2024-03-25 06:41 ftp://ftp.de.debian.org/debian/pool/main/p/progressivemauve/progressivemauve_1.2.0+4713+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 -D__GNUC__ --platform=unix64 -j1 platform: Linux-6.5.0-25-generic-x86_64-with-glibc2.35 python: 3.10.12 client-version: 1.3.55 compiler: g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 cppcheck: head 2.13.0 head-info: 51f8b53 (2024-03-24 16:07:43 +0100) count: 381 299 elapsed-time: 13.4 43.2 head-timing-info: old-timing-info: head results: mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:13:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable weight [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:26:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable weight [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:37:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable weight [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:63:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable weight [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:135:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable root [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:181:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable root [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:186:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable distance [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/RepeatHashCat.cpp:8:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STACK_TRACE_START [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/RepeatHashCat.cpp:11:2: style: Statements following 'return' will never be executed. [unreachableCode] mauvealigner-1.2.0+4713/src/UniqueMatchFinder.cpp:38:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idmer_id_lessthan [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/addUnalignedIntervals.cpp:13:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/alignmentProjector.cpp:30:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/alignmentProjector.cpp:87:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/backbone_global_to_local.cpp:13:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:31:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:98:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:308:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:350:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:375:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:438:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable iv [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:503:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:566:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:662:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:891:104: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:950:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:28:2: style: Class 'BbSeqComp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:751:15: style: Condition 'up' is always true [knownConditionTrueFalse] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:749:15: note: Assuming that condition '!up' is not redundant mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:751:15: note: Condition 'up' is always true mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:808:172: performance: Function parameter 'site_class_name' should be passed by const reference. [passedByValue] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:355:35: style: Parameter 'os' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:942:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:199:4: warning: Return value of std::remove() ignored. Elements remain in container. [uselessCallsRemove] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:200:4: warning: Return value of std::remove() ignored. Elements remain in container. [uselessCallsRemove] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:249:11: style: Variable 'cat_num' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:288:7: style: Variable 'seq_count' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:547:14: style: Variable 'sum' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:557:9: style: Variable 'sum' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:1218:12: style: Variable 'c1' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:1219:12: style: Variable 'c2' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:107:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:671:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:15:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:37:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:112:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:208:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable extents [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:234:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:197:7: performance:inconclusive: Technically the member function 'IntervalSeqManipulator::AddCopy' can be static (but you may consider moving to unnamed namespace). [functionStatic] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:191:2: style: Class 'IntervalSeqManipulator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:69:19: warning: Redundant code: Found unused array access. [constStatement] mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:216:15: warning: Redundant code: Found unused array access. [constStatement] mauvealigner-1.2.0+4713/src/bbFilter.cpp:14:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbFilter.cpp:28:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbFilter.cpp:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/bbFilter.cpp:23:7: style:inconclusive: Technically the member function 'ShorterThan::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/bbFilter.cpp:11:2: style: Class 'BbSorter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/bbFilter.cpp:39:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/bbFilter.cpp:167:25: style: Variable 'prev_in_sI' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/bbFilter.cpp:170:24: style: Variable 'prev_in_k' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/bbFilter.cpp:257:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/bbFilter.cpp:266:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/calculateBackboneCoverage.cpp:22:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/calculateBackboneCoverage.cpp:69:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/calculateBackboneCoverage.cpp:73:24: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/calculateBackboneCoverage.cpp:130:22: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/calculateBackboneCoverage2.cpp:22:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/calculateBackboneCoverage2.cpp:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/calculateBackboneCoverage2.cpp:124:22: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/calculateBackboneCoverage2.cpp:41:19: style: Unused variable: sequence_fname [unusedVariable] mauvealigner-1.2.0+4713/src/calculateCoverage.cpp:21:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/calculateCoverage.cpp:46:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/calculateCoverage.cpp:50:24: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/calculateCoverage.cpp:81:22: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/checkForLGT.cpp:29:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/checkForLGT.cpp:41:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/checkForLGT.cpp:52:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/checkForLGT.cpp:189:6: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/checkForLGT.cpp:192:6: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/checkForLGT.cpp:217:6: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/checkForLGT.cpp:220:6: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/coordinateTranslate.cpp:16:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/countInPlaceInversions.cpp:16:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/createBackboneMFA.cpp:14:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/evd.cpp:35:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INVALID_SCORE [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/evd.cpp:75:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/evd.cpp:70:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:50:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:70:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:121:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:159:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:181:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:197:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:143:7: style:inconclusive: Technically the member function 'TaxonNamePairComparator::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:91:13: style: Local variable 'childI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:68:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:91:13: note: Shadow variable mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:28:83: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/extractBackbone.cpp:21:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBackbone.cpp:44:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBackbone.cpp:43:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/extractBackbone2.cpp:21:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractBackbone2.cpp:42:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractSubalignments.cpp:32:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/extractSubalignments.cpp:85:13: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/extractSubalignments.cpp:63:8: note: Shadowed declaration mauvealigner-1.2.0+4713/src/extractSubalignments.cpp:85:13: note: Shadow variable mauvealigner-1.2.0+4713/src/extractSubalignments.cpp:28:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/gappiness.cpp:10:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/gappiness.cpp:6:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/getAlignmentWindows.cpp:26:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/getAlignmentWindows.cpp:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/getAlignmentWindows.cpp:65:54: style: C-style pointer casting [cstyleCast] mauvealigner-1.2.0+4713/src/getOrthologList.cpp:61:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/getOrthologList.cpp:77:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/getOrthologList.cpp:147:15: style: Local variable 'bbI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/getOrthologList.cpp:146:10: note: Shadowed declaration mauvealigner-1.2.0+4713/src/getOrthologList.cpp:147:15: note: Shadow variable mauvealigner-1.2.0+4713/src/getOrthologList.cpp:155:15: style: Local variable 'bbI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/getOrthologList.cpp:146:10: note: Shadowed declaration mauvealigner-1.2.0+4713/src/getOrthologList.cpp:155:15: note: Shadow variable mauvealigner-1.2.0+4713/src/getOrthologList.cpp:183:17: style: Local variable 'bbI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/getOrthologList.cpp:146:10: note: Shadowed declaration mauvealigner-1.2.0+4713/src/getOrthologList.cpp:183:17: note: Shadow variable mauvealigner-1.2.0+4713/src/getOrthologList.cpp:257:18: style: Local variable 'bbI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/getOrthologList.cpp:146:10: note: Shadowed declaration mauvealigner-1.2.0+4713/src/getOrthologList.cpp:257:18: note: Shadow variable mauvealigner-1.2.0+4713/src/getOrthologList.cpp:146:10: style: Variable 'bbI' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/joinAlignmentFiles.cpp:17:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/joinAlignmentFiles.cpp:107:2: style:inconclusive: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak] mauvealigner-1.2.0+4713/src/joinAlignmentFiles.cpp:20:19: style: Variable 'base_name' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/joinAlignmentFiles.cpp:22:19: style: Variable 'out_fname' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/makeBadgerMatrix.cpp:33:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/makeBadgerMatrix.cpp:20:2: style: Class 'livComp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/makeBadgerMatrix.cpp:103:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/makeMc4Matrix.cpp:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/makeMc4Matrix.cpp:18:2: style: Class 'livComp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/makeMc4Matrix.cpp:98:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:201:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:870:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:802:11: error: Deallocation of an auto-variable (cout) results in undefined behaviour. [autovarInvalidDeallocation] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:789:16: note: Address of variable taken here. mauvealigner-1.2.0+4713/src/mauveAligner.cpp:802:11: note: Deallocating memory that was not dynamically allocated mauvealigner-1.2.0+4713/src/mauveAligner.cpp:825:11: error: Deallocation of an auto-variable (cout) results in undefined behaviour. [autovarInvalidDeallocation] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:819:19: note: Address of variable taken here. mauvealigner-1.2.0+4713/src/mauveAligner.cpp:825:11: note: Deallocating memory that was not dynamically allocated mauvealigner-1.2.0+4713/src/mauveAligner.cpp:848:11: error: Deallocation of an auto-variable (cout) results in undefined behaviour. [autovarInvalidDeallocation] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:835:17: note: Address of variable taken here. mauvealigner-1.2.0+4713/src/mauveAligner.cpp:848:11: note: Deallocating memory that was not dynamically allocated mauvealigner-1.2.0+4713/src/mauveAligner.cpp:41:2: style: Class 'MLDeleter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:620:22: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:616:21: note: outer condition: tree_filename!="" mauvealigner-1.2.0+4713/src/mauveAligner.cpp:620:22: note: opposite inner condition: tree_filename=="" mauvealigner-1.2.0+4713/src/mauveAligner.cpp:113:9: style: The scope of the variable 'coverage_list_file' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:123:7: style: The scope of the variable 'island_break_min' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:133:9: style: The scope of the variable 'gapped_aligner' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:609:36: style: The scope of the variable 'coverage_list' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:761:7: style: The scope of the variable 'lcbI' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:650:17: style: Checking if unsigned expression 'seed_size' is less than zero. [unsignedLessThanZero] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:619:21: style: Local variable 'mi' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:82:19: note: Shadowed declaration mauvealigner-1.2.0+4713/src/mauveAligner.cpp:619:21: note: Shadow variable mauvealigner-1.2.0+4713/src/mauveAligner.cpp:500:25: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:699:24: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:717:24: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:852:22: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:90:22: style: Unused variable: seq_table [unusedVariable] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:91:22: style: Unused variable: sml_table [unusedVariable] mauvealigner-1.2.0+4713/src/mauveAligner.cpp:145:11: style: Variable 'detail_list_out' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/mauveToXMFA.cpp:14:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/mfa2xmfa.cpp:14:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/mfa2xmfa.cpp:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/mfa2xmfa.cpp:30:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/multiEVD.cpp:50:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INVALID_SCORE [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/multiEVD.cpp:93:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/multiEVD.cpp:104:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/multiEVD.cpp:99:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/multiEVD.cpp:35:7: style: Variable 'seq_count' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/multiToRawSequence.cpp:11:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/multiToRawSequence.cpp:23:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/pairCompare.cpp:14:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/pairCompare.cpp:39:9: style: Local variable 'seq_count' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/pairCompare.cpp:17:6: note: Shadowed declaration mauvealigner-1.2.0+4713/src/pairCompare.cpp:39:9: note: Shadow variable mauvealigner-1.2.0+4713/src/pairCompare.cpp:52:15: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/pairCompare.cpp:19:14: note: Shadowed declaration mauvealigner-1.2.0+4713/src/pairCompare.cpp:52:15: note: Shadow variable mauvealigner-1.2.0+4713/src/pairCompare.cpp:64:14: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/pairCompare.cpp:19:14: note: Shadowed declaration mauvealigner-1.2.0+4713/src/pairCompare.cpp:64:14: note: Shadow variable mauvealigner-1.2.0+4713/src/pairCompare.cpp:10:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:97:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:106:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:133:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:150:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:192:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable deleteRegisteredFiles [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:232:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:268:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:68:2: warning: Member variable 'OptionList::config_opt' is not initialized in the constructor. [uninitMemberVar] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:46:2: style: Class 'MLDeleter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:449:8: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:451:3: note: Found duplicate branches for 'if' and 'else'. mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:449:8: note: Found duplicate branches for 'if' and 'else'. mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:509:13: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:402:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:509:13: note: Shadow variable mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:554:15: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:402:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:554:15: note: Shadow variable mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:556:15: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:402:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:556:15: note: Shadow variable mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:659:20: style: Local variable 'mi' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:326:19: note: Shadowed declaration mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:659:20: note: Shadow variable mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:726:14: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:402:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:726:14: note: Shadow variable mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:728:14: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:402:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:728:14: note: Shadow variable mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:226:52: style: Parameter 'bbcols_fname' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:226:74: style: Parameter 'bb_fname' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:478:24: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:393:22: style: Unused variable: seq_table [unusedVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:394:22: style: Unused variable: sml_table [unusedVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:397:9: style: Variable 'output_file' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:398:9: style: Variable 'tree_filename' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:404:11: style: Variable 'detail_list_out' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/projectAndStrip.cpp:33:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/projectAndStrip.cpp:50:15: style: The scope of the variable 'not_ids' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/projectAndStrip.cpp:130:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/randomGeneSample.cpp:36:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/MatchRecord.h:101:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable subsuming_match [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/MatchRecord.h:133:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable subsuming_match [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/MatchRecord.h:234:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:56:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sar_table [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:60:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_count [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:73:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idmer_position_lessthan [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:132:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:177:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:233:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:263:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:454:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:685:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:842:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable forward [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1106:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1165:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1550:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reverse [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1620:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1648:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1748:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:14:1: style: The class 'SeedMatchEnumerator' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor] mauvealigner-1.2.0+4713/src/MatchRecord.h:167:9: performance: Variable 'spscore' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/MatchRecord.h:173:9: performance: Variable 'spscore' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/MatchRecord.h:213:7: style:inconclusive: Technically the member function 'MatchSortEntryCompare::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/MatchRecord.h:223:7: style:inconclusive: Technically the member function 'IsNullPtr::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/repeatoire.cpp:54:7: style:inconclusive: Technically the member function 'NeighborhoodListComparator::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1458:8: style:inconclusive: Technically the member function 'ProcrastinationQueue::MultiplicityHeapCompare::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1661:7: style:inconclusive: Technically the member function 'ToUPPER::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/MatchRecord.h:48:2: style: Class 'MatchRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/MatchRecord.h:80:2: style: Class 'CompactMatchRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/MatchRecord.h:170:2: style: Class 'GappedMatchRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1417:2: style: Class 'ProcrastinationQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2154:37: style: Redundant condition: two_hits. '!two_hits || (two_hits && M_i->chained_matches.size()>1)' is equivalent to '!two_hits || M_i->chained_matches.size()>1' [redundantCondition] mauvealigner-1.2.0+4713/src/repeatoire.cpp:891:15: style: C-style pointer casting [cstyleCast] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1366:32: style: C-style pointer casting [cstyleCast] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2024:28: style: C-style pointer casting [cstyleCast] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2321:14: style: C-style pointer casting [cstyleCast] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2421:63: style: C-style pointer casting [cstyleCast] mauvealigner-1.2.0+4713/src/repeatoire.cpp:220:12: style: Variable 'ok' is reassigned a value before the old one has been used. [redundantAssignment] mauvealigner-1.2.0+4713/src/repeatoire.cpp:198:16: note: ok is assigned mauvealigner-1.2.0+4713/src/repeatoire.cpp:220:12: note: ok is overwritten mauvealigner-1.2.0+4713/src/repeatoire.cpp:220:12: style: Variable 'ok' is reassigned a value before the old one has been used. [redundantAssignment] mauvealigner-1.2.0+4713/src/repeatoire.cpp:207:16: note: ok is assigned mauvealigner-1.2.0+4713/src/repeatoire.cpp:220:12: note: ok is overwritten mauvealigner-1.2.0+4713/src/repeatoire.cpp:1231:21: style: Redundant initialization for 'left_extend_length'. The initialized value is overwritten before it is read. [redundantInitialization] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1159:25: note: left_extend_length is initialized mauvealigner-1.2.0+4713/src/repeatoire.cpp:1231:21: note: left_extend_length is overwritten mauvealigner-1.2.0+4713/src/repeatoire.cpp:1232:22: style: Redundant initialization for 'right_extend_length'. The initialized value is overwritten before it is read. [redundantInitialization] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1160:26: note: right_extend_length is initialized mauvealigner-1.2.0+4713/src/repeatoire.cpp:1232:22: note: right_extend_length is overwritten mauvealigner-1.2.0+4713/src/repeatoire.cpp:1184:68: style: Same value in both branches of ternary operator. [duplicateValueTernary] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1197:80: style: Same value in both branches of ternary operator. [duplicateValueTernary] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1211:80: style: Same value in both branches of ternary operator. [duplicateValueTernary] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1223:80: style: Same value in both branches of ternary operator. [duplicateValueTernary] mauvealigner-1.2.0+4713/src/MatchRecord.h:228:38: style: The scope of the variable 'iv_matches' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1241:19: style: The scope of the variable 'leftExtension_aln' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1242:19: style: The scope of the variable 'rightExtension_aln' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1336:17: style: The scope of the variable 'extension_bb' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2075:8: style: The scope of the variable 'extended' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/repeatoire.cpp:715:9: style: Local variable 'changed' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:596:10: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:715:9: note: Shadow variable mauvealigner-1.2.0+4713/src/repeatoire.cpp:2097:33: style: Local variable 'novel_subset_list' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1978:31: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:2097:33: note: Shadow variable mauvealigner-1.2.0+4713/src/repeatoire.cpp:2132:33: style: Local variable 'novel_subset_list' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1978:31: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:2132:33: note: Shadow variable mauvealigner-1.2.0+4713/src/repeatoire.cpp:2232:33: style: Local variable 'novel_subset_list' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1978:31: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:2232:33: note: Shadow variable mauvealigner-1.2.0+4713/src/repeatoire.cpp:2190:70: style: Local variable 'mplt_sort_list' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1947:47: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:2190:70: note: Shadow variable mauvealigner-1.2.0+4713/src/repeatoire.cpp:2192:29: style: Local variable 'compI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1948:9: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:2192:29: note: Shadow variable mauvealigner-1.2.0+4713/src/repeatoire.cpp:2325:12: style: Local variable 'direction' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2063:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:2325:12: note: Shadow variable mauvealigner-1.2.0+4713/src/repeatoire.cpp:2340:12: style: Local variable 'direction' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2063:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:2340:12: note: Shadow variable mauvealigner-1.2.0+4713/src/repeatoire.cpp:2452:17: style: Local variable 'compI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1948:9: note: Shadowed declaration mauvealigner-1.2.0+4713/src/repeatoire.cpp:2452:17: note: Shadow variable mauvealigner-1.2.0+4713/src/MatchRecord.h:29:109: performance: Function parameter 'comp_map' should be passed by const reference. [passedByValue] mauvealigner-1.2.0+4713/src/MatchRecord.h:327:31: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/repeatoire.cpp:293:79: style: Parameter 'ji_component_map' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/repeatoire.cpp:522:104: style: Parameter 'group_members' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/repeatoire.cpp:522:152: style: Parameter 'neighborhood_list' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/repeatoire.cpp:571:71: style: Parameter 'left_list' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/repeatoire.cpp:571:111: style: Parameter 'right_list' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2398:6: error: Iterator 'subset_list.begin()+sI' referring to container 'left_deferred_subsets' is used with container 'subset_list'. [mismatchingContainerIterator] mauvealigner-1.2.0+4713/src/MatchRecord.h:296:48: style: Variable 'chain_begin' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:640:18: style: Variable 'ik_parity' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:596:10: style: Variable 'changed' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1118:17: style: Variable 'changed' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1348:20: style: Variable 'cgalen' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1349:23: style: Variable 'resultlen' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1147:7: style: Variable 'novel_hss_regions_support' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1148:7: style: Variable 'danger_zone_active' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1327:7: style: Variable 'boundaries_improved' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1339:10: style: Variable 'isnovel' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2259:31: style: Variable 'changed' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1667:10: style: Variable 'debug_extension' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1877:32: style: Unused variable: it [unusedVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1913:10: style: Variable 'all_components_overlap' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1915:10: style: Variable 'prev_overlaps' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1916:10: style: Variable 'mi_multiplicity' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1917:10: style: Variable 'mi2_multiplicity' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1918:10: style: Variable 'num_components' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1919:9: style: Variable 'overlap_size' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1920:9: style: Variable 'hit_match' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1997:7: style: Variable 'curr_extensions' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:1998:7: style: Variable 'max_extensions' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2073:20: style: Unused variable: alignment [unusedVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2074:19: style: Unused variable: scores [unusedVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2147:24: style: Variable 'e' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2191:70: style: Unused variable: final_mplt_sort_list [unusedVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2506:12: style: Variable 'e' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/repeatoire.cpp:2509:10: style: Variable 'alignment_count' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:82:34: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/rootTrees.cpp:29:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/rootTrees.cpp:48:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/rootTrees.cpp:90:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/rootTrees.cpp:117:32: style: Checking if unsigned expression 'treeI' is less than zero. [unsignedLessThanZero] mauvealigner-1.2.0+4713/src/rootTrees.cpp:70:13: style: Local variable 'childI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/rootTrees.cpp:46:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/rootTrees.cpp:70:13: note: Shadow variable mauvealigner-1.2.0+4713/src/rootTrees.cpp:86:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/rootTrees.cpp:108:19: style: Unused variable: tree_list [unusedVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:119:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/scoreALU.cpp:163:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/scoreALU.cpp:79:2: performance: Variable 'queryId' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:80:2: performance: Variable 'start' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:81:2: performance: Variable 'end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:82:2: performance: Variable 'remaining' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:83:2: performance: Variable 'strand' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:84:2: performance: Variable 'repeatId' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:85:2: performance: Variable 'repeatClass' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:86:2: performance: Variable 'prior' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:87:2: performance: Variable 'startDB' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:88:2: performance: Variable 'endDB' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] mauvealigner-1.2.0+4713/src/scoreALU.cpp:504:14: style: Condition 'inall||1' is always true [knownConditionTrueFalse] mauvealigner-1.2.0+4713/src/scoreALU.cpp:420:9: style: The scope of the variable 'debug_pos' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/scoreALU.cpp:494:14: style: Checking if unsigned expression 'rnum' is less than zero. [unsignedLessThanZero] mauvealigner-1.2.0+4713/src/scoreALU.cpp:509:11: style: Local variable 'rnum' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:422:9: note: Shadowed declaration mauvealigner-1.2.0+4713/src/scoreALU.cpp:509:11: note: Shadow variable mauvealigner-1.2.0+4713/src/scoreALU.cpp:721:22: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/scoreALU.cpp:92:17: style: Variable 'seq_count' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:99:12: style: Variable 'seqI' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:105:18: style: Variable 'line_count' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:100:19: style: Unused variable: lengths [unusedVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:103:9: style: Unused variable: empty_line [unusedVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:104:19: style: Unused variable: aln_mat [unusedVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:231:7: style: Variable 'seqI' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:307:6: style: Variable 'aluhits' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:328:18: style: Unused variable: specificity [unusedVariable] mauvealigner-1.2.0+4713/src/scoreALU.cpp:635:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/scoreALU.cpp:641:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:89:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:102:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:45:15: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:39:15: note: Virtual function in base class mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:45:15: note: Function in derived class mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:46:15: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:40:15: note: Virtual function in base class mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:46:15: note: Function in derived class mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:74:15: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:39:15: note: Virtual function in base class mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:74:15: note: Function in derived class mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:75:15: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:40:15: note: Virtual function in base class mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:75:15: note: Function in derived class mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:459:22: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:99:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:68:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:155:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:381:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:114:7: style:inconclusive: Technically the member function 'PairFirstComparator < std :: pair < unsigned long , uint > >::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:188:9: style: The scope of the variable 'component_pair_count' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:133:14: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:125:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:133:14: note: Shadow variable mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:152:15: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:125:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:152:15: note: Shadow variable mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:172:15: style: Local variable 'seqI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:125:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:172:15: note: Shadow variable mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:450:22: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:269:33: style: Variable 'last_int2' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:434:26: style: Unused variable: align_matrix [unusedVariable] mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:435:19: style: Unused variable: leftend [unusedVariable] mauvealigner-1.2.0+4713/src/sortContigs.cpp:19:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/sortContigs.cpp:32:7: style: The scope of the variable 'ref_seqI' can be reduced. [variableScope] mauvealigner-1.2.0+4713/src/sortContigs.cpp:114:26: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/sortContigs.cpp:122:25: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/sortContigs.cpp:178:21: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/stripGapColumns.cpp:16:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/stripSubsetLCBs.cpp:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/stripSubsetLCBs.cpp:123:22: style: Condition 'min_genome_count==-1' is always false [knownConditionTrueFalse] mauvealigner-1.2.0+4713/src/stripSubsetLCBs.cpp:169:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/stripSubsetLCBs.cpp:161:8: style: Variable 'i' is assigned a value that is never used. [unreadVariable] mauvealigner-1.2.0+4713/src/stripSubsetLCBs.cpp:162:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/toEvoHighwayFormat.cpp:40:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/toEvoHighwayFormat.cpp:12:37: style: Parameter 'chr_lens' can be declared as reference to const [constParameterReference] mauvealigner-1.2.0+4713/src/toEvoHighwayFormat.cpp:145:21: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/toGBKsequence.cpp:15:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/toGBKsequence.cpp:33:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/toGrimmFormat.cpp:17:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/toGrimmFormat.cpp:81:21: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/toMultiFastA.cpp:14:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/toRawSequence.cpp:15:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/toRawSequence.cpp:22:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/transposeCoordinates.cpp:21:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/transposeCoordinates.cpp:33:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/unalign.cpp:16:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/unalign.cpp:57:55: style: C-style pointer casting [cstyleCast] mauvealigner-1.2.0+4713/src/unalign.cpp:80:22: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/uniqueMerCount.cpp:20:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/uniqueMerCount.cpp:36:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/uniqueMerCount.cpp:34:23: style: Variable 'gne' can be declared as reference to const [constVariableReference] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:48:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:68:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:119:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:157:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:179:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:195:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:141:7: style:inconclusive: Technically the member function 'TaxonNamePairComparator::operator()' can be const. [functionConst] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:89:13: style: Local variable 'childI' shadows outer variable [shadowVariable] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:66:7: note: Shadowed declaration mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:89:13: note: Shadow variable mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:191:27: style: Parameter 'argv' can be declared as const array [constParameter] mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:26:83: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] mauvealigner-1.2.0+4713/src/xmfa2maf.cpp:11:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] mauvealigner-1.2.0+4713/src/xmfa2maf.cpp:50:19: style: C-style pointer casting [cstyleCast] diff: head mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:135:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable root [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:181:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable root [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:186:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable distance [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:26:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable weight [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:37:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable weight [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/AlignmentTree.cpp:63:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable weight [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/MatchRecord.h:133:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable subsuming_match [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/MatchRecord.h:234:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:132:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:56:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sar_table [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:60:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq_count [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/SeedMatchEnumerator.h:73:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable idmer_position_lessthan [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:308:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:350:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:355:35: style: Parameter 'os' can be declared as reference to const [constParameterReference] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:375:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:438:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable iv [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:503:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:566:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:662:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:891:104: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:942:27: style: Parameter 'argv' can be declared as const array [constParameter] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:950:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbAnalyze.cpp:98:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:112:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:208:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable extents [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:234:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbBreakOnGenes.cpp:37:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbFilter.cpp:28:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/bbFilter.cpp:39:27: style: Parameter 'argv' can be declared as const array [constParameter] head mauvealigner-1.2.0+4713/src/bbFilter.cpp:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/calculateBackboneCoverage.cpp:69:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/calculateBackboneCoverage2.cpp:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/calculateCoverage.cpp:46:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/checkForLGT.cpp:41:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/checkForLGT.cpp:52:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/evd.cpp:75:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:121:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:159:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:181:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:197:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/extractBCITrees.cpp:70:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/extractBackbone.cpp:44:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/extractBackbone2.cpp:42:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/getAlignmentWindows.cpp:47:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/getAlignmentWindows.cpp:65:54: style: C-style pointer casting [cstyleCast] head mauvealigner-1.2.0+4713/src/getOrthologList.cpp:77:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/mauveAligner.cpp:870:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/mfa2xmfa.cpp:31:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/multiEVD.cpp:104:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/multiEVD.cpp:93:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:106:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:133:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:150:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:192:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable deleteRegisteredFiles [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:232:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/progressiveMauve.cpp:268:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:1106:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:1165:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:1242:19: style: The scope of the variable 'rightExtension_aln' can be reduced. [variableScope] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:1550:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable reverse [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:1620:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:1648:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:1748:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:177:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:233:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] 2.13.0 mauvealigner-1.2.0+4713/src/repeatoire.cpp:2398:6: error: Iterator 'subset_list.begin()+sI' from different container 'subset_list' are used together. [mismatchingContainerIterator] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:2398:6: error: Iterator 'subset_list.begin()+sI' referring to container 'left_deferred_subsets' is used with container 'subset_list'. [mismatchingContainerIterator] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:263:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:454:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_MATCH [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:685:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/repeatoire.cpp:842:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable forward [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/rootTrees.cpp:48:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/rootTrees.cpp:90:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/scoreALU.cpp:163:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/scoreALU.cpp:504:14: style: Condition 'inall||1' is always true [knownConditionTrueFalse] 2.13.0 mauvealigner-1.2.0+4713/src/scoreALU.cpp:531:13: style: Condition 'debug_pos' is always false [knownConditionTrueFalse] mauvealigner-1.2.0+4713/src/scoreALU.cpp:420:21: note: Assignment 'debug_pos=false', assigned value is 0 mauvealigner-1.2.0+4713/src/scoreALU.cpp:531:13: note: Condition 'debug_pos' is always false 2.13.0 mauvealigner-1.2.0+4713/src/scoreALU.cpp:582:13: style: Condition 'debug_pos' is always false [knownConditionTrueFalse] mauvealigner-1.2.0+4713/src/scoreALU.cpp:420:21: note: Assignment 'debug_pos=false', assigned value is 0 mauvealigner-1.2.0+4713/src/scoreALU.cpp:582:13: note: Condition 'debug_pos' is always false head mauvealigner-1.2.0+4713/src/scoreAlignment.cpp:102:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/scoreProcrastAlignment.cpp:381:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/transposeCoordinates.cpp:33:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/uniqueMerCount.cpp:36:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:119:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:157:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:179:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:195:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head mauvealigner-1.2.0+4713/src/uniquifyTrees.cpp:68:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable children [valueFlowBailoutIncompleteVar] DONE