1.4.4/src/alignment.cpp:133:21: note: Assuming condition is false ivar-1.4.4/src/alignment.cpp:156:11: note: Negative array index ivar-1.4.4/src/alignment.cpp:157:11: error: Array 'h[500][60]' accessed at index h[*][-1], which is out of bounds. [negativeIndex] ivar-1.4.4/src/alignment.cpp:124:72: note: Assignment 'max_j=0', assigned value is 0 ivar-1.4.4/src/alignment.cpp:133:21: note: Assuming condition is false ivar-1.4.4/src/alignment.cpp:157:11: note: Negative array index ivar-1.4.4/src/alignment.cpp:158:11: error: Array 'h[500][60]' accessed at index h[-1][*], which is out of bounds. [negativeIndex] ivar-1.4.4/src/alignment.cpp:124:61: note: Assignment 'max_i=0', assigned value is 0 ivar-1.4.4/src/alignment.cpp:133:21: note: Assuming condition is false ivar-1.4.4/src/alignment.cpp:158:11: note: Negative array index ivar-1.4.4/src/alignment.cpp:113:16: style: Condition 'j==1' is always true [knownConditionTrueFalse] ivar-1.4.4/src/alignment.cpp:111:11: note: Assuming that condition 'j==0' is not redundant ivar-1.4.4/src/alignment.cpp:110:21: note: Assuming that condition 'j<2' is not redundant ivar-1.4.4/src/alignment.cpp:113:16: note: Condition 'j==1' is always true ivar-1.4.4/src/alignment.cpp:152:7: style: The scope of the variable '_t' can be reduced. [variableScope] ivar-1.4.4/tests/test_trim.cpp:9:12: warning: Member variable 'result_t::flag' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/alignment.cpp:152:11: style: The scope of the variable '_l' can be reduced. [variableScope] ivar-1.4.4/tests/test_trim.cpp:10:12: warning: Member variable 'result_t::n_cigar' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/tests/test_trim.cpp:12:11: warning: Member variable 'result_t::fail' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/alignment.cpp:152:15: style: The scope of the variable '_d' can be reduced. [variableScope] ivar-1.4.4/src/alignment.cpp:63:72: performance: Function parameter 'read' should be passed by const reference. [passedByValue] ivar-1.4.4/src/alignment.cpp:64:31: performance: Function parameter 'adap' should be passed by const reference. [passedByValue] ivar-1.4.4/src/alignment.cpp:85:74: performance: Function parameter 'read' should be passed by const reference. [passedByValue] ivar-1.4.4/src/alignment.cpp:86:33: performance: Function parameter 'adap' should be passed by const reference. [passedByValue] ivar-1.4.4/src/alignment.cpp:122:29: performance: Function parameter 'read' should be passed by const reference. [passedByValue] ivar-1.4.4/src/alignment.cpp:122:47: performance: Function parameter 'adap' should be passed by const reference. [passedByValue] ivar-1.4.4/src/alignment.cpp:63:23: style: Parameter 'h' can be declared as const array [constParameter] ivar-1.4.4/src/alignment.cpp:85:25: style: Parameter 'h' can be declared as const array [constParameter] ivar-1.4.4/src/alignment.cpp:108:27: style: Parameter 'a' can be declared as const array [constParameter] ivar-1.4.4/tests/test_trim.cpp:16:69: performance: Function parameter 'testname' should be passed by const reference. [passedByValue] ivar-1.4.4/tests/test_trim.cpp:30:23: style: Variable 'region_' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/tests/test_common_variants.cpp:10:15: style: Variable 'files' can be declared as const array [constVariable] ivar-1.4.4/tests/test_common_variants.cpp:56:16: style: Variable 'count_values' can be declared as const array [constVariable] ivar-1.4.4/tests/test_common_variants.cpp:48:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/tests/test_common_variants.cpp:72:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/get_masked_amplicons.cpp:16:16: style: The scope of the variable 'ctr' can be reduced. [variableScope] ivar-1.4.4/src/get_masked_amplicons.cpp:16:21: style: The scope of the variable 'pos' can be reduced. [variableScope] ivar-1.4.4/src/get_masked_amplicons.cpp:3:45: performance: Function parameter 'bed' should be passed by const reference. [passedByValue] ivar-1.4.4/src/get_masked_amplicons.cpp:3:62: performance: Function parameter 'vpath' should be passed by const reference. [passedByValue] ivar-1.4.4/src/get_masked_amplicons.cpp:4:62: performance: Function parameter 'primer_pair_file' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:35:16: style: The member function 'ref_antd::reverse_complement_codon' can be static. [functionStatic] ivar-1.4.4/src/ref_seq.h:22:8: note: The member function 'ref_antd::reverse_complement_codon' can be static. ivar-1.4.4/src/ref_seq.cpp:35:16: note: The member function 'ref_antd::reverse_complement_codon' can be static. ivar-1.4.4/src/ref_seq.cpp:81:36: style: Condition 'codon_start_pos+i>=edit_pos-1' is always true [knownConditionTrueFalse] ivar-1.4.4/src/ref_seq.cpp:78:36: note: Assuming that condition 'codon_start_pos+i=edit_pos-1' is always true ivar-1.4.4/src/ref_seq.cpp:138:36: style: Condition 'codon_start_pos+i>=edit_pos-1' is always true [knownConditionTrueFalse] ivar-1.4.4/src/ref_seq.cpp:135:29: note: Assuming that condition 'codon_start_pos+i=edit_pos-1' is always true ivar-1.4.4/src/ref_seq.cpp:211:9: style: The scope of the variable 'ref_codon' can be reduced. [variableScope] ivar-1.4.4/src/ref_seq.cpp:211:21: style: The scope of the variable 'alt_codon' can be reduced. [variableScope] ivar-1.4.4/src/ref_seq.cpp:24:50: style: Argument 'region' shadows outer member [shadowMember] ivar-1.4.4/src/ref_seq.h:36:15: note: Shadowed member ivar-1.4.4/src/ref_seq.cpp:24:50: note: Shadow argument ivar-1.4.4/src/ref_seq.cpp:42:52: style: Argument 'region' shadows outer member [shadowMember] ivar-1.4.4/src/ref_seq.h:36:15: note: Shadowed member ivar-1.4.4/src/ref_seq.cpp:42:52: note: Shadow argument ivar-1.4.4/src/ref_seq.cpp:102:52: style: Argument 'region' shadows outer member [shadowMember] ivar-1.4.4/src/ref_seq.h:36:15: note: Shadowed member ivar-1.4.4/src/ref_seq.cpp:102:52: note: Shadow argument ivar-1.4.4/src/ref_seq.cpp:202:43: style: Argument 'region' shadows outer member [shadowMember] ivar-1.4.4/src/ref_seq.h:36:15: note: Shadowed member ivar-1.4.4/src/ref_seq.cpp:202:43: note: Shadow argument ivar-1.4.4/src/ref_seq.cpp:24:50: performance: Function parameter 'region' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:42:52: performance: Function parameter 'region' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:102:52: performance: Function parameter 'region' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:169:35: performance: Function parameter 'path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:175:35: performance: Function parameter 'path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:186:32: performance: Function parameter 'ref_path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:191:32: performance: Function parameter 'ref_path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:191:54: performance: Function parameter 'gff_path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:202:43: performance: Function parameter 'region' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ref_seq.cpp:203:51: style: Parameter 'line_stream' can be declared as reference to const [constParameterReference] ivar-1.4.4/src/ref_seq.cpp:212:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/call_variants.cpp:62:7: style: The scope of the variable 'ctr' can be reduced. [variableScope] ivar-1.4.4/src/call_variants.cpp:68:8: style: The scope of the variable 'ref' can be reduced. [variableScope] ivar-1.4.4/src/call_variants.cpp:15:12: performance: Function parameter 'a' should be passed by const reference. [passedByValue] ivar-1.4.4/src/call_variants.cpp:34:61: performance: Function parameter 'ref_path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/call_variants.cpp:35:41: performance: Function parameter 'gff_path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/call_variants.cpp:5:67: style: Parameter 'ad' can be declared as reference to const [constParameterReference] ivar-1.4.4/src/allele_functions.cpp:54:8: style: The scope of the variable 'beg' can be reduced. [variableScope] ivar-1.4.4/src/allele_functions.cpp:54:13: style: The scope of the variable 'end' can be reduced. [variableScope] ivar-1.4.4/src/allele_functions.cpp:74:12: style: The scope of the variable 'tmp' can be reduced. [variableScope] ivar-1.4.4/src/call_variants.cpp:8:28: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] ivar-1.4.4/src/call_variants.cpp:131:20: error: Uninitialized variables: a.beg, a.end, a.tmp_mean_qual [uninitvar] ivar-1.4.4/src/allele_functions.cpp:10:46: performance: Function parameter 'ad' should be passed by const reference. [passedByValue] ivar-1.4.4/src/allele_functions.cpp:23:37: performance: Function parameter 'n' should be passed by const reference. [passedByValue] ivar-1.4.4/src/allele_functions.cpp:23:60: performance: Function parameter 'ad' should be passed by const reference. [passedByValue] ivar-1.4.4/src/allele_functions.cpp:33:44: performance: Function parameter 'ad' should be passed by const reference. [passedByValue] ivar-1.4.4/src/allele_functions.cpp:44:63: performance: Function parameter 'bases' should be passed by const reference. [passedByValue] ivar-1.4.4/src/call_variants.cpp:131:20: error: Uninitialized struct member: a.beg [uninitStructMember] ivar-1.4.4/src/allele_functions.cpp:45:53: performance: Function parameter 'qualities' should be passed by const reference. [passedByValue] ivar-1.4.4/src/call_variants.cpp:131:20: error: Uninitialized struct member: a.end [uninitStructMember] ivar-1.4.4/src/call_variants.cpp:131:20: error: Uninitialized struct member: a.tmp_mean_qual [uninitStructMember] ivar-1.4.4/src/call_variants.cpp:62:11: style: Variable 'ctr' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/allele_functions.cpp:38:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/allele_functions.cpp:25:34: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] ivar-1.4.4/tests/test_primer_trim.cpp:38:7: style: Variable 'primer_indices' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_trim.cpp:39:11: style: Variable 'cigar_flag' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_trim.cpp:49:12: style: Variable 'cigar_len' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_trim.cpp:54:12: style: Variable 'read_start_pos' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_trim.cpp:57:11: style: Variable 'condense_cigar_flag' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_trim.cpp:65:12: style: Variable 'condense_cigar_len' can be declared as const array [constVariable] ivar-1.4.4/tests/test_primer_trim.cpp:70:16: style: Variable 'overlapping_primer_sizes' can be declared as const array [constVariable] ivar-1.4.4/src/trim_primer_quality.cpp:143:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CSOFT_CLIP [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/trim_primer_quality.cpp:171:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/trim_primer_quality.cpp:195:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/trim_primer_quality.cpp:333:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/src/trim_primer_quality.cpp:557:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] ivar-1.4.4/tests/test_unpaired_trim.cpp:36:13: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer] ivar-1.4.4/tests/test_unpaired_trim.cpp:38:7: style: Variable 'forward_primer_indices' can be declared as const array [constVariable] ivar-1.4.4/tests/test_unpaired_trim.cpp:39:7: style: Variable 'rev_primer_indices' can be declared as const array [constVariable] ivar-1.4.4/tests/test_unpaired_trim.cpp:40:11: style: Variable 'cigar_flag' can be declared as const array [constVariable] ivar-1.4.4/tests/test_unpaired_trim.cpp:52:12: style: Variable 'cigar_len' can be declared as const array [constVariable] ivar-1.4.4/tests/test_unpaired_trim.cpp:58:12: style: Variable 'read_start_pos' can be declared as const array [constVariable] ivar-1.4.4/tests/test_unpaired_trim.cpp:59:11: style: Variable 'condense_cigar_flag' can be declared as const array [constVariable] ivar-1.4.4/tests/test_unpaired_trim.cpp:69:12: style: Variable 'condense_cigar_len' can be declared as const array [constVariable] ivar-1.4.4/tests/test_unpaired_trim.cpp:75:16: style: Variable 'fwd_overlapping_primer_sizes' can be declared as const array [constVariable] ivar-1.4.4/tests/test_unpaired_trim.cpp:76:16: style: Variable 'rev_overlapping_primer_sizes' can be declared as const array [constVariable] ivar-1.4.4/src/call_consensus.cpp:93:3: warning: If memory allocation fails, then there is a possible null pointer dereference: nuc [nullPointerOutOfMemory] ivar-1.4.4/src/call_consensus.cpp:163:35: note: Assuming allocation function fails ivar-1.4.4/src/call_consensus.cpp:163:21: note: Assignment 'nuc=(char*)malloc(30*sizeof(char))', assigned value is 0 ivar-1.4.4/src/call_consensus.cpp:164:51: note: Calling function 'get_consensus_indel', 3rd argument 'nuc' value is 0 ivar-1.4.4/src/call_consensus.cpp:72:21: note: Assuming condition is false ivar-1.4.4/src/call_consensus.cpp:93:3: note: Null pointer dereference ivar-1.4.4/src/call_consensus.cpp:89:13: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:125:17: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:137:19: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:141:15: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:144:15: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:147:15: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:150:15: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:163:21: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:168:21: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/call_consensus.cpp:71:8: style: The scope of the variable 'n' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus.cpp:99:15: style: The scope of the variable 'region_' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus.cpp:123:32: style: The scope of the variable 's' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus.cpp:123:35: style: The scope of the variable 'd' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus.cpp:125:61: style: The scope of the variable 'r' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus.cpp:180:24: style: Local variable 'i' shadows outer variable [shadowVariable] ivar-1.4.4/src/call_consensus.cpp:135:16: note: Shadowed variable ivar-1.4.4/src/call_consensus.cpp:180:24: note: Shadow local variable ivar-1.4.4/src/call_consensus.cpp:125:61: style: Variable 'r' can be declared as pointer to const [constVariablePointer] ivar-1.4.4/src/call_consensus.cpp:141:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer] ivar-1.4.4/src/call_consensus.cpp:144:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer] ivar-1.4.4/src/call_consensus.cpp:147:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer] ivar-1.4.4/src/call_consensus.cpp:150:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer] ivar-1.4.4/src/call_consensus.cpp:67:13: style: Variable 'q' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/suffix_tree.cpp:19:19: style:inconclusive: Technically the member function 'suffix_node::is_leaf_node' can be const. [functionConst] ivar-1.4.4/src/suffix_tree.h:19:8: note: Technically the member function 'suffix_node::is_leaf_node' can be const. ivar-1.4.4/src/suffix_tree.cpp:19:19: note: Technically the member function 'suffix_node::is_leaf_node' can be const. ivar-1.4.4/src/suffix_tree.cpp:21:19: style:inconclusive: Technically the member function 'suffix_node::contains_child' can be const. [functionConst] ivar-1.4.4/src/suffix_tree.h:20:8: note: Technically the member function 'suffix_node::contains_child' can be const. ivar-1.4.4/src/suffix_tree.cpp:21:19: note: Technically the member function 'suffix_node::contains_child' can be const. ivar-1.4.4/src/suffix_tree.cpp:25:18: style:inconclusive: Technically the member function 'suffix_node::get_length' can be const. [functionConst] ivar-1.4.4/src/suffix_tree.h:21:7: note: Technically the member function 'suffix_node::get_length' can be const. ivar-1.4.4/src/suffix_tree.cpp:25:18: note: Technically the member function 'suffix_node::get_length' can be const. ivar-1.4.4/src/suffix_tree.cpp:78:26: style:inconclusive: Technically the member function 'suffix_node::get_path' can be const. [functionConst] ivar-1.4.4/src/suffix_tree.h:24:15: note: Technically the member function 'suffix_node::get_path' can be const. ivar-1.4.4/src/suffix_tree.cpp:78:26: note: Technically the member function 'suffix_node::get_path' can be const. ivar-1.4.4/src/suffix_tree.cpp:10:9: warning: Class 'suffix_node' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor] ivar-1.4.4/src/suffix_tree.cpp:10:9: warning: Class 'suffix_node' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq] ivar-1.4.4/src/suffix_tree.h:17:17: style: Class 'suffix_node' is unsafe, 'suffix_node::children' can leak by wrong usage. [unsafeClassCanLeak] ivar-1.4.4/src/suffix_tree.cpp:269:23: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/suffix_tree.cpp:53:15: style: The scope of the variable 'str' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:138:34: style: The scope of the variable 'new_node' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:263:19: style: The scope of the variable 'l2' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:263:37: style: The scope of the variable 's' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:263:40: style: The scope of the variable 'cmn' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:263:45: style: The scope of the variable 'trmd_read' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:264:24: style: The scope of the variable 'beg' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:265:16: style: The scope of the variable 'pos' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:271:22: style: The scope of the variable 'adp_pos' can be reduced. [variableScope] ivar-1.4.4/src/suffix_tree.cpp:40:38: performance: Function parameter 's1' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:40:54: performance: Function parameter 's2' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:51:67: performance: Function parameter 's1' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:52:67: performance: Function parameter 's2' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:78:47: performance: Function parameter 's' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:105:37: performance: Function parameter 's' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:229:63: performance: Function parameter 'p' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:240:65: performance: Function parameter 'l' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:241:48: performance: Function parameter 'adp' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:261:30: performance: Function parameter 'f1' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:261:46: performance: Function parameter 'f2' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:261:62: performance: Function parameter 'adp_path' should be passed by const reference. [passedByValue] ivar-1.4.4/src/suffix_tree.cpp:32:16: style: Variable 'n' can be declared as pointer to const [constVariablePointer] ivar-1.4.4/src/suffix_tree.cpp:336:12: error: Memory is allocated but not initialized: t [uninitdata] ivar-1.4.4/src/suffix_tree.cpp:335:10: error: Memory is allocated but not initialized: root [uninitdata] ivar-1.4.4/src/suffix_tree.cpp:138:43: style: Variable 'new_node' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/suffix_tree.cpp:138:62: style: Variable 'new_cur_node' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/suffix_tree.cpp:170:22: style: Variable 'new_node' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/suffix_tree.cpp:263:30: style: Unused variable: l2_rc [unusedVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:35:8: style: The scope of the variable 'n' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:36:23: style: The scope of the variable 'max_depth' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:36:38: style: The scope of the variable 'tmp_depth' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:37:33: style: The scope of the variable 'gap_depth' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:39:23: style: The scope of the variable 'ctr' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:40:10: style: The scope of the variable 'q' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:40:17: style: The scope of the variable 'tq' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:177:7: style: The scope of the variable 'ctr' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:180:8: style: The scope of the variable 'ref' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:221:11: style: The scope of the variable 't' can be reduced. [variableScope] ivar-1.4.4/src/call_consensus_pileup.cpp:42:38: style: Local variable 'it' shadows outer variable [shadowVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:41:33: note: Shadowed variable ivar-1.4.4/src/call_consensus_pileup.cpp:42:38: note: Shadow local variable ivar-1.4.4/src/call_consensus_pileup.cpp:160:61: performance: Function parameter 'seq_id' should be passed by const reference. [passedByValue] ivar-1.4.4/src/call_consensus_pileup.cpp:68:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/call_consensus_pileup.cpp:72:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/call_consensus_pileup.cpp:85:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/call_consensus_pileup.cpp:104:7: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/call_consensus_pileup.cpp:117:7: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/call_consensus_pileup.cpp:134:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] ivar-1.4.4/src/call_consensus_pileup.cpp:93:25: warning: Uninitialized variables: tmp_a.beg, tmp_a.end, tmp_a.tmp_mean_qual [uninitvar] ivar-1.4.4/src/call_consensus_pileup.cpp:93:25: error: Uninitialized struct member: tmp_a.beg [uninitStructMember] ivar-1.4.4/src/call_consensus_pileup.cpp:93:25: error: Uninitialized struct member: tmp_a.end [uninitStructMember] ivar-1.4.4/src/call_consensus_pileup.cpp:93:25: error: Uninitialized struct member: tmp_a.tmp_mean_qual [uninitStructMember] ivar-1.4.4/src/call_consensus_pileup.cpp:36:33: style: Variable 'max_depth' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:36:48: style: Variable 'tmp_depth' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:37:43: style: Variable 'gap_depth' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:39:27: style: Variable 'ctr' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:40:12: style: Variable 'q' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:40:20: style: Variable 'tq' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:32:15: style: Variable 'cnuc' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/call_consensus_pileup.cpp:177:11: style: Variable 'ctr' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/ivar.cpp:30:11: warning: Member variable 'args_t::min_qual' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:31:11: warning: Member variable 'args_t::sliding_window' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:32:10: warning: Member variable 'args_t::min_threshold' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:33:10: warning: Member variable 'args_t::min_insert_threshold' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:34:7: warning: Member variable 'args_t::min_length' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:38:12: warning: Member variable 'args_t::min_depth' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:39:8: warning: Member variable 'args_t::gap' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:40:8: warning: Member variable 'args_t::keep_min_coverage' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:42:11: warning: Member variable 'args_t::primer_offset' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:44:8: warning: Member variable 'args_t::write_no_primers_flag' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:46:8: warning: Member variable 'args_t::keep_for_reanalysis' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:47:8: warning: Member variable 'args_t::gapped_depth' has no initializer. [uninitMemberVarNoCtor] ivar-1.4.4/src/ivar.cpp:593:20: style: C-style pointer casting [cstyleCast] ivar-1.4.4/src/ivar.cpp:585:23: style: The scope of the variable 'ctr' can be reduced. [variableScope] ivar-1.4.4/src/ivar.cpp:253:56: performance: Function parameter 'f' should be passed by const reference. [passedByValue] ivar-1.4.4/src/ivar.cpp:288:11: style: Variable 'opt' is assigned a value that is never used. [unreadVariable] ivar-1.4.4/src/trim_primer_quality.cpp:144:26: style: Condition 'del_len=n' is not redundant ivar-1.4.4/src/trim_primer_quality.cpp:144:26: note: Condition 'del_len=n' is not redundant ivar-1.4.4/src/trim_primer_quality.cpp:256:26: note: Condition 'del_len