2025-11-22 12:24
ftp://ftp.de.debian.org/debian/pool/main/libs/libsmithwaterman/libsmithwaterman_0.0+git20160702.2610e25.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j4
platform: Linux-5.4.0-216-generic-x86_64-with-glibc2.29
python: 3.8.10
client-version: 1.3.69
compiler: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
cppcheck: head 2.18.0
head-info: 602da94 (2025-11-21 17:16:29 +0100)
count: 107 106
elapsed-time: 1.3 2.0
head-timing-info:

old-timing-info:

head results:
libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.cpp:23:18: style:inconclusive: Technically the member function 'IndelAllele::referenceLength' can be const. [functionConst]
libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.h:18:9: note: Technically the member function 'IndelAllele::referenceLength' can be const.
libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.cpp:23:18: note: Technically the member function 'IndelAllele::referenceLength' can be const.
libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.cpp:15:18: style:inconclusive: Technically the member function 'IndelAllele::readLength' can be const. [functionConst]
libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.h:19:9: note: Technically the member function 'IndelAllele::readLength' can be const.
libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.cpp:15:18: note: Technically the member function 'IndelAllele::readLength' can be const.
libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.h:26:54: performance: Function parameter 's' should be passed by const reference. [passedByValue]
libsmithwaterman-0.0+git20160702.2610e25/IndelAllele.cpp:31:25: performance: Function parameter 'sequence' should be passed by const reference. [passedByValue]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.h:101:35: performance:inconclusive: Technically the member function 'CBandedSmithWaterman::UpdateBestScore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.h:52:14: note: Technically the member function 'CBandedSmithWaterman::UpdateBestScore' can be static (but you may consider moving to unnamed namespace).
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.h:101:35: note: Technically the member function 'CBandedSmithWaterman::UpdateBestScore' can be static (but you may consider moving to unnamed namespace).
libsmithwaterman-0.0+git20160702.2610e25/Repeats.cpp:3:40: style:inconclusive: Function 'repeatCounts' argument 1 names different: declaration 'pos' definition 'position'. [funcArgNamesDifferent]
libsmithwaterman-0.0+git20160702.2610e25/Repeats.h:7:40: note: Function 'repeatCounts' argument 1 names different: declaration 'pos' definition 'position'.
libsmithwaterman-0.0+git20160702.2610e25/Repeats.cpp:3:40: note: Function 'repeatCounts' argument 1 names different: declaration 'pos' definition 'position'.
libsmithwaterman-0.0+git20160702.2610e25/Repeats.cpp:3:64: style:inconclusive: Function 'repeatCounts' argument 2 names different: declaration 'seq' definition 'sequence'. [funcArgNamesDifferent]
libsmithwaterman-0.0+git20160702.2610e25/Repeats.h:7:59: note: Function 'repeatCounts' argument 2 names different: declaration 'seq' definition 'sequence'.
libsmithwaterman-0.0+git20160702.2610e25/Repeats.cpp:3:64: note: Function 'repeatCounts' argument 2 names different: declaration 'seq' definition 'sequence'.
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:43:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:54:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:96:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:49:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:54:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:808:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:75:9: style: The scope of the variable 'c' can be reduced. [variableScope]
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:238:31: style: Local variable 'c' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:75:9: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:238:31: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:274:49: style: Local variable 'c' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:75:9: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:274:49: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:275:17: style: Local variable 'len' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:235:13: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:275:17: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/smithwaterman.cpp:94:30: style: Variable 'long_options' can be declared as const array [constVariable]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:17:23: warning: Member variable 'CBandedSmithWaterman::mHomoPolymerGapOpenPenalty' is not initialized in the constructor. [uninitMemberVar]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:266:28: style:inconclusive: Technically the member function 'CBandedSmithWaterman::CorrectHomopolymerGapOrder' can be const. [functionConst]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.h:44:7: note: Technically the member function 'CBandedSmithWaterman::CorrectHomopolymerGapOrder' can be const.
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:266:28: note: Technically the member function 'CBandedSmithWaterman::CorrectHomopolymerGapOrder' can be const.
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:42:3: warning: Class 'CBandedSmithWaterman' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:42:3: warning: Class 'CBandedSmithWaterman' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:511:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:511:9: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:372:32: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:373:21: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:375:32: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:376:21: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:380:32: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:381:21: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:385:32: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:386:21: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:405:32: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:406:21: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:412:32: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:413:21: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:419:32: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:420:21: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:281:7: style: The scope of the variable 'hasReferenceGap' can be reduced. [variableScope]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:281:32: style: The scope of the variable 'hasQueryGap' can be reduced. [variableScope]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:59:69: style:inconclusive: Function 'Align' argument 2 names different: declaration 'stringAl' definition 'cigarAl'. [funcArgNamesDifferent]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.h:35:48: note: Function 'Align' argument 2 names different: declaration 'stringAl' definition 'cigarAl'.
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:59:69: note: Function 'Align' argument 2 names different: declaration 'stringAl' definition 'cigarAl'.
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:517:73: style:inconclusive: Function 'Traceback' argument 2 names different: declaration 'stringAl' definition 'cigarAl'. [funcArgNamesDifferent]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.h:50:52: note: Function 'Traceback' argument 2 names different: declaration 'stringAl' definition 'cigarAl'.
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:517:73: note: Function 'Traceback' argument 2 names different: declaration 'stringAl' definition 'cigarAl'.
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:282:8: style: Variable 'pNonGapSeq' can be declared as pointer to const [constVariablePointer]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:281:23: style: Variable 'hasReferenceGap' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:281:44: style: Variable 'hasQueryGap' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:547:16: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:546:8: note: outer condition: !last.insertion
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:547:16: note: opposite inner condition: last.insertion
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:35:9: style: The if condition is the same as the previous if condition [duplicateCondition]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:34:9: note: First condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:35:9: note: Second condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:195:9: style: The if condition is the same as the previous if condition [duplicateCondition]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:190:9: note: First condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:195:9: note: Second condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:286:9: style: The if condition is the same as the previous if condition [duplicateCondition]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:280:9: note: First condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:286:9: note: Second condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:425:9: style: The if condition is the same as the previous if condition [duplicateCondition]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:420:9: note: First condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:425:9: note: Second condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:573:11: style: The if condition is the same as the previous if condition [duplicateCondition]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:572:11: note: First condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:573:11: note: Second condition
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:26:24: style:inconclusive: Function 'leftAlign' argument 1 names different: declaration 'alternateQuery' definition 'querySequence'. [funcArgNamesDifferent]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.h:23:24: note: Function 'leftAlign' argument 1 names different: declaration 'alternateQuery' definition 'querySequence'.
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:26:24: note: Function 'leftAlign' argument 1 names different: declaration 'alternateQuery' definition 'querySequence'.
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:26:62: style:inconclusive: Function 'leftAlign' argument 3 names different: declaration 'referenceSequence' definition 'baseReferenceSequence'. [funcArgNamesDifferent]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.h:23:63: note: Function 'leftAlign' argument 3 names different: declaration 'referenceSequence' definition 'baseReferenceSequence'.
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:26:62: note: Function 'leftAlign' argument 3 names different: declaration 'referenceSequence' definition 'baseReferenceSequence'.
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:783:29: style:inconclusive: Function 'stablyLeftAlign' argument 1 names different: declaration 'alternateQuery' definition 'querySequence'. [funcArgNamesDifferent]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.h:24:29: note: Function 'stablyLeftAlign' argument 1 names different: declaration 'alternateQuery' definition 'querySequence'.
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:783:29: note: Function 'stablyLeftAlign' argument 1 names different: declaration 'alternateQuery' definition 'querySequence'.
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:121:17: style: Local variable 'steppos' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:115:13: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:121:17: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:122:17: style: Local variable 'readsteppos' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:115:22: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:122:17: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:378:7: style: Local variable 'minsize' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:320:10: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:378:7: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:379:7: style: Local variable 'flankingLength' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:321:10: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:379:7: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:380:10: style: Local variable 'flanking' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:323:13: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:380:10: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:383:10: style: Local variable 'p' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:326:13: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:383:10: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:746:66: performance: Function parameter 'referenceSequence' should be passed by const reference. [passedByValue]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:204:26: style: Variable 'indel' can be declared as reference to const [constVariableReference]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:746:29: style: Parameter 'querySequence' can be declared as reference to const [constParameterReference]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:746:52: style: Parameter 'cigar' can be declared as reference to const [constParameterReference]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:344:16: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:381:19: style: Variable 'indelRefEnd' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:574:19: style: Variable 'mindist' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:381:7: style: Variable 'indelRefEnd' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/LeftAlign.cpp:574:11: style: Variable 'mindist' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:12:22: warning: Member variable 'CSmithWatermanGotoh::BestScore' is not initialized in the constructor. [uninitMemberVar]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:12:22: warning: Member variable 'CSmithWatermanGotoh::mHomoPolymerGapOpenPenalty' is not initialized in the constructor. [uninitMemberVar]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:12:22: warning: Member variable 'CSmithWatermanGotoh::mEntropyGapOpenPenalty' is not initialized in the constructor. [uninitMemberVar]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:12:22: warning: Member variable 'CSmithWatermanGotoh::mRepeatGapExtensionPenalty' is not initialized in the constructor. [uninitMemberVar]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:12:22: warning: Member variable 'CSmithWatermanGotoh::mMaxRepeatGapExtensionPenalty' is not initialized in the constructor. [uninitMemberVar]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:663:27: style:inconclusive: Technically the member function 'CSmithWatermanGotoh::CorrectHomopolymerGapOrder' can be const. [functionConst]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.h:41:10: note: Technically the member function 'CSmithWatermanGotoh::CorrectHomopolymerGapOrder' can be const.
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:663:27: note: Technically the member function 'CSmithWatermanGotoh::CorrectHomopolymerGapOrder' can be const.
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:83:12: style: C-style pointer casting [cstyleCast]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:155:13: style: C-style pointer casting [cstyleCast]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:159:13: style: C-style pointer casting [cstyleCast]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:238:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:238:12: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:584:35: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:585:24: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:589:35: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:590:24: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:594:35: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:595:24: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:614:35: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:615:24: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:621:35: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:622:24: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:628:35: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:629:24: style: Same expression on both sides of '-'. [duplicateExpression]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:352:7: style: Variable 'referenceGapExtendScore' is assigned an expression that holds the same value. [redundantAssignment]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:312:30: note: referenceGapExtendScore is assigned 'currentAnchorGapScore-mGapExtendPenalty' here.
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:352:7: note: Variable 'referenceGapExtendScore' is assigned an expression that holds the same value.
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:149:9: style: The scope of the variable 'entropyWindowSize' can be reduced. [variableScope]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:240:50: style: The scope of the variable 'bestScoreDiagonal' can be reduced. [variableScope]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:242:59: style: The scope of the variable 'currentAnchorGapScore' can be reduced. [variableScope]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:677:10: style: The scope of the variable 'hasReferenceGap' can be reduced. [variableScope]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:677:35: style: The scope of the variable 'hasQueryGap' can be reduced. [variableScope]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:135:10: style: Local variable 'queryEndRepeatBases' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:95:9: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:135:10: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:142:10: style: Local variable 'queryBeginRepeatBases' shadows outer variable [shadowVariable]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:94:9: note: Shadowed declaration
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:142:10: note: Shadow variable
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:282:21: style: Variable 'repeats' can be declared as reference to const [constVariableReference]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:331:21: style: Variable 'repeats' can be declared as reference to const [constVariableReference]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:678:11: style: Variable 'pNonGapSeq' can be declared as pointer to const [constVariablePointer]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:94:9: style: Variable 'queryBeginRepeatBases' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:95:9: style: Variable 'queryEndRepeatBases' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:677:26: style: Variable 'hasReferenceGap' is assigned a value that is never used. [unreadVariable]
libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:677:47: style: Variable 'hasQueryGap' is assigned a value that is never used. [unreadVariable]
diff:
2.18.0 libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:42:3: warning: Class 'CBandedSmithWaterman' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:42:3: warning: Class 'CBandedSmithWaterman' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
2.18.0 libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:42:3: warning: Class 'CBandedSmithWaterman' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head libsmithwaterman-0.0+git20160702.2610e25/BandedSmithWaterman.cpp:42:3: warning: Class 'CBandedSmithWaterman' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
head libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:352:7: style: Variable 'referenceGapExtendScore' is assigned an expression that holds the same value. [redundantAssignment]
     libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:312:30: note: referenceGapExtendScore is assigned 'currentAnchorGapScore-mGapExtendPenalty' here.
     libsmithwaterman-0.0+git20160702.2610e25/SmithWatermanGotoh.cpp:352:7: note: Variable 'referenceGapExtendScore' is assigned an expression that holds the same value.


DONE