2025-07-25 20:44
ftp://ftp.de.debian.org/debian/pool/main/d/dindel/dindel_1.01-wu1-3+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=boost  --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 -j6
platform: Linux-6.1.0-37-amd64-x86_64-with-glibc2.36
python: 3.11.2
client-version: 1.3.67
compiler: g++ (Debian 12.2.0-14+deb12u1) 12.2.0
cppcheck: head 2.18.0
head-info: 55e2dc6 (2025-07-24 17:37:42 +0200)
count: 658 658
elapsed-time: 9.6 9.9
head-timing-info:

old-timing-info:

head results:
dindel-tgi-1.01-wu1-3/Variant.hpp:68:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:104:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:136:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SNP [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/MLAlignment.hpp:74:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:212:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:354:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:382:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:27:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:64:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:98:102: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:178:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortFunc [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Faster.cpp:191:0: debug: Function::addArguments found argument 'hash' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/Faster.cpp:131:0: debug: Function::addArguments found argument 'hash' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:152:19: debug: Scope::checkVariable found variable 'begin_' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:153:19: debug: Scope::checkVariable found variable 'end_' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:163:15: debug: Scope::checkVariable found variable 'row_' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:165:15: debug: Scope::checkVariable found variable 'begin1_' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:166:15: debug: Scope::checkVariable found variable 'end1_' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:198:11: debug: Scope::checkVariable found variable 'it' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:240:11: debug: Scope::checkVariable found variable 'it' with varid 0. [varid0]
dindel-tgi-1.01-wu1-3/Variant.hpp:33:2: warning:inconclusive: Member variable 'Variant::type' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:33:2: warning:inconclusive: Member variable 'Variant::length' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::startHap' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::endHap' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::startRead' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::endRead' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::leftFlankHap' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::rightFlankHap' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::leftFlankRead' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::rightFlankRead' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::freq' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Variant.hpp:81:2: warning:inconclusive: Member variable 'AlignedVariant::addComb' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MLAlignment.hpp:35:2: warning: Member variable 'MLAlignment::firstBase' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MLAlignment.hpp:35:2: warning: Member variable 'MLAlignment::lastBase' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MLAlignment.hpp:35:2: warning: Member variable 'MLAlignment::nBQT' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MLAlignment.hpp:35:2: warning: Member variable 'MLAlignment::nmmBQT' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MLAlignment.hpp:35:2: warning: Member variable 'MLAlignment::mLogBQ' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MLAlignment.hpp:35:2: warning: Member variable 'MLAlignment::nMMLeft' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MLAlignment.hpp:35:2: warning: Member variable 'MLAlignment::nMMRight' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:318:2: warning: Member variable 'HapHash::hap_ptr' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:89:3: performance: Variable 'seq' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:121:3: performance: Variable 'seq' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:130:3: performance: Variable 'seq' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:135:3: performance: Variable 'indel' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:136:3: performance: Variable 'align' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:138:3: performance: Variable 'snps' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:139:3: performance: Variable 'indels' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:140:3: performance: Variable 'ml' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:352:7: performance:inconclusive: Technically the member function 'HapHash::print' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:364:13: performance:inconclusive: Technically the member function 'HapHash::map_char' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:380:7: style:inconclusive: Technically the member function 'HapHash::makeHash' can be const. [functionConst]
dindel-tgi-1.01-wu1-3/Variant.hpp:34:2: style: Class 'Variant' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:111:2: style: Class 'Haplotype' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:225:7: style: Condition 'addVariant' is always true [knownConditionTrueFalse]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:209:19: note: Assignment 'addVariant=true', assigned value is 1
dindel-tgi-1.01-wu1-3/Haplotype.hpp:225:7: note: Condition 'addVariant' is always true
dindel-tgi-1.01-wu1-3/Haplotype.hpp:226:8: style: Same expression used in consecutive assignments of 'readStart' and 'readEnd'. [duplicateAssignExpression]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:227:8: note: Same expression used in consecutive assignments of 'readStart' and 'readEnd'.
dindel-tgi-1.01-wu1-3/Haplotype.hpp:226:8: note: Same expression used in consecutive assignments of 'readStart' and 'readEnd'.
dindel-tgi-1.01-wu1-3/HapBlock.cpp:32:7: style: The scope of the variable 'found' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:59:38: style:inconclusive: Function 'HapBlock' argument 1 names different: declaration 'seq' definition 'h'. [funcArgNamesDifferent]
dindel-tgi-1.01-wu1-3/HapBlock.hpp:35:29: note: Function 'HapBlock' argument 1 names different: declaration 'seq' definition 'h'.
dindel-tgi-1.01-wu1-3/HapBlock.cpp:59:38: note: Function 'HapBlock' argument 1 names different: declaration 'seq' definition 'h'.
dindel-tgi-1.01-wu1-3/HapBlock.cpp:119:17: style: Local variable 'length' shadows outer function [shadowFunction]
dindel-tgi-1.01-wu1-3/HapBlock.hpp:40:11: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/HapBlock.cpp:119:17: note: Shadow variable
dindel-tgi-1.01-wu1-3/Haplotype.hpp:258:86: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:267:69: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:76:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:32:12: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:35:41: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:222:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:257:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:266:82: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Haplotype.hpp:353:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:33:92: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:75:80: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:78:80: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:88:92: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:102:92: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:109:80: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HapBlock.cpp:172:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:156:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:208:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dec [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:175:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:318:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:477:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:53:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:76:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FMUNMAP [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:227:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Library.hpp:54:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Library.hpp:70:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Library.hpp:124:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Library.hpp:172:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Library.hpp:246:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:140:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_rev_table [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:200:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:201:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FMUNMAP [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:202:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FMREVERSE [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:203:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:204:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:275:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:358:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:384:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FDUP [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Read.hpp:410:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModel.hpp:68:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:51:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Faster.cpp:86:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Faster.cpp:146:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Faster.cpp:193:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Faster.cpp:259:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Faster.cpp:763:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:152:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:333:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:74:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:129:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:223:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INS [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:272:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:353:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:414:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:98:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:108:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:283:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tid [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:716:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:734:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:757:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:766:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:897:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1008:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1081:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1558:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1720:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1780:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Utils.hpp:33:13: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
dindel-tgi-1.01-wu1-3/Utils.hpp:36:13: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
dindel-tgi-1.01-wu1-3/Library.hpp:39:2: warning:inconclusive: Member variable 'Library::modeInsertSize' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Library.hpp:39:2: warning:inconclusive: Member variable 'Library::maxins' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Library.hpp:39:2: warning:inconclusive: Member variable 'Library::ninetyfifth_pct_prob' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MyBam.hpp:36:2: warning: Member variable 'MyBam::bh' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/MyBam.hpp:36:2: warning: Member variable 'MyBam::idx' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Read.hpp:58:2: warning: Member variable 'Read::mapQual' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Read.hpp:58:2: warning: Member variable 'Read::bamHeader' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Read.hpp:58:2: warning: Member variable 'Read::bam' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Read.hpp:62:2: warning: Member variable 'Read::mapQual' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Read.hpp:62:2: warning: Member variable 'Read::bamHeader' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Read.hpp:62:2: warning: Member variable 'Read::bam' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::llMatch' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::bMid' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::hlen' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::rlen' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::llOff' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::llOffHMQ' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::pOffFirst' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::pOffFirstHMQ' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::hap_ptr' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::read_ptr' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::hapStart' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::likelihoodComputed' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/Faster.hpp:66:2: warning:inconclusive: Member variable 'ObservationModelS::bMidError' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModel.hpp:32:4: performance: Variable 'modelType' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/ObservationModel.hpp:66:8: style:inconclusive: Technically the member function 'ObservationModelParameters::print' can be const. [functionConst]
dindel-tgi-1.01-wu1-3/Library.hpp:42:2: style: Class 'Library' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/Library.hpp:50:2: style: Class 'Library' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/MyBam.hpp:37:2: style: Class 'MyBam' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/Read.hpp:62:2: style: Class 'Read' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/ObservationModel.hpp:35:3: style: Class 'ObservationModelParameters' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/Faster.cpp:360:16: style: Expression is always true because 'else if' condition is opposite to previous condition at line 356. [multiCondition]
dindel-tgi-1.01-wu1-3/Faster.cpp:356:9: note: first condition
dindel-tgi-1.01-wu1-3/Faster.cpp:360:16: note: else if condition is opposite to first condition
dindel-tgi-1.01-wu1-3/Read.hpp:388:6: style: Exception should be caught by reference. [catchExceptionByValue]
dindel-tgi-1.01-wu1-3/Read.hpp:143:35: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/Read.hpp:178:14: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/Read.hpp:382:22: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/Read.hpp:188:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
dindel-tgi-1.01-wu1-3/Read.hpp:248:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
dindel-tgi-1.01-wu1-3/Read.hpp:249:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
dindel-tgi-1.01-wu1-3/Read.hpp:250:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
dindel-tgi-1.01-wu1-3/Read.hpp:251:44: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
dindel-tgi-1.01-wu1-3/Read.hpp:252:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
dindel-tgi-1.01-wu1-3/Read.hpp:252:43: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
dindel-tgi-1.01-wu1-3/Faster.cpp:637:10: style:inconclusive: Same expression used in consecutive assignments of 'hapStart' and 'hapEnd'. [duplicateAssignExpression]
dindel-tgi-1.01-wu1-3/Faster.cpp:638:10: note: Same expression used in consecutive assignments of 'hapStart' and 'hapEnd'.
dindel-tgi-1.01-wu1-3/Faster.cpp:637:10: note: Same expression used in consecutive assignments of 'hapStart' and 'hapEnd'.
dindel-tgi-1.01-wu1-3/Library.hpp:176:9: style: Redundant initialization for 'it'. The initialized value is overwritten before it is read. [redundantInitialization]
dindel-tgi-1.01-wu1-3/Library.hpp:175:43: note: it is initialized
dindel-tgi-1.01-wu1-3/Library.hpp:176:9: note: it is overwritten
dindel-tgi-1.01-wu1-3/Library.hpp:225:6: style: Redundant initialization for 'it'. The initialized value is overwritten before it is read. [redundantInitialization]
dindel-tgi-1.01-wu1-3/Library.hpp:224:40: note: it is initialized
dindel-tgi-1.01-wu1-3/Library.hpp:225:6: note: it is overwritten
dindel-tgi-1.01-wu1-3/Faster.cpp:399:4: style: Variable 'ns' is assigned an expression that holds the same value. [redundantAssignment]
dindel-tgi-1.01-wu1-3/Faster.cpp:398:11: note: ics is assigned 'cs+S' here.
dindel-tgi-1.01-wu1-3/Faster.cpp:399:4: note: Variable 'ns' is assigned an expression that holds the same value.
dindel-tgi-1.01-wu1-3/Faster.cpp:67:11: style: The scope of the variable 'olStart' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/Faster.cpp:67:20: style: The scope of the variable 'olEnd' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/Faster.cpp:68:6: style: The scope of the variable 'mid' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/Faster.cpp:406:13: style: Local variable 'ns' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/Faster.cpp:388:8: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/Faster.cpp:406:13: note: Shadow variable
dindel-tgi-1.01-wu1-3/Faster.cpp:455:13: style: Local variable 'ns' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/Faster.cpp:440:8: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/Faster.cpp:455:13: note: Shadow variable
dindel-tgi-1.01-wu1-3/Faster.cpp:560:8: style: Local variable 'hp' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/Faster.cpp:490:6: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/Faster.cpp:560:8: note: Shadow variable
dindel-tgi-1.01-wu1-3/Faster.cpp:617:9: style: Local variable 'hapStart' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/Faster.hpp:96:9: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/Faster.cpp:617:9: note: Shadow variable
dindel-tgi-1.01-wu1-3/Faster.cpp:637:10: style: Local variable 'hapStart' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/Faster.hpp:96:9: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/Faster.cpp:637:10: note: Shadow variable
dindel-tgi-1.01-wu1-3/Faster.cpp:655:11: style: Local variable 'hapStart' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/Faster.hpp:96:9: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/Faster.cpp:655:11: note: Shadow variable
dindel-tgi-1.01-wu1-3/Read.hpp:264:13: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/OutputData.hpp:63:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/OutputData.hpp:106:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:295:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:58:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:101:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:202:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:236:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:294:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:337:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:347:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable h1 [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:373:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:404:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:699:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:751:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:898:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1337:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1514:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1555:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1720:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offHapHMQ [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1757:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1812:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hash [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1867:159: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1951:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numIndels [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2129:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ll [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2953:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ll [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3690:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ll [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3772:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3902:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dec [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:4029:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
dindel-tgi-1.01-wu1-3/Faster.cpp:454:7: style: Variable 'ics' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/Library.hpp:247:80: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Faster.cpp:161:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Faster.cpp:174:91: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Faster.cpp:671:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Faster.cpp:675:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Faster.cpp:747:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/Faster.cpp:766:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:162:8: style: Boolean value assigned to floating point variable. [assignBoolToFloat]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:41:2: warning: Member variable 'AlignedCandidates::centerPos' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:41:2: warning: Member variable 'AlignedCandidates::leftPos' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:41:2: warning: Member variable 'AlignedCandidates::rightPos' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:76:2: warning: Member variable 'HDHapBlock::start' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:76:2: warning: Member variable 'HDHapBlock::end' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:76:2: warning: Member variable 'HDHapBlock::type' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:43:3: performance: Variable 'tid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:47:3: performance: Variable 'tid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:48:3: performance: Variable 'variants' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:82:4: performance: Variable 'tid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:88:4: performance: Variable 'tid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:91:4: performance: Variable 'variants' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:92:4: performance: Variable 'freqs' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:198:29: performance:inconclusive: Technically the member function 'HaplotypeDistribution::updateBlock' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:57:7: note: Technically the member function 'HaplotypeDistribution::updateBlock' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:198:29: note: Technically the member function 'HaplotypeDistribution::updateBlock' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/VariantFile.hpp:103:2: style: Class 'VariantFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:54:17: performance: Function 'getIndelsAtMidPos()' should return member 'indelsAtMidPos' by const reference. [returnByReference]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:229:9: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:227:11: note: outer condition: !is.eof()
dindel-tgi-1.01-wu1-3/VariantFile.hpp:229:9: note: identical inner condition: !is.eof()
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:480:8: style: The if condition is the same as the previous if condition [duplicateCondition]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:476:8: note: First condition
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:480:8: note: Second condition
dindel-tgi-1.01-wu1-3/VariantFile.hpp:175:17: style: Condition '!error' is always true [knownConditionTrueFalse]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:175:7: note: Assuming that condition 'error' is not redundant
dindel-tgi-1.01-wu1-3/VariantFile.hpp:175:17: note: Condition '!error' is always true
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:301:10: style: Condition 'lenB==0' is always false [knownConditionTrueFalse]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:293:16: note: Assuming that condition 'seq.size()==0' is not redundant
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:297:28: note: Assuming condition is false
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:300:24: note: Assignment 'lenB=seq.size()', assigned value is greater than 0
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:301:10: note: Condition 'lenB==0' is always false
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:309:7: style: Condition 'lenB' is always true [knownConditionTrueFalse]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:301:10: note: Assuming that condition 'lenB==0' is not redundant
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:309:7: note: Condition 'lenB' is always true
dindel-tgi-1.01-wu1-3/VariantFile.hpp:155:5: style: Exception should be caught by reference. [catchExceptionByValue]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:276:5: style: Exception should be caught by reference. [catchExceptionByValue]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:70:4: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:137:3: style: Statements following 'throw' will never be executed. [unreachableCode]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:192:12: style: The scope of the variable 'pos' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:253:12: style: The scope of the variable 'changed' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:282:14: style: The scope of the variable 'nuc' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:355:8: style: The scope of the variable 'found' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:299:11: style: The scope of the variable 'lenA' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:255:15: style: Local variable 'col' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:224:10: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/VariantFile.hpp:255:15: note: Shadow variable
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:300:3: style: Local variable 'hap' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:489:12: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:300:3: note: Shadow variable
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:305:3: style: Local variable 'hap' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:489:12: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:305:3: note: Shadow variable
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:468:15: style: Local variable 'x' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:410:10: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:468:15: note: Shadow variable
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:96:11: style: Local variable 'len' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:63:11: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:96:11: note: Shadow variable
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:176:4: performance: Range variable 'var' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:245:4: performance: Range variable 'var' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:305:3: performance: Range variable 'hap' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:255:15: style: Variable 'col' can be declared as reference to const [constVariableReference]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:296:13: style: Variable 'block' can be declared as reference to const [constVariableReference]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:88:12: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/VariantFile.hpp:61:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:306:9: style: Consider using std::copy algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:344:45: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:419:9: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:447:108: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:456:10: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:223:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:226:50: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:451:5: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:476:5: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:129:28: warning: Uninitialized variable: idx [uninitvar]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:126:21: note: Assuming condition is false
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:129:28: note: Uninitialized variable: idx
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:355:13: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:365:10: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:166:91: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:341:93: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:343:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:359:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:368:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:435:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.hpp:447:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:59:93: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:189:80: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:222:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:449:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:465:96: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:474:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/HaplotypeDistribution.cpp:485:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:826:72: style:inconclusive: Boolean expression 'maxIdx[bMid]!=0' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:152:20: warning: Invalid std::log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:129:17: note: Assignment 'logLikelihood=0.0', assigned value is 0.0
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:138:16: note: Assuming condition is false
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:152:20: note: Invalid argument
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:153:27: warning: Invalid std::log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:130:24: note: Assignment 'logLikelihoodNoPrior=0.0', assigned value is 0.0
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:138:16: note: Assuming condition is false
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:153:27: note: Invalid argument
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::logLikelihood' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::logLikelihoodNoPrior' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::obsInitialized' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::memAllocated' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::HMMInitialized' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::HMMConsistent' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::likelihoodComputed' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::forwardDone' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::backwardDone' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::marginalsComputed' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::makeObsVector' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::obsVector' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::hapSize' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::readSize' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::ROState' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::bMid' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::hapStart' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::numT' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::numS' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::logpLOgLO' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::logpFirstgLO' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::logpInsgIns' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::logpInsgNoIns' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::logpNoInsgNoIns' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:30:2: warning:inconclusive: Member variable 'ObservationModelFB::logpNoInsgIns' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::logLikelihood' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::logLikelihoodNoPrior' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::obsVector' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::hapSize' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::readSize' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::ROState' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::numT' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::numS' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::logpLOgLO' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::logpFirstgLO' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::logpInsgIns' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::logpInsgNoIns' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::logpNoInsgNoIns' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:21: warning: Member variable 'ObservationModelFB::logpNoInsgIns' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/ReadIndelErrorModel.hpp:31:3: performance: Variable 'baselineProbs' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:318:26: performance:inconclusive: Technically the member function 'ObservationModelFB::getObsVector' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:35:7: note: Technically the member function 'ObservationModelFB::getObsVector' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:318:26: note: Technically the member function 'ObservationModelFB::getObsVector' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:388:26: style:inconclusive: Technically the member function 'ObservationModelFB::passMessageOneInc' can be const. [functionConst]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:62:7: note: Technically the member function 'ObservationModelFB::passMessageOneInc' can be const.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:388:26: note: Technically the member function 'ObservationModelFB::passMessageOneInc' can be const.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:432:26: style:inconclusive: Technically the member function 'ObservationModelFB::passMessageOneDec' can be const. [functionConst]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:63:7: note: Technically the member function 'ObservationModelFB::passMessageOneDec' can be const.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:432:26: note: Technically the member function 'ObservationModelFB::passMessageOneDec' can be const.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:711:26: style:inconclusive: Technically the member function 'ObservationModelFB::printMarginalsInt' can be const. [functionConst]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:70:7: note: Technically the member function 'ObservationModelFB::printMarginalsInt' can be const.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:711:26: note: Technically the member function 'ObservationModelFB::printMarginalsInt' can be const.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:630:26: performance:inconclusive: Technically the member function 'ObservationModelFB::_badValue' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:72:7: note: Technically the member function 'ObservationModelFB::_badValue' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:630:26: note: Technically the member function 'ObservationModelFB::_badValue' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:128:7: performance:inconclusive: Technically the member function 'ObservationModelFBMax::printMarginals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:129:7: performance:inconclusive: Technically the member function 'ObservationModelFBMax::computeMarginals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:130:7: performance:inconclusive: Technically the member function 'ObservationModelFBMax::computeXMarginals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:877:36: performance:inconclusive: Technically the member function 'ObservationModelFBMax::updateMax' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:151:14: note: Technically the member function 'ObservationModelFBMax::updateMax' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:877:36: note: Technically the member function 'ObservationModelFBMax::updateMax' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/ReadIndelErrorModel.hpp:36:9: style:inconclusive: Technically the member function 'ReadIndelErrorModel::getViterbiHPError' can be const. [functionConst]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:52:15: style: Virtual function 'Init' is called from constructor 'ObservationModelFB(const Haplotype&_hap,const Read&r,uint32_t hapStart,const ObservationModelParameters&params)' at line 31. Dynamic binding is not used. [virtualCallInConstructor]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:31:2: note: Calling Init
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:52:15: note: Init is a virtual function
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:59:15: style: Virtual function 'deleteMemory' is called from destructor '~ObservationModelFB()' at line 864. Dynamic binding is not used. [virtualCallInConstructor]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:864:2: note: Calling deleteMemory
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:59:15: note: deleteMemory is a virtual function
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:128:7: warning: The class 'ObservationModelFBMax' defines member function with name 'printMarginals' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:732:26: note: Parent function 'ObservationModelFB::printMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:128:7: note: Derived function 'ObservationModelFBMax::printMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:129:7: warning: The class 'ObservationModelFBMax' defines member function with name 'computeMarginals' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:648:26: note: Parent function 'ObservationModelFB::computeMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:129:7: note: Derived function 'ObservationModelFBMax::computeMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:130:7: warning: The class 'ObservationModelFBMax' defines member function with name 'computeXMarginals' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:693:26: note: Parent function 'ObservationModelFB::computeXMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:130:7: note: Derived function 'ObservationModelFBMax::computeXMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1477:29: warning: The class 'ObservationModelFBMax' defines member function with name 'printAlignment' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:761:26: note: Parent function 'ObservationModelFB::printAlignment'
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1477:29: note: Derived function 'ObservationModelFBMax::printAlignment'
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1068:36: warning: The class 'ObservationModelFBMax' defines member function with name 'calcLikelihood' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:171:33: note: Parent function 'ObservationModelFB::calcLikelihood'
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1068:36: note: Derived function 'ObservationModelFBMax::calcLikelihood'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:140:7: warning: The class 'ObservationModelFBMax' defines member function with name 'passMessageOneInc' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:388:26: note: Parent function 'ObservationModelFB::passMessageOneInc'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:140:7: note: Derived function 'ObservationModelFBMax::passMessageOneInc'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:141:7: warning: The class 'ObservationModelFBMax' defines member function with name 'passMessageOneDec' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:432:26: note: Parent function 'ObservationModelFB::passMessageOneDec'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:141:7: note: Derived function 'ObservationModelFBMax::passMessageOneDec'
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1583:29: warning: The class 'ObservationModelFBMax' defines member function with name 'computeBackwardMessages' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:609:26: note: Parent function 'ObservationModelFB::computeBackwardMessages'
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1583:29: note: Derived function 'ObservationModelFBMax::computeBackwardMessages'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:137:3: style: The destructor '~ObservationModelFBMax' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:31:11: note: Virtual destructor in base class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:137:3: note: Destructor in derived class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:144:7: style: The function 'allocateMemory' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:58:15: note: Virtual function in base class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:144:7: note: Function in derived class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:145:7: style: The function 'deleteMemory' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:59:15: note: Virtual function in base class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:145:7: note: Function in derived class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:147:7: style: The function 'computeForwardMessages' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:67:15: note: Virtual function in base class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:147:7: note: Function in derived class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:149:7: style: The function 'calcLikelihoodFromLastSlice' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:69:15: note: Virtual function in base class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:149:7: note: Function in derived class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:163:7: style: The function 'setupTransitionProbs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:55:15: note: Virtual function in base class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:163:7: note: Function in derived class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:164:7: style: The function 'passMessageTwoInc' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:142:15: note: Virtual function in base class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:164:7: note: Function in derived class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:165:7: style: The function 'passMessageTwoDec' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:143:15: note: Virtual function in base class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:165:7: note: Function in derived class
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:48:17: performance: Function 'getOffHapLik()' should return member 'likOffHap' by const reference. [returnByReference]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:826:72: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1417:10: style:inconclusive: Same expression used in consecutive assignments of 'hapStart' and 'hapEnd'. [duplicateAssignExpression]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1418:10: note: Same expression used in consecutive assignments of 'hapStart' and 'hapEnd'.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1417:10: note: Same expression used in consecutive assignments of 'hapStart' and 'hapEnd'.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:125:2: style: Statements following 'throw' will never be executed. [unreachableCode]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:54:11: style: The scope of the variable 'olStart' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:54:20: style: The scope of the variable 'olEnd' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:55:6: style: The scope of the variable 'mid' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:223:6: style: The scope of the variable 'b' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:134: style:inconclusive: Function 'ObservationModelFB' argument 4 names different: declaration 'params' definition '_params'. [funcArgNamesDifferent]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:120:115: note: Function 'ObservationModelFB' argument 4 names different: declaration 'params' definition '_params'.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:28:134: note: Function 'ObservationModelFB' argument 4 names different: declaration 'params' definition '_params'.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:867:140: style:inconclusive: Function 'ObservationModelFBMax' argument 4 names different: declaration 'params' definition '_params'. [funcArgNamesDifferent]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:134:118: note: Function 'ObservationModelFBMax' argument 4 names different: declaration 'params' definition '_params'.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:867:140: note: Function 'ObservationModelFBMax' argument 4 names different: declaration 'params' definition '_params'.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1631:146: style:inconclusive: Function 'ObservationModelFBMaxErr' argument 4 names different: declaration 'params' definition '_params'. [funcArgNamesDifferent]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:160:121: note: Function 'ObservationModelFBMaxErr' argument 4 names different: declaration 'params' definition '_params'.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1631:146: note: Function 'ObservationModelFBMaxErr' argument 4 names different: declaration 'params' definition '_params'.
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:141:10: style: Local variable 'mar' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:99:18: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:141:10: note: Shadow variable
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1754:11: style: Local variable 'x' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1750:6: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1754:11: note: Shadow variable
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1763:11: style: Local variable 'x' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1750:6: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1763:11: note: Shadow variable
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:126:10: style: Variable 'alpha_l' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:127:10: style: Variable 'beta_l' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:128:10: style: Variable 'obs_l' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:318:54: style: Parameter 'vec' can be declared as pointer to const [constParameterPointer]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:698:11: style: Variable '_mar' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:774:11: style: Variable 'm' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1078:10: style: Variable 'alpha_l' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1079:10: style: Variable 'beta_l' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1080:10: style: Variable 'obs_l' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ReadIndelErrorModel.hpp:30:10: style: Variable 'hp' can be declared as const array [constVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:203:31: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1661:31: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:781:13: warning: Uninitialized variable: idx [uninitvar]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:776:17: note: Assuming condition is false
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:781:13: note: Uninitialized variable: idx
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:775:13: style: Variable 'entropy[b]' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:777:14: style: Variable 'entropy[b]' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:780:10: style: Variable 'maxP[b]' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:785:12: style: Variable 'obsLik[b]' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:786:25: style: Variable 'obsLik[b]' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1465:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1469:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1542:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/ObservationModelFB.cpp:1561:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:309:3: performance: Variable 'score' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:313:3: performance: Variable 'params' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:68:4: performance: Variable 'seq' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:39:7: performance:inconclusive: Technically the member function 'Realign::getFlankingCoordinatesBetter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:260:30: performance:inconclusive: Technically the member function 'GetCandidatesFromCIGAR::realignCandidateFile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:90:7: note: Technically the member function 'GetCandidatesFromCIGAR::realignCandidateFile' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:260:30: note: Technically the member function 'GetCandidatesFromCIGAR::realignCandidateFile' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:305:30: performance:inconclusive: Technically the member function 'GetCandidatesFromCIGAR::outputLibraries' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:103:7: note: Technically the member function 'GetCandidatesFromCIGAR::outputLibraries' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:305:30: note: Technically the member function 'GetCandidatesFromCIGAR::outputLibraries' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/Fasta.hpp:38:2: style: Class 'Fasta' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:37:2: style: Class 'GetCandidates' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:93:3: style: The destructor '~GetCandidatesFromCIGAR' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:45:11: note: Virtual destructor in base class
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:93:3: note: Destructor in derived class
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:128:4: style: Exception should be caught by reference. [catchExceptionByValue]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:142:4: style: Exception should be caught by reference. [catchExceptionByValue]
dindel-tgi-1.01-wu1-3/Fasta.hpp:51:9: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:39:21: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:448:36: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:216:10: style: Redundant initialization for 'it'. The initialized value is overwritten before it is read. [redundantInitialization]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:199:56: note: it is initialized
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:216:10: note: it is overwritten
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:86:11: style: The scope of the variable 'newiseq' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:98:9: style: The scope of the variable 'eq' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:113:9: style: The scope of the variable 'eq' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:70:6: style: The scope of the variable 'lastop' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:387:49: style:inconclusive: Function 'get' argument 1 names different: declaration 'bamFile' definition '_bamFile'. [funcArgNamesDifferent]
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:92:26: note: Function 'get' argument 1 names different: declaration 'bamFile' definition '_bamFile'.
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:387:49: note: Function 'get' argument 1 names different: declaration 'bamFile' definition '_bamFile'.
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:183:8: style: Local variable 'pos' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:155:6: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:183:8: note: Shadow variable
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:231:64: style: Local variable 'it' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:199:54: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:231:64: note: Shadow variable
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:39:42: performance: Function parameter 'tid' should be passed by const reference. [passedByValue]
dindel-tgi-1.01-wu1-3/GetCandidates.hpp:64:61: performance: Function parameter '_seq' should be passed by const reference. [passedByValue]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:223:4: performance: Range variable 'aid' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:289:4: performance: Range variable 'var' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:67:12: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:57:15: style: Variable 'newpos' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:63:13: style: Variable 'newpos' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:72:13: style: Variable 'newpos' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:93:15: style: Variable 'newpos' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:98:12: style: Variable 'eq' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:101:9: style: Variable 'eq' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:102:13: style: Variable 'newpos' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:103:14: style: Variable 'newiseq' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:113:11: style: Variable 'eq' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:116:8: style: Variable 'eq' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:117:13: style: Variable 'newpos' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:70:12: style: Variable 'lastop' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:71:18: style: Variable 'lastPos' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:95:10: style: Variable 'lastPos' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:99:9: style: Variable 'lastop' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:116:27: style: Unused variable: alIndel [unusedVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:116:36: style: Unused variable: alSNP [unusedVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:178:10: style: Unused variable: align [unusedVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:276:20: style: Unused variable: variants [unusedVariable]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:329:11: style: Variable 'pct' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:353:91: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/ObservationModelSeqAn.hpp:357:87: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:181:89: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:216:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:217:88: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:231:105: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:237:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:242:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:312:76: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:323:62: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:333:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:345:62: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:349:62: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/GetCandidates.cpp:358:62: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.hpp:179:3: warning: Member variable 'InDel::type' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:192:3: warning: Member variable 'Parameters::maxHapReadProd' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:192:3: warning: Member variable 'Parameters::checkBaseQualThreshold' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:192:3: warning: Member variable 'Parameters::scaleErr' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:192:3: warning: Member variable 'Parameters::alignAgainstReference' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:192:3: warning: Member variable 'Parameters::varFileIsOneBased' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:192:3: warning: Member variable 'Parameters::meanInsert' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:192:3: warning: Member variable 'Parameters::stdInsert' is not initialized in the constructor. [uninitMemberVar]
dindel-tgi-1.01-wu1-3/DInDel.hpp:100:5: performance: Variable 'av' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/DInDel.hpp:194:4: performance: Variable 'tid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/DInDel.hpp:195:4: performance: Variable 'fileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
dindel-tgi-1.01-wu1-3/DInDel.cpp:363:16: performance:inconclusive: Technically the member function 'DetInDel::outputHapsAndFreqs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:126:7: note: Technically the member function 'DetInDel::outputHapsAndFreqs' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:363:16: note: Technically the member function 'DetInDel::outputHapsAndFreqs' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:290:18: performance:inconclusive: Technically the member function 'DetInDel::getMaxHap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:130:9: note: Technically the member function 'DetInDel::getMaxHap' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:290:18: note: Technically the member function 'DetInDel::getMaxHap' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:342:16: performance:inconclusive: Technically the member function 'DetInDel::outputTopHaps' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:132:7: note: Technically the member function 'DetInDel::outputTopHaps' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:342:16: note: Technically the member function 'DetInDel::outputTopHaps' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:1742:16: performance:inconclusive: Technically the member function 'DetInDel::computeHapPosition' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:138:7: note: Technically the member function 'DetInDel::computeHapPosition' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:1742:16: note: Technically the member function 'DetInDel::computeHapPosition' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:3855:16: performance:inconclusive: Technically the member function 'DetInDel::statisticsHaplotypePair' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:142:7: note: Technically the member function 'DetInDel::statisticsHaplotypePair' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:3855:16: note: Technically the member function 'DetInDel::statisticsHaplotypePair' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:3665:16: style:inconclusive: Technically the member function 'DetInDel::estimateHaplotypeFrequencies' can be const. [functionConst]
dindel-tgi-1.01-wu1-3/DInDel.hpp:144:7: note: Technically the member function 'DetInDel::estimateHaplotypeFrequencies' can be const.
dindel-tgi-1.01-wu1-3/DInDel.cpp:3665:16: note: Technically the member function 'DetInDel::estimateHaplotypeFrequencies' can be const.
dindel-tgi-1.01-wu1-3/DInDel.cpp:670:16: performance:inconclusive: Technically the member function 'DetInDel::writeRealignedBAMFile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:175:7: note: Technically the member function 'DetInDel::writeRealignedBAMFile' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:670:16: note: Technically the member function 'DetInDel::writeRealignedBAMFile' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:644:16: performance:inconclusive: Technically the member function 'DetInDel::writeUnalignedBAMFile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:176:7: note: Technically the member function 'DetInDel::writeUnalignedBAMFile' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.cpp:644:16: note: Technically the member function 'DetInDel::writeUnalignedBAMFile' can be static (but you may consider moving to unnamed namespace).
dindel-tgi-1.01-wu1-3/DInDel.hpp:246:14: performance:inconclusive: Technically the member function 'DetInDel::Parameters::makeOutputData' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:262:14: performance:inconclusive: Technically the member function 'DetInDel::Parameters::makeGLFOutputData' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/DInDel.hpp:278:14: performance:inconclusive: Technically the member function 'DetInDel::Parameters::makeGLFv2OutputData' can be static (but you may consider moving to unnamed namespace). [functionStatic]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:128:7: warning: The class 'ObservationModelFBMax' defines member function with name 'printMarginals' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:43:7: note: Parent function 'ObservationModelFB::printMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:128:7: note: Derived function 'ObservationModelFBMax::printMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:129:7: warning: The class 'ObservationModelFBMax' defines member function with name 'computeMarginals' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:44:7: note: Parent function 'ObservationModelFB::computeMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:129:7: note: Derived function 'ObservationModelFBMax::computeMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:130:7: warning: The class 'ObservationModelFBMax' defines member function with name 'computeXMarginals' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:45:7: note: Parent function 'ObservationModelFB::computeXMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:130:7: note: Derived function 'ObservationModelFBMax::computeXMarginals'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:132:7: warning: The class 'ObservationModelFBMax' defines member function with name 'printAlignment' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:46:7: note: Parent function 'ObservationModelFB::printAlignment'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:132:7: note: Derived function 'ObservationModelFBMax::printAlignment'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:133:14: warning: The class 'ObservationModelFBMax' defines member function with name 'calcLikelihood' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:32:14: note: Parent function 'ObservationModelFB::calcLikelihood'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:133:14: note: Derived function 'ObservationModelFBMax::calcLikelihood'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:140:7: warning: The class 'ObservationModelFBMax' defines member function with name 'passMessageOneInc' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:62:7: note: Parent function 'ObservationModelFB::passMessageOneInc'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:140:7: note: Derived function 'ObservationModelFBMax::passMessageOneInc'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:141:7: warning: The class 'ObservationModelFBMax' defines member function with name 'passMessageOneDec' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:63:7: note: Parent function 'ObservationModelFB::passMessageOneDec'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:141:7: note: Derived function 'ObservationModelFBMax::passMessageOneDec'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:148:7: warning: The class 'ObservationModelFBMax' defines member function with name 'computeBackwardMessages' also defined in its parent class 'ObservationModelFB'. [duplInheritedMember]
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:68:7: note: Parent function 'ObservationModelFB::computeBackwardMessages'
dindel-tgi-1.01-wu1-3/ObservationModelFB.hpp:148:7: note: Derived function 'ObservationModelFBMax::computeBackwardMessages'
dindel-tgi-1.01-wu1-3/OutputData.hpp:36:2: style: Class 'OutputData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/OutputData.hpp:68:3: style: Class 'Line' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3447:13: style: The if condition is the same as the previous if condition [duplicateCondition]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3404:13: note: First condition
dindel-tgi-1.01-wu1-3/DInDel.cpp:3447:13: note: Second condition
dindel-tgi-1.01-wu1-3/DInDel.cpp:1135:41: style: Condition 'reads[r].mateIsUnmapped()==true' is always true [knownConditionTrueFalse]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1098:41: note: Assuming that condition 'reads[r].mateIsUnmapped()==false' is not redundant
dindel-tgi-1.01-wu1-3/DInDel.cpp:1135:41: note: Condition 'reads[r].mateIsUnmapped()==true' is always true
dindel-tgi-1.01-wu1-3/DInDel.cpp:2505:10: style: Condition '0&&llOld>llNew+1e-5' is always false [knownConditionTrueFalse]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1369:3: style: Exception should be caught by reference. [catchExceptionByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1635:2: style: Exception should be caught by reference. [catchExceptionByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:277:2: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
dindel-tgi-1.01-wu1-3/DInDel.cpp:277:2: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
dindel-tgi-1.01-wu1-3/DInDel.cpp:276:8: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/DInDel.cpp:694:18: style: C-style pointer casting [cstyleCast]
dindel-tgi-1.01-wu1-3/DInDel.cpp:922:11: style: Same expression used in consecutive assignments of 'rightFetchReadPos' and 'rightMostReadPos'. [duplicateAssignExpression]
dindel-tgi-1.01-wu1-3/DInDel.cpp:923:11: note: Same expression used in consecutive assignments of 'rightFetchReadPos' and 'rightMostReadPos'.
dindel-tgi-1.01-wu1-3/DInDel.cpp:922:11: note: Same expression used in consecutive assignments of 'rightFetchReadPos' and 'rightMostReadPos'.
dindel-tgi-1.01-wu1-3/DInDel.cpp:925:11: style: Same expression used in consecutive assignments of 'leftFetchReadPos' and 'leftMostReadPos'. [duplicateAssignExpression]
dindel-tgi-1.01-wu1-3/DInDel.cpp:926:11: note: Same expression used in consecutive assignments of 'leftFetchReadPos' and 'leftMostReadPos'.
dindel-tgi-1.01-wu1-3/DInDel.cpp:925:11: note: Same expression used in consecutive assignments of 'leftFetchReadPos' and 'leftMostReadPos'.
dindel-tgi-1.01-wu1-3/DInDel.cpp:2263:17: style: The comparison 'sSnp == 1' is always true. [knownConditionTrueFalse]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2252:15: note: 'sSnp' is assigned value '1' here.
dindel-tgi-1.01-wu1-3/DInDel.cpp:2263:17: note: The comparison 'sSnp == 1' is always true.
dindel-tgi-1.01-wu1-3/DInDel.cpp:2267:19: style: The comparison 'sIndel == 1' is always true. [knownConditionTrueFalse]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2252:27: note: 'sIndel' is assigned value '1' here.
dindel-tgi-1.01-wu1-3/DInDel.cpp:2267:19: note: The comparison 'sIndel == 1' is always true.
dindel-tgi-1.01-wu1-3/DInDel.cpp:3083:9: style:inconclusive: Same expression used in consecutive assignments of 'max_ll_indel' and 'max_ll_noindel'. [duplicateAssignExpression]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3084:9: note: Same expression used in consecutive assignments of 'max_ll_indel' and 'max_ll_noindel'.
dindel-tgi-1.01-wu1-3/DInDel.cpp:3083:9: note: Same expression used in consecutive assignments of 'max_ll_indel' and 'max_ll_noindel'.
dindel-tgi-1.01-wu1-3/DInDel.cpp:599:72: style: Redundant initialization for 'hmax'. The initialized value is overwritten before it is read. [redundantInitialization]
dindel-tgi-1.01-wu1-3/DInDel.cpp:597:16: note: hmax is initialized
dindel-tgi-1.01-wu1-3/DInDel.cpp:599:72: note: hmax is overwritten
dindel-tgi-1.01-wu1-3/DInDel.cpp:3516:7: style: Redundant initialization for 'ml'. The initialized value is overwritten before it is read. [redundantInitialization]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3509:24: note: ml is initialized
dindel-tgi-1.01-wu1-3/DInDel.cpp:3516:7: note: ml is overwritten
dindel-tgi-1.01-wu1-3/DInDel.cpp:165:10: style: The scope of the variable 'offset' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:385:21: style: The scope of the variable 'likPairs' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:931:7: style: The scope of the variable 'leftOverlapsPrevious' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1628:7: style: The scope of the variable 'nh' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1981:10: style: The scope of the variable 'numdelcovered' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2003:12: style: The scope of the variable 'cov' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2415:26: style: The scope of the variable 'eNew' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2429:18: style: The scope of the variable 'llNew' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2665:17: style: The scope of the variable 'support' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2700:13: style: The scope of the variable 'mlidx' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2980:6: style: The scope of the variable 'ref_hap_idx' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3429:9: style: The scope of the variable 'offBoth' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3700:25: style: The scope of the variable 'eNew' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3772:30: style: The scope of the variable 'hpm' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3772:35: style: The scope of the variable 'hmm' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3773:9: style: The scope of the variable 'midx' can be reduced. [variableScope]
dindel-tgi-1.01-wu1-3/OutputData.hpp:54:16: style: Local variable 'out' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/OutputData.hpp:109:11: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/OutputData.hpp:54:16: note: Shadow variable
dindel-tgi-1.01-wu1-3/OutputData.hpp:92:17: style: Local variable 'out' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/OutputData.hpp:109:11: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/OutputData.hpp:92:17: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:735:12: style: Local variable 'debug' shadows outer function [shadowFunction]
dindel-tgi-1.01-wu1-3/DInDel.hpp:150:7: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:735:12: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:1458:12: style: Local variable 'start' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1429:11: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:1458:12: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:1459:12: style: Local variable 'end' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1430:11: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:1459:12: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:1866:28: style: Local variable 'indels' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.hpp:370:23: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:1866:28: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:2177:23: style: Local variable 'indels' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.hpp:370:23: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:2177:23: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:2214:24: style: Local variable 'indels' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.hpp:370:23: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:2214:24: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:2242:24: style: Local variable 'indels' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.hpp:370:23: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:2242:24: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:2528:10: style: Local variable 'z' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2115:17: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:2528:10: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:2438:8: style: Local variable 'idx' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2123:6: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:2438:8: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:2605:18: style: Local variable 'prior' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2582:17: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:2605:18: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:2672:8: style: Local variable 'nr' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2111:9: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:2672:8: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:3134:39: style: Local variable 'indels' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.hpp:370:23: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:3134:39: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:3329:7: style: Local variable 'nr' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2937:9: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:3329:7: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:3419:50: style: Local variable 'it' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3310:48: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:3419:50: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:3526:34: style: Local variable 'it' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3310:48: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:3526:34: note: Shadow variable
dindel-tgi-1.01-wu1-3/DInDel.cpp:3547:13: style: Local variable 'mq' shadows outer variable [shadowVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3505:11: note: Shadowed declaration
dindel-tgi-1.01-wu1-3/DInDel.cpp:3547:13: note: Shadow variable
dindel-tgi-1.01-wu1-3/OutputData.hpp:41:3: performance: Range variable 'label' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/DInDel.hpp:192:42: performance: Function parameter '_fileName' should be passed by const reference. [passedByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1515:4: performance: Range variable 'av' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1556:3: performance: Range variable 'v' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1839:2: performance: Range variable 'avar' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1885:2: performance: Range variable 'indel' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1897:2: performance: Range variable 'indel' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2103:362: performance: Function parameter 'program' should be passed by const reference. [passedByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2213:3: performance: Range variable 's' should be declared as const reference. [iterateByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2933:336: performance: Function parameter 'program' should be passed by const reference. [passedByValue]
dindel-tgi-1.01-wu1-3/DInDel.cpp:290:130: style: Parameter 'likPairs' can be declared as reference to const [constParameterReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:342:123: style: Parameter 'likPairs' can be declared as reference to const [constParameterReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:380:193: style: Parameter 'oData' can be declared as reference to const [constParameterReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:473:20: style: Variable 'hr' can be declared as reference to const [constVariableReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:885:95: style: Parameter 'oldLeftPos' can be declared as reference to const [constParameterReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1427:84: style: Parameter 'leftPos' can be declared as reference to const [constParameterReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1427:104: style: Parameter 'rightPos' can be declared as reference to const [constParameterReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2933:147: style: Parameter 'hapFreqs' can be declared as reference to const [constParameterReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2933:182: style: Parameter 'posteriors' can be declared as reference to const [constParameterReference]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1748:12: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
dindel-tgi-1.01-wu1-3/DInDel.cpp:649:53: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2530:5: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2689:9: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
dindel-tgi-1.01-wu1-3/DInDel.cpp:302:19: warning: Uninitialized variable: midx [uninitvar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:295:16: note: Assuming condition is false
dindel-tgi-1.01-wu1-3/DInDel.cpp:302:19: note: Uninitialized variable: midx
dindel-tgi-1.01-wu1-3/DInDel.cpp:2541:15: warning: Uninitialized variable: loglik [uninitvar]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2431:10: note: Assuming condition is false
dindel-tgi-1.01-wu1-3/DInDel.cpp:2541:15: note: Uninitialized variable: loglik
dindel-tgi-1.01-wu1-3/DInDel.cpp:143:12: style: Variable 'll' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:143:19: style: Variable 'l1' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:143:27: style: Variable 'l2' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:154:6: style: Variable 'l1' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:155:6: style: Variable 'l2' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:156:6: style: Variable 'll' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:607:28: style: Variable 'hx' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:609:30: style: Variable 'ml' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:931:28: style: Variable 'leftOverlapsPrevious' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:942:18: style: Variable 'rend' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:956:25: style: Variable 'leftOverlapsPrevious' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1087:10: style: Variable 'tf' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1097:8: style: Variable 'tf' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1130:11: style: Variable 'tf' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1151:9: style: Variable 'tf' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1165:85: style: Variable 'tf' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1202:10: style: Variable 'tf' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1429:16: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1430:14: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1434:11: style: Variable 'print' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1429:11: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1430:11: style: Variable 'end' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1434:6: style: Variable 'print' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1543:18: style: Unused variable: indelVariants [unusedVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1975:16: style: Variable 'leftV' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1976:17: style: Variable 'rightV' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2003:16: style: Variable 'cov' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2005:13: style: Variable 'cov' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2175:10: style: Variable 'PRID' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2191:7: style: Variable 'PRID' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2230:7: style: Variable 'PRID' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2248:20: style: Variable 'maxStateSnp' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2249:22: style: Variable 'maxStateIndel' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2284:8: style: Variable 'PRID' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2377:20: style: Variable 'sites[pav.first]' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2551:10: style: Variable 'post[a]' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2582:22: style: Variable 'prior' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2704:13: style: Variable 'mlidx' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2980:18: style: Variable 'ref_hap_idx' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2991:16: style: Variable 'ref_hap_idx' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3326:12: style: Variable 'totnf' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3326:21: style: Variable 'totnr' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3429:17: style: Variable 'offBoth' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3431:14: style: Variable 'offBoth' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3516:7: style: Variable 'ml' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3519:7: style: Variable 'ml' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3557:16: style: Variable 'msq' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3557:46: style: Variable 'msq' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3558:8: style: Variable 'totnf' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3559:8: style: Variable 'totnr' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3811:7: style: Variable 'hpm' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3812:7: style: Variable 'hmm' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3813:8: style: Variable 'midx' is assigned a value that is never used. [unreadVariable]
dindel-tgi-1.01-wu1-3/DInDel.cpp:330:89: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:332:89: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:334:85: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:336:85: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:351:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:353:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:355:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:357:86: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:370:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1497:101: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1498:97: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1508:98: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1513:99: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1867:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1871:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1876:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1880:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:1962:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2089:110: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2163:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2202:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2241:116: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2399:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2785:105: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:2999:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3009:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3022:69: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3139:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3144:97: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3310:104: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3419:107: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3598:82: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3799:101: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3800:101: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3801:97: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3802:97: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3877:100: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3878:100: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3879:96: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
dindel-tgi-1.01-wu1-3/DInDel.cpp:3880:96: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
diff:


DONE