2021-09-19 01:35
ftp://ftp.de.debian.org/debian/pool/main/k/kmer/kmer_0~20150903+r2013.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=python -j1 --showtime=top5 --check-library --inconclusive --enable=style,information --template=daca2 -rp=temp -D__GNUC__ --platform=unix64 temp
platform: Linux-5.4.0-84-generic-x86_64-with-glibc2.29
python: 3.8.10
client-version: 1.3.12
compiler: g++ (Ubuntu 10.3.0-1ubuntu1~20.04) 10.3.0
cppcheck: head 2.5
head-info: 9e9a982c6 (2021-09-18 22:23:05 +0200)
count: 1349 1295
elapsed-time: 107.5 101.1
head-timing-info:
 Tokenizer::simplifyTokens1: 18.7889s (avg. 0.066392s - 283 result(s))
 Tokenizer::simplifyTokens1::ValueFlow: 15.1804s (avg. 0.0604796s - 251 result(s))
 Tokenizer::simplifyTokens1::createSymbolDatabase: 1.28538s (avg. 0.00512102s - 251 result(s))
 Tokenizer::createTokens: 0.701908s (avg. 0.00248024s - 283 result(s))
 Other::runChecks: 0.447792s (avg. 0.00178403s - 251 result(s))
 Overall time: 38.9066s

old-timing-info:
 Tokenizer::simplifyTokens1: 17.5829s (avg. 0.0621304s - 283 result(s))
 Tokenizer::simplifyTokens1::ValueFlow: 13.8921s (avg. 0.0553469s - 251 result(s))
 Tokenizer::simplifyTokens1::createSymbolDatabase: 1.27923s (avg. 0.00509652s - 251 result(s))
 Tokenizer::createTokens: 0.700971s (avg. 0.00247693s - 283 result(s))
 Other::runChecks: 0.410859s (avg. 0.00163689s - 251 result(s))
 Overall time: 36.2852s

head results:
kmer-code-2013-trunk/ESTmapper/terminate.C:60:12: style:inconclusive: Technically the member function 'iidReaderWriter::thisIID' can be const. [functionConst]
kmer-code-2013-trunk/ESTmapper/terminate.C:32:7: warning: Class 'iidReaderWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/ESTmapper/terminate.C:32:7: warning: Class 'iidReaderWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/ESTmapper/terminate.C:69:5: warning: Possible leak in public function. The pointer 'iids' is not deallocated before it is allocated. [publicAllocationError]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-span.H:37:5: performance: Variable '_iid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-span.H:38:5: performance: Variable '_beg' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-span.H:39:5: performance: Variable '_end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-span.H:40:5: performance: Variable '_matchesLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-span.H:41:5: performance: Variable '_matchesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-stats.H:32:5: performance: Variable 'histMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-stats.H:34:5: performance: Variable 'sum' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:75:7: performance: Variable 'count' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:76:7: performance: Variable 'len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-stats.H:52:11: style:inconclusive: Technically the member function 'histogram::getSum' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-stats.H:33:5: warning: Class 'histogram' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-stats.H:33:5: warning: Class 'histogram' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:123:15: style: Condition 'beg==gap' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:106:19: note: beg is assigned 'i-1' here.
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:107:21: note: Assignment 'gap=i', assigned value is symbolic=beg+1
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:123:15: note: Condition 'beg==gap' is always false
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-spanTree.H:65:12: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-spanTree.H:95:14: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:84:32: style: Parameter 'x' can be declared with const [constParameter]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-printAnno.C:46:19: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-process.C:41:21: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/alignOverlap/overlap.C:123:43: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:107:16: style: The scope of the variable 'tpdel' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:172:9: style: The scope of the variable 'tmpcost' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:405:20: style:inconclusive: Function 'halignStart' argument 1 names different: declaration 'string1' definition 's1'. [funcArgNamesDifferent]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.H:41:24: note: Function 'halignStart' argument 1 names different: declaration 'string1' definition 's1'.
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:405:20: note: Function 'halignStart' argument 1 names different: declaration 'string1' definition 's1'.
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:406:20: style:inconclusive: Function 'halignStart' argument 2 names different: declaration 'string2' definition 's2'. [funcArgNamesDifferent]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.H:42:24: note: Function 'halignStart' argument 2 names different: declaration 'string2' definition 's2'.
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:406:20: note: Function 'halignStart' argument 2 names different: declaration 'string2' definition 's2'.
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:474:36: style:inconclusive: Function 'iterateUngappedAlignSharpEnds' argument 6 names different: declaration 'nmat' definition 'nmatInSeg'. [funcArgNamesDifferent]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.H:51:40: note: Function 'iterateUngappedAlignSharpEnds' argument 6 names different: declaration 'nmat' definition 'nmatInSeg'.
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:474:36: note: Function 'iterateUngappedAlignSharpEnds' argument 6 names different: declaration 'nmat' definition 'nmatInSeg'.
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:107:25: style: Variable 'tpdel' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:297:11: style: Variable 'cost1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:316:11: style: Variable 'cost2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:347:11: style: Variable 'cost1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:374:11: style: Variable 'cost2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:507:14: style: Variable 'nmat' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/halign/halign.C:519:21: style: Variable 'nmat' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.H:33:24: warning: Assert statement modifies 'newp'. [assignmentInAssert]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.H:42:24: warning: Assert statement modifies 'newp'. [assignmentInAssert]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:1134:7: error: Common realloc mistake: 'BrevC' nulled but not freed upon failure [memleakOnRealloc]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:1032:13: style: The comparison 'j == 0' is always true. [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:1030:11: note: 'j' is assigned value '0' here.
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:1032:13: note: The comparison 'j == 0' is always true.
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:147:9: style: The scope of the variable 'c' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:254:12: style: The scope of the variable 'disconnect' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:599:10: style: The scope of the variable 'inserted' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:872:7: style: The scope of the variable 'j' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:872:15: style: The scope of the variable 'indel' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:873:10: style: The scope of the variable 'pcnt' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:1106:16: style: The scope of the variable 'BseqLen' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:1109:25: style: Variable 'hits' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.C:1111:26: style: Variable 'traps' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:479:9: style: Variable 'abeg' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:465:13: note: abeg is assigned
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:479:9: note: abeg is overwritten
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:480:9: style: Variable 'bbeg' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:466:13: note: bbeg is assigned
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:480:9: note: bbeg is overwritten
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:105:7: style: The scope of the variable 'tracespace' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:100:36: style:inconclusive: Function 'AS_Local_Trace' argument 1 names different: declaration 'local_overlap' definition 'O'. [funcArgNamesDifferent]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_local.H:268:37: note: Function 'AS_Local_Trace' argument 1 names different: declaration 'local_overlap' definition 'O'.
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_loverlapper.C:100:36: note: Function 'AS_Local_Trace' argument 1 names different: declaration 'local_overlap' definition 'O'.
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_overlap.C:773:22: style: The scope of the variable 'sg' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_overlap.C:774:22: style: The scope of the variable 'ln' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_overlap.C:118:44: style: Parameter 'x' can be declared with const [constParameter]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_overlap.C:647:9: style: Variable 'beg' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:172:45: style: Parameter 'trace' can be declared with const [constParameter]
kmer-code-2013-trunk/atac-driver/chimera/happy-clones-span-clumps.C:21:5: performance: Variable 'clumpsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/chimera/happy-clones-span-clumps.C:22:5: performance: Variable 'clumpsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/chimera/happy-clones-span-clumps.C:187:5: performance: Variable 'scaffoldsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/chimera/happy-clones-span-clumps.C:23:5: warning: Class 'atacClumpCoordTreeScaffold' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/chimera/happy-clones-span-clumps.C:23:5: warning: Class 'atacClumpCoordTreeScaffold' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/chimera/happy-clones-span-clumps.C:188:5: warning: Class 'atacClumpCoordTree' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/chimera/happy-clones-span-clumps.C:188:5: warning: Class 'atacClumpCoordTree' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/chimera/happy-clones-span-clumps.C:316:5: error: Resource leak: inf [resourceLeak]
kmer-code-2013-trunk/atac-driver/clumpMaker/clumpMaker.C:87:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/clumpMaker/clumpMaker.C:88:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/clumpMaker/clumpMaker.C:109:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/clumpMaker/clumpMaker.C:110:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/clumpMaker/clumpMaker.C:220:12: style: The scope of the variable 'isSorted' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/clumpMaker/clumpMaker.C:220:25: style: Variable 'isSorted' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/clumpMaker/clumpMaker.C:235:16: style: Variable 'isSorted' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/gapShifter/coalesceMatches.C:36:19: style: The scope of the variable 'r' can be reduced. [variableScope]
kmer-code-2013-trunk/atac-driver/gapShifter/coalesceMatches.C:36:21: style: Variable 'r' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/gapShifter/correctGaps.C:76:18: style: Variable 'S1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/gapShifter/correctGaps.C:77:18: style: Variable 'S2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/gapShifter/extractUnmapped.C:180:5: performance: Variable 'matchesLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/gapShifter/extractUnmapped.C:181:5: performance: Variable 'matchesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/gapShifter/extractUnmapped.C:192:10: style:inconclusive: Technically the member function 'extractMatchList::len' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/gapShifter/extractUnmapped.C:182:5: warning: Class 'extractMatchList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/gapShifter/extractUnmapped.C:182:5: warning: Class 'extractMatchList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/gapShifter/gapShifter.C:700:24: style: Variable 'logFileName' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/atac-driver/lengthFilter/lengthFilter.C:114:46: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/atac-driver/libatac/atacFeature.C:109:81: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchOrder.H:42:3: warning: Member variable 'atacMatchOrder::_ML' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchOrder.H:45:3: warning: Member variable 'atacMatchOrder::_ML' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/atac-driver/libatac/atacFeature.H:52:3: warning:inconclusive: Member variable 'atacFeature::featureuid' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/atac-driver/libatac/atacFeature.H:52:3: warning:inconclusive: Member variable 'atacFeature::parentuid' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/atac-driver/libatac/atacFeature.H:52:3: warning:inconclusive: Member variable 'atacFeature::type' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:35:5: performance: Variable 'matchiid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:37:5: performance: Variable 'iid1' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:37:12: performance: Variable 'pos1' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:37:19: performance: Variable 'len1' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:37:26: performance: Variable 'fwd1' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:38:5: performance: Variable 'iid2' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:38:12: performance: Variable 'pos2' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:38:19: performance: Variable 'len2' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:38:26: performance: Variable 'fwd2' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:28:3: performance: Variable '_featuresLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:29:3: performance: Variable '_featuresMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchList.H:37:18: style:inconclusive: Technically the member function 'atacMatchList::numMatches' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchList.H:38:18: style:inconclusive: Technically the member function 'atacMatchList::numberOfMatches' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchOrder.H:52:21: style:inconclusive: Technically the member function 'atacMatchOrder::numMatches' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchOrder.H:53:21: style:inconclusive: Technically the member function 'atacMatchOrder::numberOfMatches' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchOrder.H:68:21: style:inconclusive: Technically the member function 'atacMatchOrder::index' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.H:34:18: style:inconclusive: Technically the member function 'atacFeatureList::numberOfFeatures' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/fasta-accessor.H:117:8: style:inconclusive: Technically the member function 'FastAAccessor::isValid' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/fasta-accessor.H:156:10: style:inconclusive: Technically the member function 'FastAAccessor::getRangeBegin' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/fasta-accessor.H:157:10: style:inconclusive: Technically the member function 'FastAAccessor::getRangeEnd' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/fasta-accessor.H:158:10: style:inconclusive: Technically the member function 'FastAAccessor::getRangeLength' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:30:3: warning: Class 'atacFeatureList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:30:3: warning: Class 'atacFeatureList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.H:40:3: style: Class 'atacMatch' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchOrder.H:42:3: style: Class 'atacMatchOrder' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchOrder.H:45:3: style: Class 'atacMatchOrder' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atacFeature.H:53:3: style: Class 'atacFeature' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/atac-driver/libatac/fasta-accessor.H:60:3: style: Class 'FastAAccessor' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/atac-driver/libatac/fasta-accessor.H:64:3: style: Class 'FastAAccessor' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atac.H:74:3: style: Class 'atacFileStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atac.H:117:3: style: Class 'atacFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:58:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:59:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:73:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:74:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:89:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/libatac/atacFeatureList.C:90:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:45:5: warning: Class 'atacFileStream' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:45:5: warning: Class 'atacFileStream' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:43:17: style: Condition 'filename!=0L' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:38:16: note: Assuming that condition 'filename==0L' is not redundant
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:43:17: note: Condition 'filename!=0L' is always true
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:122:17: style: Condition 'filename!=0L' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:116:16: note: Assuming that condition 'filename==0L' is not redundant
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:122:17: note: Condition 'filename!=0L' is always true
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:255:7: style: Condition '_fileA' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:262:7: style: Condition '_fileB' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:29:16: style: Parameter 'inLine' can be declared with const [constParameter]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:84:34: style: Parameter 'type' can be declared with const [constParameter]
kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:298:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
kmer-code-2013-trunk/atac-driver/libatac/atacFileStreamMerge.C:49:3: performance: Variable '_filesLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacFileStreamMerge.C:50:3: performance: Variable '_filesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacFileStreamMerge.C:52:3: performance: Variable '_theMatchIID' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacFileStreamMerge.C:53:3: performance: Variable '_theFeatureIID' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacFileStreamMerge.C:51:3: warning: Class 'atacFileStreamMerge' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atacFileStreamMerge.C:51:3: warning: Class 'atacFileStreamMerge' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/libatac/atacMatch.C:131:84: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchList.C:28:3: performance: Variable '_matchesLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchList.C:29:3: performance: Variable '_matchesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchList.C:30:3: warning: Class 'atacMatchList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/libatac/atacMatchList.C:30:3: warning: Class 'atacMatchList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/matchExtender/match.H:40:5: warning:inconclusive: The buffer '_matchId' may not be null-terminated after the call to strncpy(). [terminateStrncpy]
kmer-code-2013-trunk/atac-driver/matchExtender/match.H:100:8: style:inconclusive: Technically the member function 'match_s::isDeleted' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/matchExtender/match.H:43:5: warning: Class 'match_s' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/atac-driver/matchExtender/match.H:43:5: warning: Class 'match_s' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender-func.C:355:31: style: Condition 'good_run_len>minEndRunLen' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender-func.C:352:31: note: Assuming that condition 'good_run_len==minEndRunLen' is not redundant
kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender-func.C:355:31: note: Condition 'good_run_len>minEndRunLen' is always true
kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender.C:50:7: style:inconclusive: Technically the member function 'MatchCompare::operator()' can be const. [functionConst]
kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender.C:146:7: style: Condition 'fail' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender.C:118:18: note: Assignment 'fail=false', assigned value is 0
kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender.C:146:7: note: Condition 'fail' is always false
kmer-code-2013-trunk/atac-driver/statsGenerator/statsGenerator.C:507:40: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:345:11: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:339:12: note: outer condition: node1
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:345:11: note: identical inner condition: node1
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:357:11: style: Condition 'node2' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:339:21: note: Assuming that condition 'node2' is not redundant
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:357:11: note: Condition 'node2' is always true
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:114:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:115:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:158:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:180:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:209:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:261:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:262:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:263:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:264:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:346:19: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:358:19: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:546:20: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:667:20: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/leaff/blocks.C:20:16: style: Local variable 'S' shadows outer variable [shadowVariable]
kmer-code-2013-trunk/leaff/blocks.C:7:16: note: Shadowed declaration
kmer-code-2013-trunk/leaff/blocks.C:20:16: note: Shadow variable
kmer-code-2013-trunk/leaff/blocks.C:7:22: style: Variable 'S' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/leaff/dups.C:36:18: style: Variable 's1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/leaff/dups.C:37:18: style: Variable 's2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/leaff/fragmenter.C:136:32: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/leaff/leaff.C:774:17: style: Array index 'pos' is used before limits check. [arrayIndexThenCheck]
kmer-code-2013-trunk/leaff/leaff.C:778:17: style: Array index 'pos' is used before limits check. [arrayIndexThenCheck]
kmer-code-2013-trunk/leaff/leaff.C:649:14: style: The scope of the variable 'l' can be reduced. [variableScope]
kmer-code-2013-trunk/leaff/leaff.C:773:15: style: Local variable 'pos' shadows outer variable [shadowVariable]
kmer-code-2013-trunk/leaff/leaff.C:716:11: note: Shadowed declaration
kmer-code-2013-trunk/leaff/leaff.C:773:15: note: Shadow variable
kmer-code-2013-trunk/leaff/leaff.C:452:17: style: Variable 'bases' can be declared with const [constVariable]
kmer-code-2013-trunk/leaff/partition.C:62:30: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/leaff/simseq.C:58:10: style: The scope of the variable 'num' can be reduced. [variableScope]
kmer-code-2013-trunk/leaff/simseq.C:58:15: style: The scope of the variable 'optype' can be reduced. [variableScope]
kmer-code-2013-trunk/leaff/simseq.C:196:17: style: The scope of the variable 'start' can be reduced. [variableScope]
kmer-code-2013-trunk/leaff/stats.C:115:30: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/libbio/halign.c:66:9: warning: Identical condition 'x>M', second condition is always false [identicalConditionAfterEarlyExit]
kmer-code-2013-trunk/libbio/halign.c:63:8: note: If condition 'x>M' is true, the function will return/exit
kmer-code-2013-trunk/libbio/halign.c:66:9: note: Testing identical condition 'x>M'
kmer-code-2013-trunk/libbio/halign.c:394:20: style:inconclusive: Function 'halign' argument 1 names different: declaration 'string1' definition 'seq1'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libbio/bio.h:34:20: note: Function 'halign' argument 1 names different: declaration 'string1' definition 'seq1'.
kmer-code-2013-trunk/libbio/halign.c:394:20: note: Function 'halign' argument 1 names different: declaration 'string1' definition 'seq1'.
kmer-code-2013-trunk/libbio/halign.c:395:20: style:inconclusive: Function 'halign' argument 2 names different: declaration 'string2' definition 'seq2'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libbio/bio.h:35:20: note: Function 'halign' argument 2 names different: declaration 'string2' definition 'seq2'.
kmer-code-2013-trunk/libbio/halign.c:395:20: note: Function 'halign' argument 2 names different: declaration 'string2' definition 'seq2'.
kmer-code-2013-trunk/libbio/halign.c:32:16: style: struct member 'edit_script_list::offset1' is never used. [unusedStructMember]
kmer-code-2013-trunk/libbio/halign.c:32:25: style: struct member 'edit_script_list::offset2' is never used. [unusedStructMember]
kmer-code-2013-trunk/libbio/halign.c:33:16: style: struct member 'edit_script_list::len1' is never used. [unusedStructMember]
kmer-code-2013-trunk/libbio/halign.c:33:22: style: struct member 'edit_script_list::len2' is never used. [unusedStructMember]
kmer-code-2013-trunk/libbio/halign.c:34:16: style: struct member 'edit_script_list::score' is never used. [unusedStructMember]
kmer-code-2013-trunk/libbio/halign.c:35:16: style: struct member 'edit_script_list::first' is never used. [unusedStructMember]
kmer-code-2013-trunk/libbio/halign.c:36:16: style: struct member 'edit_script_list::script' is never used. [unusedStructMember]
kmer-code-2013-trunk/libbio/merCovering.H:24:7: performance: Variable '_lo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/merCovering.H:25:7: performance: Variable '_hi' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/merCovering.H:40:5: performance: Variable '_width' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/merCovering.H:41:5: performance: Variable '_pieces' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/merList.H:9:5: performance: Variable '_ptrsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/merList.H:10:5: performance: Variable '_ptrsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/merList.H:13:5: performance: Variable '_mersWid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:4:3: performance: Variable '_style' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:6:3: performance: Variable '_merSize' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:8:3: performance: Variable '_merSizeValidIs' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:9:3: performance: Variable '_merSizeValidZero' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:15:3: performance: Variable '_compression' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:16:3: performance: Variable '_compressionIndex' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:17:3: performance: Variable '_compressionFirstIndex' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:19:3: performance: Variable '_compressionCurrentLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:21:3: performance: Variable '_templateSpan' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:22:3: performance: Variable '_templateLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:24:3: performance: Variable '_templatePos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:25:3: performance: Variable '_templateMer' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/kmer.C:26:3: performance: Variable '_templateFirst' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libbio/merCovering.H:66:17: style:inconclusive: Technically the member function 'merCovering::sumOfLengths' can be const. [functionConst]
kmer-code-2013-trunk/libbio/merCovering.H:75:17: style:inconclusive: Technically the member function 'merCovering::numberOfPieces' can be const. [functionConst]
kmer-code-2013-trunk/libbio/merList.H:46:9: style:inconclusive: Technically the member function 'merList::getMer' can be const. [functionConst]
kmer-code-2013-trunk/libbio/kmer.H:63:8: performance:inconclusive: Technically the member function 'kMerBuilder::addBaseCompressedSpaced' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libbio/kmer.C:493:14: note: Technically the member function 'kMerBuilder::addBaseCompressedSpaced' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libbio/kmer.H:63:8: note: Technically the member function 'kMerBuilder::addBaseCompressedSpaced' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libbio/kmer.H:97:17: style:inconclusive: Technically the member function 'kMerBuilder::theFMer' can be const. [functionConst]
kmer-code-2013-trunk/libbio/kmer.H:98:17: style:inconclusive: Technically the member function 'kMerBuilder::theRMer' can be const. [functionConst]
kmer-code-2013-trunk/libbio/kmer.H:101:17: style:inconclusive: Technically the member function 'kMerBuilder::merSize' can be const. [functionConst]
kmer-code-2013-trunk/libbio/kmer.H:102:17: style:inconclusive: Technically the member function 'kMerBuilder::templateSpan' can be const. [functionConst]
kmer-code-2013-trunk/libbio/kmer.H:104:17: style:inconclusive: Technically the member function 'kMerBuilder::baseSpan' can be const. [functionConst]
kmer-code-2013-trunk/libbio/merList.H:11:5: warning: Class 'merList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libbio/merList.H:11:5: warning: Class 'merList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libbio/kmer.C:141:5: warning: Class 'kMerBuilder' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libbio/kmer.C:141:5: warning: Class 'kMerBuilder' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libbio/merCovering.H:38:3: style: Class 'merCovering' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libbio/kmertiny.H:142:29: style:inconclusive: Function 'merToString' argument 1 names different: declaration 'instr' definition 'str'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libbio/kmertiny.H:104:30: note: Function 'merToString' argument 1 names different: declaration 'instr' definition 'str'.
kmer-code-2013-trunk/libbio/kmertiny.H:142:29: note: Function 'merToString' argument 1 names different: declaration 'instr' definition 'str'.
kmer-code-2013-trunk/libbio/test/halign-test.C:12:6: style: Variable 's1' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libbio/test/halign-test.C:9:6: note: s1 is assigned
kmer-code-2013-trunk/libbio/test/halign-test.C:12:6: note: s1 is overwritten
kmer-code-2013-trunk/libbio/test/halign-test.C:13:6: style: Variable 's2' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libbio/test/halign-test.C:10:6: note: s2 is assigned
kmer-code-2013-trunk/libbio/test/halign-test.C:13:6: note: s2 is overwritten
kmer-code-2013-trunk/libbio/test/test-bigmer-msf.C:41:10: style: Variable 'dna' can be declared with const [constVariable]
kmer-code-2013-trunk/libkmer/existDB.H:56:15: style:inconclusive: Technically the member function 'existDB::isForward' can be const. [functionConst]
kmer-code-2013-trunk/libkmer/existDB.H:57:15: style:inconclusive: Technically the member function 'existDB::isCanonical' can be const. [functionConst]
kmer-code-2013-trunk/libkmer/existDB.H:76:16: style:inconclusive: Technically the member function 'existDB::HASH' can be const. [functionConst]
kmer-code-2013-trunk/libkmer/existDB.H:80:16: style:inconclusive: Technically the member function 'existDB::CHECK' can be const. [functionConst]
kmer-code-2013-trunk/libkmer/existDB.H:147:8: performance:inconclusive: Technically the member function 'existDB::clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libkmer/existDB.H:35:3: style: Class 'existDB' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libkmer/driver-existDB.C:52:41: style: Condition 'ee!=eg' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/libkmer/driver-existDB.C:52:27: note: Assuming that condition 'ef!=eg' is not redundant
kmer-code-2013-trunk/libkmer/driver-existDB.C:52:13: note: Assuming that condition 'ee!=ef' is not redundant
kmer-code-2013-trunk/libkmer/driver-existDB.C:52:41: note: Condition 'ee!=eg' is always false
kmer-code-2013-trunk/libkmer/driver-existDB.C:55:41: style: Condition 'ce!=cg' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/libkmer/driver-existDB.C:55:27: note: Assuming that condition 'cf!=cg' is not redundant
kmer-code-2013-trunk/libkmer/driver-existDB.C:55:13: note: Assuming that condition 'ce!=cf' is not redundant
kmer-code-2013-trunk/libkmer/driver-existDB.C:55:41: note: Condition 'ce!=cg' is always false
kmer-code-2013-trunk/libkmer/positionDB.H:143:16: style:inconclusive: Technically the member function 'positionDB::HASH' can be const. [functionConst]
kmer-code-2013-trunk/libkmer/positionDB.H:147:16: style:inconclusive: Technically the member function 'positionDB::CHECK' can be const. [functionConst]
kmer-code-2013-trunk/libkmer/existDB-create-from-fasta.C:254:19: style: The comparison 'rebuilding == false' is always true because 'rebuilding' and 'false' represent the same value. [knownConditionTrueFalse]
kmer-code-2013-trunk/libkmer/existDB-create-from-fasta.C:17:35: note: 'rebuilding' is assigned value 'false' here.
kmer-code-2013-trunk/libkmer/existDB-create-from-fasta.C:254:19: note: The comparison 'rebuilding == false' is always true because 'rebuilding' and 'false' represent the same value.
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:53:7: style: Condition 'beVerbose' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:18:34: note: Assignment 'beVerbose=false', assigned value is 0
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:26:15: note: Assuming condition is false
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:53:7: note: Condition 'beVerbose' is always false
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:64:7: style: Condition 'beVerbose' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:18:34: note: Assignment 'beVerbose=false', assigned value is 0
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:26:15: note: Assuming condition is false
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:64:7: note: Condition 'beVerbose' is always false
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:10:39: style:inconclusive: Function 'createFromMeryl' argument 1 names different: declaration 'filename' definition 'prefix'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libkmer/existDB.H:67:44: note: Function 'createFromMeryl' argument 1 names different: declaration 'filename' definition 'prefix'.
kmer-code-2013-trunk/libkmer/existDB-create-from-meryl.C:10:39: note: Function 'createFromMeryl' argument 1 names different: declaration 'filename' definition 'prefix'.
kmer-code-2013-trunk/libkmer/existDB-create-from-sequence.C:254:19: style: The comparison 'rebuilding == false' is always true because 'rebuilding' and 'false' represent the same value. [knownConditionTrueFalse]
kmer-code-2013-trunk/libkmer/existDB-create-from-sequence.C:17:35: note: 'rebuilding' is assigned value 'false' here.
kmer-code-2013-trunk/libkmer/existDB-create-from-sequence.C:254:19: note: The comparison 'rebuilding == false' is always true because 'rebuilding' and 'false' represent the same value.
kmer-code-2013-trunk/libkmer/existDB-state.C:24:3: warning:inconclusive: The buffer 'cigam' may not be null-terminated after the call to strncpy(). [terminateStrncpy]
kmer-code-2013-trunk/libkmer/existDB-state.C:77:5: error: Resource leak: F [resourceLeak]
kmer-code-2013-trunk/libkmer/positionDB.H:73:15: performance:inconclusive: Technically the member function 'positionDB::reallocateSpace' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libkmer/positionDB-access.C:6:13: note: Technically the member function 'positionDB::reallocateSpace' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libkmer/positionDB.H:73:15: note: Technically the member function 'positionDB::reallocateSpace' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libkmer/positionDB-access.C:36:36: style:inconclusive: Function 'loadPositions' argument 1 names different: declaration 'v' definition 'J'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libkmer/positionDB.H:78:41: note: Function 'loadPositions' argument 1 names different: declaration 'v' definition 'J'.
kmer-code-2013-trunk/libkmer/positionDB-access.C:36:36: note: Function 'loadPositions' argument 1 names different: declaration 'v' definition 'J'.
kmer-code-2013-trunk/libkmer/positionDB-access.C:8:41: style: Parameter 'posnLen' can be declared with const [constParameter]
kmer-code-2013-trunk/libkmer/positionDB-file.C:116:5: error: Resource leak: F [resourceLeak]
kmer-code-2013-trunk/libkmer/positionDB-mismatch.C:305:41: style:inconclusive: Function 'getUpToNMismatches' argument 2 names different: declaration 'maxMismatches' definition 'numMismatches'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libkmer/positionDB.H:100:46: note: Function 'getUpToNMismatches' argument 2 names different: declaration 'maxMismatches' definition 'numMismatches'.
kmer-code-2013-trunk/libkmer/positionDB-mismatch.C:305:41: note: Function 'getUpToNMismatches' argument 2 names different: declaration 'maxMismatches' definition 'numMismatches'.
kmer-code-2013-trunk/libkmer/positionDB-mismatch.C:93:12: style: Variable 'err' can be declared with const [constVariable]
kmer-code-2013-trunk/libkmer/positionDB-sort.C:86:80: debug: Wrong data detected by condition !tok->next()->astOperand2() [DacaWrongData]
kmer-code-2013-trunk/libkmer/positionDB.C:200:35: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/libkmer/test/test-maskonly.C:63:8: style: Variable 'thrs' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libmeryl/libmeryl.H:25:19: style:inconclusive: Technically the member function 'merylStreamReader::theCount' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:27:19: style:inconclusive: Technically the member function 'merylStreamReader::hasPositions' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:29:19: style:inconclusive: Technically the member function 'merylStreamReader::getPosition' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:31:19: style:inconclusive: Technically the member function 'merylStreamReader::merSize' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:32:19: style:inconclusive: Technically the member function 'merylStreamReader::merCompression' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:34:19: style:inconclusive: Technically the member function 'merylStreamReader::prefixSize' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:36:19: style:inconclusive: Technically the member function 'merylStreamReader::numberOfUniqueMers' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:37:19: style:inconclusive: Technically the member function 'merylStreamReader::numberOfDistinctMers' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:38:19: style:inconclusive: Technically the member function 'merylStreamReader::numberOfTotalMers' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:40:19: style:inconclusive: Technically the member function 'merylStreamReader::histogram' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:41:19: style:inconclusive: Technically the member function 'merylStreamReader::histogramLength' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:42:19: style:inconclusive: Technically the member function 'merylStreamReader::histogramHuge' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:43:19: style:inconclusive: Technically the member function 'merylStreamReader::histogramMaximumCount' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.H:46:19: style:inconclusive: Technically the member function 'merylStreamReader::validMer' can be const. [functionConst]
kmer-code-2013-trunk/libmeryl/libmeryl.C:25:3: warning: Class 'merylStreamReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libmeryl/libmeryl.C:25:3: warning: Class 'merylStreamReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libmeryl/libmeryl.C:204:3: warning: Class 'merylStreamWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libmeryl/libmeryl.C:204:3: warning: Class 'merylStreamWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libmeryl/libmeryl.H:21:3: style: Class 'merylStreamReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libmeryl/libmeryl.C:195:50: style:inconclusive: Function 'merylStreamWriter' argument 1 names different: declaration 'filePrefix' definition 'fn'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libmeryl/libmeryl.H:110:33: note: Function 'merylStreamWriter' argument 1 names different: declaration 'filePrefix' definition 'fn'.
kmer-code-2013-trunk/libmeryl/libmeryl.C:195:50: note: Function 'merylStreamWriter' argument 1 names different: declaration 'filePrefix' definition 'fn'.
kmer-code-2013-trunk/libmeryl/libmeryl.C:49:17: style: Variable 'Pmagic[i]' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libseq/seqFile.H:16:3: warning: Member variable 'seqFile::_filename' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libseq/seqFile.H:16:3: warning: Member variable 'seqFile::_typename' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libseq/seqFile.H:16:3: warning: Member variable 'seqFile::_randomAccessSupported' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libseq/seqFile.H:17:3: warning:inconclusive: Member variable 'seqFile::_filename' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libseq/seqFile.H:17:3: warning:inconclusive: Member variable 'seqFile::_typename' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libseq/seqFile.H:17:3: warning:inconclusive: Member variable 'seqFile::_randomAccessSupported' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libseq/fastaFile.C:24:3: warning: Class 'fastaFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libseq/fastaFile.C:24:3: warning: Class 'fastaFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libseq/fastaFile.H:27:3: style: Class 'fastaFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libseq/fastaFile.H:34:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaFile.H:34:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaFile.H:37:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaFile.H:37:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaFile.H:39:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaFile.H:39:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaFile.H:40:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaFile.H:40:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaFile.H:43:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaFile.H:43:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaFile.C:354:5: error: Resource leak: I [resourceLeak]
kmer-code-2013-trunk/libseq/fastaStdin.C:17:5: warning: Class 'fastaStdin' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libseq/fastaStdin.C:17:5: warning: Class 'fastaStdin' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libseq/fastaStdin.H:12:3: style: Class 'fastaStdin' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libseq/fastaStdin.H:19:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaStdin.H:19:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaStdin.H:22:23: style: The function 'getNumberOfSequences' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:31:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaStdin.H:22:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaStdin.H:25:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaStdin.H:25:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaStdin.H:27:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaStdin.H:27:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaStdin.H:28:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaStdin.H:28:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaStdin.H:31:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastaStdin.H:31:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastaStdin.C:110:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libseq/fastqFile.C:24:3: warning: Class 'fastqFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libseq/fastqFile.C:24:3: warning: Class 'fastqFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libseq/fastqFile.H:27:3: style: Class 'fastqFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libseq/fastqFile.H:34:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqFile.H:34:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqFile.H:37:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqFile.H:37:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqFile.H:39:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqFile.H:39:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqFile.H:40:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqFile.H:40:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqFile.H:43:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqFile.H:43:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqFile.C:351:5: error: Resource leak: I [resourceLeak]
kmer-code-2013-trunk/libseq/fastqStdin.C:17:5: warning: Class 'fastqStdin' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libseq/fastqStdin.C:17:5: warning: Class 'fastqStdin' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libseq/fastqStdin.H:12:3: style: Class 'fastqStdin' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libseq/fastqStdin.H:19:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqStdin.H:19:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqStdin.H:22:23: style: The function 'getNumberOfSequences' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:31:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqStdin.H:22:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqStdin.H:25:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqStdin.H:25:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqStdin.H:27:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqStdin.H:27:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqStdin.H:28:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqStdin.H:28:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqStdin.H:31:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/fastqStdin.H:31:23: note: Function in derived class
kmer-code-2013-trunk/libseq/fastqStdin.C:110:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libseq/merStream.C:11:3: performance: Variable '_beg' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/merStream.C:12:3: performance: Variable '_end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.H:32:21: style:inconclusive: Technically the member function 'seqStream::eof' can be const. [functionConst]
kmer-code-2013-trunk/libseq/seqStream.H:68:21: style:inconclusive: Technically the member function 'seqStream::seqPos' can be const. [functionConst]
kmer-code-2013-trunk/libseq/seqStream.H:69:21: style:inconclusive: Technically the member function 'seqStream::seqIID' can be const. [functionConst]
kmer-code-2013-trunk/libseq/seqStream.H:70:21: style:inconclusive: Technically the member function 'seqStream::strPos' can be const. [functionConst]
kmer-code-2013-trunk/libseq/seqStream.H:72:21: style:inconclusive: Technically the member function 'seqStream::numberOfSequences' can be const. [functionConst]
kmer-code-2013-trunk/libseq/seqStream.H:77:21: style:inconclusive: Technically the member function 'seqStream::lengthOf' can be const. [functionConst]
kmer-code-2013-trunk/libseq/seqStream.H:78:21: style:inconclusive: Technically the member function 'seqStream::IIDOf' can be const. [functionConst]
kmer-code-2013-trunk/libseq/seqStream.H:79:21: style:inconclusive: Technically the member function 'seqStream::startOf' can be const. [functionConst]
kmer-code-2013-trunk/libseq/seqStream.H:18:3: style: Class 'seqStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libseq/selftest.C:16:26: error: syntax error [syntaxError]
kmer-code-2013-trunk/libseq/seqCache.H:11:5: performance: Variable '_idx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqCache.H:15:5: performance: Variable '_headerLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqCache.H:18:5: performance: Variable '_seqLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqCache.H:67:3: style: Class 'seqCache' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libseq/seqFactory.C:13:3: performance: Variable '_filesNum' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqFactory.C:14:3: performance: Variable '_filesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqFactory.C:15:3: warning: Class 'seqFactory' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libseq/seqFactory.C:15:3: warning: Class 'seqFactory' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libseq/seqStore.H:72:3: style: Class 'seqStore' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libseq/seqStore.H:79:23: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/seqStore.H:79:23: note: Function in derived class
kmer-code-2013-trunk/libseq/seqStore.H:82:23: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/seqStore.H:82:23: note: Function in derived class
kmer-code-2013-trunk/libseq/seqStore.H:84:23: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/seqStore.H:84:23: note: Function in derived class
kmer-code-2013-trunk/libseq/seqStore.H:85:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/seqStore.H:85:23: note: Function in derived class
kmer-code-2013-trunk/libseq/seqStore.H:88:23: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/seqStore.H:88:23: note: Function in derived class
kmer-code-2013-trunk/libseq/seqStore.C:410:3: warning: memset() called to fill 0 bytes. [memsetZeroBytes]
kmer-code-2013-trunk/libseq/seqStore.C:28:3: warning: Class 'seqStore' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libseq/seqStore.C:28:3: warning: Class 'seqStore' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libseq/seqStore.C:72:5: error: Resource leak: F [resourceLeak]
kmer-code-2013-trunk/libseq/seqStore.C:594:20: style: Variable 'HEAD._indexStart' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libseq/seqStore.C:583:28: note: HEAD._indexStart is assigned
kmer-code-2013-trunk/libseq/seqStore.C:594:20: note: HEAD._indexStart is overwritten
kmer-code-2013-trunk/libseq/seqStore.C:598:20: style: Variable 'HEAD._blockStart' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libseq/seqStore.C:584:28: note: HEAD._blockStart is assigned
kmer-code-2013-trunk/libseq/seqStore.C:598:20: note: HEAD._blockStart is overwritten
kmer-code-2013-trunk/libseq/seqStore.C:602:20: style: Variable 'HEAD._namesStart' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libseq/seqStore.C:585:28: note: HEAD._namesStart is assigned
kmer-code-2013-trunk/libseq/seqStore.C:602:20: note: HEAD._namesStart is overwritten
kmer-code-2013-trunk/libseq/seqStore.C:372:35: style: Parameter 'b' can be declared with const [constParameter]
kmer-code-2013-trunk/libseq/seqStream.C:46:3: performance: Variable '_currentIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:47:3: performance: Variable '_currentPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:48:3: performance: Variable '_streamPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:50:3: performance: Variable '_bufferMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:51:3: performance: Variable '_bufferLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:52:3: performance: Variable '_bufferPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:53:3: performance: Variable '_bufferSep' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:56:3: performance: Variable '_idxLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:69:3: performance: Variable '_lengthOfSequences' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:74:3: performance: Variable '_separatorLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:76:3: performance: Variable '_bgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:77:3: performance: Variable '_end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libseq/seqStream.C:17:3: warning: Class 'seqStream' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libseq/seqStream.C:17:3: warning: Class 'seqStream' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libseq/sffFile.C:17:3: warning: Class 'sffFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libseq/sffFile.C:17:3: warning: Class 'sffFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libseq/sffFile.H:64:3: style: Class 'sffFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libseq/sffFile.H:71:17: style: The function 'openFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:23:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/sffFile.H:71:17: note: Function in derived class
kmer-code-2013-trunk/libseq/sffFile.H:74:17: style: The function 'find' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:34:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/sffFile.H:74:17: note: Function in derived class
kmer-code-2013-trunk/libseq/sffFile.H:79:17: style: The function 'getSequenceLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:36:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/sffFile.H:79:17: note: Function in derived class
kmer-code-2013-trunk/libseq/sffFile.H:81:17: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:37:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/sffFile.H:81:17: note: Function in derived class
kmer-code-2013-trunk/libseq/sffFile.H:84:17: style: The function 'getSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
kmer-code-2013-trunk/libseq/seqFile.H:40:25: note: Virtual function in base class
kmer-code-2013-trunk/libseq/sffFile.H:84:17: note: Function in derived class
kmer-code-2013-trunk/libseq/sffFile.C:111:5: error: Resource leak: F [resourceLeak]
kmer-code-2013-trunk/libseq/sffFile.C:11:30: style:inconclusive: Function 'sffFile' argument 1 names different: declaration 'filename' definition 'name'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libseq/sffFile.H:64:23: note: Function 'sffFile' argument 1 names different: declaration 'filename' definition 'name'.
kmer-code-2013-trunk/libseq/sffFile.C:11:30: note: Function 'sffFile' argument 1 names different: declaration 'filename' definition 'name'.
kmer-code-2013-trunk/libseq/test-merStream.C:43:16: warning: Assert statement calls a function which may have desired side effects: 'thePositionInSequence'. [assertWithSideEffect]
kmer-code-2013-trunk/libseq/test-merStream.C:44:16: warning: Assert statement calls a function which may have desired side effects: 'thePositionInStream'. [assertWithSideEffect]
kmer-code-2013-trunk/libseq/test-merStream.C:45:16: warning: Assert statement calls a function which may have desired side effects: 'theSequenceNumber'. [assertWithSideEffect]
kmer-code-2013-trunk/libseq/test-merStream.C:22:7: style: Condition 'verbose' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/libseq/test-merStream.C:19:22: note: Assignment 'verbose=true', assigned value is 1
kmer-code-2013-trunk/libseq/test-merStream.C:22:7: note: Condition 'verbose' is always true
kmer-code-2013-trunk/libseq/test-merStream.C:32:9: style: Condition 'verbose' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/libseq/test-merStream.C:19:22: note: Assignment 'verbose=true', assigned value is 1
kmer-code-2013-trunk/libseq/test-merStream.C:32:9: note: Condition 'verbose' is always true
kmer-code-2013-trunk/libseq/test-correctSequence.H:25:13: style: Variable 'bases' can be declared with const [constVariable]
kmer-code-2013-trunk/libseq/test-merStream.C:15:71: style: Parameter 'SP' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.H:113:5: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::type' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::masknum' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::seedLength' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::matchedLength' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:16:3: warning:inconclusive: Member variable 'mss_t::shifts' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libsim4/sim4core/exon.H:123:5: performance: Variable '_listLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/exon.H:124:5: performance: Variable '_listMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/exon.H:127:5: performance: Variable '_curLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/exon.H:128:5: performance: Variable '_curMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:52:5: performance: Variable '_estFrom' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:53:5: performance: Variable '_estTo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:54:5: performance: Variable '_genFrom' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:55:5: performance: Variable '_genTo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:56:5: performance: Variable '_numMatches' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:57:5: performance: Variable '_numMatchesN' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:58:5: performance: Variable '_percentIdentity' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:59:5: performance: Variable '_intronOrientation' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.H:41:10: performance:inconclusive: Technically the member function 'mspManager::transitionFunction' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.H:79:17: style:inconclusive: Technically the member function 'mspManager::tooManyMSPs' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.H:80:17: style:inconclusive: Technically the member function 'mspManager::numberOfMSPs' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4parameters.H:134:19: style:inconclusive: Technically the member function 'sim4parameters::getOutputFormat' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:68:10: style:inconclusive: Technically the member function 'sim4command::externalSeedsExist' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:69:10: style:inconclusive: Technically the member function 'sim4command::numberOfExternalSeeds' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:70:10: style:inconclusive: Technically the member function 'sim4command::externalSeedESTPosition' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:71:10: style:inconclusive: Technically the member function 'sim4command::externalSeedGENPosition' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:72:10: style:inconclusive: Technically the member function 'sim4command::externalSeedLength' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:86:10: style:inconclusive: Technically the member function 'sim4command::doForward' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:87:10: style:inconclusive: Technically the member function 'sim4command::doReverse' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:100:19: style:inconclusive: Technically the member function 'sim4command::getGENidx' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:101:19: style:inconclusive: Technically the member function 'sim4command::getGENlo' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:102:19: style:inconclusive: Technically the member function 'sim4command::getGENhi' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.H:19:17: style:inconclusive: Technically the member function 'sim4polishList::length' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:252:7: style:inconclusive: Technically the member function 'Sim4::snake' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:263:7: style:inconclusive: Technically the member function 'Sim4::rsnake' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:487:8: performance:inconclusive: Technically the member function 'Sim4::fatal' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:519:1: performance:inconclusive: Technically the member function 'Sim4::script_flip_list' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:532:9: performance:inconclusive: Technically the member function 'Sim4::computePercentIdentity' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:644:10: performance:inconclusive: Technically the member function 'Sim4::ckfree' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/exon.H:125:5: warning: Class 'exonManager' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libsim4/sim4core/exon.H:125:5: warning: Class 'exonManager' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:17:3: style: Class 'mss_t' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:161:3: style: Class 'sim4polish' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.H:13:3: style: Class 'sim4polishList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:544:3: style: Class 'Sim4' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:81:24: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:88:24: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:179:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:186:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:197:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:204:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:346:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:352:27: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:445:34: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:452:34: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:464:34: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:471:34: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:378:41: style: Parameter 'target' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:43:24: style: Parameter 's1' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:311:24: style: Parameter 's1' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:243:8: performance:inconclusive: Technically the member function 'Sim4::Flip_script' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/align.C:802:7: note: Technically the member function 'Sim4::Flip_script' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:243:8: note: Technically the member function 'Sim4::Flip_script' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:249:8: performance:inconclusive: Technically the member function 'Sim4::align_reverse' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/align.C:820:7: note: Technically the member function 'Sim4::align_reverse' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:249:8: note: Technically the member function 'Sim4::align_reverse' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/align.C:619:29: style: Condition 'j2-i2<j1-i1' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/libsim4/sim4core/align.C:593:22: note: Assuming that condition 'j2-i2==j1-i1' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/align.C:619:29: note: Condition 'j2-i2<j1-i1' is always true
kmer-code-2013-trunk/libsim4/sim4core/align.C:260:15: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:270:13: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:281:15: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:290:17: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:295:15: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:306:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:316:17: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:321:15: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:332:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:574:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:584:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:594:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:601:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:604:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:608:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:611:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:621:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:624:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:628:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:631:33: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/align.C:143:19: style: The scope of the variable 't1' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/align.C:143:27: style: The scope of the variable 't' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/align.C:822:7: style: The scope of the variable 'auxi' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/align.C:158:24: error: Uninitialized variable: SS [uninitvar]
kmer-code-2013-trunk/libsim4/sim4core/align.C:159:24: error: Uninitialized variable: DD [uninitvar]
kmer-code-2013-trunk/libsim4/sim4core/align.C:160:24: error: Uninitialized variable: II [uninitvar]
kmer-code-2013-trunk/libsim4/sim4core/exon_cores.C:44:27: style: The scope of the variable 'j' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/exon_cores.C:14:24: performance: Function parameter 'MSS' should be passed by const reference. [passedByValue]
kmer-code-2013-trunk/libsim4/sim4core/extend.C:7:23: style: Parameter 's1' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/extend.C:7:33: style: Parameter 's2' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/extend.C:169:23: style: Parameter 's1' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/extend.C:169:33: style: Parameter 's2' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:235:16: warning: Possible null pointer dereference: buff [nullPointer]
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:223:26: note: Assignment 'buff=NULL', assigned value is 0
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:227:11: note: Assuming condition is false
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:235:16: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:363:13: warning: Possible null pointer dereference: buff [nullPointer]
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:352:26: note: Assignment 'buff=NULL', assigned value is 0
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:357:22: note: Assuming condition is false
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:363:13: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:326:8: style: Variable 'pos' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:317:16: note: pos is assigned
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:326:8: note: pos is overwritten
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:414:10: style: The scope of the variable 'Clean_Exit_Msg_Line' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:438:10: style: The scope of the variable 'Clean_Exit_Msg_Line' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:460:10: style: The scope of the variable 'Clean_Exit_Msg_Line' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:299:40: style:inconclusive: Function 'Full_Window_Prob' argument 1 names different: declaration 'p' definition 'icm'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:31:39: note: Function 'Full_Window_Prob' argument 1 names different: declaration 'p' definition 'icm'.
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:299:40: note: Function 'Full_Window_Prob' argument 1 names different: declaration 'p' definition 'icm'.
kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:221:38: style: Parameter 'perm' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:313:19: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:73:26: style: Variable 'n0' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:74:29: style: Variable 'OFFSET1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:74:48: style: Variable 'OFFSET2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:75:25: style: Variable 's1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:75:34: style: Variable 's2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:117:26: style: Variable 'n0' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:118:29: style: Variable 'OFFSET1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:118:48: style: Variable 'OFFSET2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:119:25: style: Variable 's1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:119:34: style: Variable 's2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:313:22: style: Variable 's1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/greedy.C:313:31: style: Variable 's2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:17:3: performance: Variable '_allocMSPs' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:18:3: performance: Variable '_numMSPs' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:29:3: performance: Variable '_mspLimitAbsolute' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:19:3: warning: Class 'mspManager' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:19:3: warning: Class 'mspManager' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:86:0: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:87:0: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:167:7: style: The scope of the variable 'f1' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:167:11: style: The scope of the variable 'f2' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/mspManager.C:167:21: style: The scope of the variable 'diag' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:68:16: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:88:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:268:14: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:281:14: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:36:9: style: The scope of the variable 'a' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:36:13: style: The scope of the variable 'b' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:32:25: style:inconclusive: Function 'pluri_align' argument 2 names different: declaration 'lblock' definition 'theExons'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:364:28: note: Function 'pluri_align' argument 2 names different: declaration 'lblock' definition 'theExons'.
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:32:25: note: Function 'pluri_align' argument 2 names different: declaration 'lblock' definition 'theExons'.
kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:9:40: style: Parameter 'head' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:501:8: performance:inconclusive: Technically the member function 'Sim4::get_polyAT' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:7:7: note: Technically the member function 'Sim4::get_polyAT' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:501:8: note: Technically the member function 'Sim4::get_polyAT' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/poly.C:531:7: style: Condition 'exons_head' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:521:17: note: Assuming that condition '!Exons->next_exon' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/poly.C:529:14: note: exons_head is assigned 'Exons->next_exon' here.
kmer-code-2013-trunk/libsim4/sim4core/poly.C:531:7: note: Condition 'exons_head' is always true
kmer-code-2013-trunk/libsim4/sim4core/poly.C:117:7: warning: Either the condition 'prev==0L' is redundant or there is possible null pointer dereference: prev. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:109:16: note: Assuming that condition 'prev==0L' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/poly.C:117:7: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/poly.C:255:5: warning: Either the condition 'prev==0L' is redundant or there is possible null pointer dereference: prev. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:247:14: note: Assuming that condition 'prev==0L' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/poly.C:255:5: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/poly.C:296:10: warning: Either the condition 'exons_tail' is redundant or there is possible null pointer dereference: exons_tail. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:301:7: note: Assuming that condition 'exons_tail' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/poly.C:296:10: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/poly.C:90:17: style: The scope of the variable 'num' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:282:9: style: The scope of the variable 'b' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:282:13: style: The scope of the variable 'end' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:283:7: style: The scope of the variable 'numA' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:284:7: style: The scope of the variable 'startPos' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:351:17: style: The scope of the variable 'num' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:515:9: style: The scope of the variable 't' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:516:9: style: The scope of the variable 'b' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:516:13: style: The scope of the variable 'end' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:517:7: style: The scope of the variable 'numT' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:518:7: style: The scope of the variable 'startPos' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:7:24: warning: Function 'get_polyAT' argument order different: declaration 'seq, len, pA, pT, flag' definition 'seq, len, pT, pA, flag' [funcArgOrderDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:501:25: note: Function 'get_polyAT' argument order different: declaration 'seq, len, pA, pT, flag' definition 'seq, len, pT, pA, flag'
kmer-code-2013-trunk/libsim4/sim4core/poly.C:7:24: note: Function 'get_polyAT' argument order different: declaration 'seq, len, pA, pT, flag' definition 'seq, len, pT, pA, flag'
kmer-code-2013-trunk/libsim4/sim4core/poly.C:284:15: style: Variable 'startPos' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/poly.C:518:15: style: Variable 'startPos' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:350:10: performance:inconclusive: Technically the member function 'Sim4::resolve_overlap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:7:7: note: Technically the member function 'Sim4::resolve_overlap' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:350:10: note: Technically the member function 'Sim4::resolve_overlap' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:104:5: warning: Either the condition 'prev==0L' is redundant or there is possible null pointer dereference: prev. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:92:14: note: Assuming that condition 'prev==0L' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:104:5: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:105:5: warning: Either the condition 'prev==0L' is redundant or there is possible null pointer dereference: prev. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:92:14: note: Assuming that condition 'prev==0L' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:105:5: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:9:10: style: The scope of the variable 'GTAG_score' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:9:22: style: The scope of the variable 'CTAC_score' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1.C:73:22: style: Variable 'Lblock' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1.C:64:24: note: Lblock is assigned
kmer-code-2013-trunk/libsim4/sim4core/sim4b1.C:73:22: note: Lblock is overwritten
kmer-code-2013-trunk/libsim4/sim4core/sim4b1.C:280:21: style: Same value in both branches of ternary operator. [duplicateValueTernary]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1.C:16:11: style: The scope of the variable 'rollbflag' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.C:8:3: performance: Variable 'mask' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:28:11: style:inconclusive: Technically the member function 'mss_t::mask_shift' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.C:92:8: note: Technically the member function 'mss_t::mask_shift' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.H:28:11: note: Technically the member function 'mss_t::mask_shift' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4b1_s.C:13:10: style: The scope of the variable 'total' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:26:3: performance: Variable '_estIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:31:3: performance: Variable '_ESTsequenceLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:33:3: performance: Variable '_genIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:34:3: performance: Variable '_genLo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:35:3: performance: Variable '_genHi' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:40:3: performance: Variable '_GENsequenceLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:45:3: performance: Variable '_externalSeedsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:46:3: performance: Variable '_externalSeedsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:58:3: performance: Variable '_estIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:93:3: performance: Variable '_estIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:98:3: performance: Variable '_ESTsequenceLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:100:3: performance: Variable '_genIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:101:3: performance: Variable '_genLo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:102:3: performance: Variable '_genHi' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:107:3: performance: Variable '_GENsequenceLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:112:3: performance: Variable '_externalSeedsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:113:3: performance: Variable '_externalSeedsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:95:19: style:inconclusive: Technically the member function 'sim4command::getESTidx' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:176:14: note: Technically the member function 'sim4command::getESTidx' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:95:19: note: Technically the member function 'sim4command::getESTidx' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:184:16: style: The scope of the variable 'xxx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:222:9: style: The scope of the variable 'xxx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:23:38: style:inconclusive: Function 'sim4command' argument 7 names different: declaration 'doForward' definition 'doFor'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:29:29: note: Function 'sim4command' argument 7 names different: declaration 'doForward' definition 'doFor'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:23:38: note: Function 'sim4command' argument 7 names different: declaration 'doForward' definition 'doFor'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:24:38: style:inconclusive: Function 'sim4command' argument 8 names different: declaration 'doReverse' definition 'doRev'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:30:29: note: Function 'sim4command' argument 8 names different: declaration 'doReverse' definition 'doRev'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:24:38: note: Function 'sim4command' argument 8 names different: declaration 'doReverse' definition 'doRev'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:55:38: style:inconclusive: Function 'sim4command' argument 5 names different: declaration 'doForward' definition 'doFor'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:39:27: note: Function 'sim4command' argument 5 names different: declaration 'doForward' definition 'doFor'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:55:38: note: Function 'sim4command' argument 5 names different: declaration 'doForward' definition 'doFor'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:56:38: style:inconclusive: Function 'sim4command' argument 6 names different: declaration 'doReverse' definition 'doRev'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:40:27: note: Function 'sim4command' argument 6 names different: declaration 'doReverse' definition 'doRev'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:56:38: note: Function 'sim4command' argument 6 names different: declaration 'doReverse' definition 'doRev'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:91:44: style:inconclusive: Function 'sim4command' argument 7 names different: declaration 'doForward' definition 'doFor'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:51:33: note: Function 'sim4command' argument 7 names different: declaration 'doForward' definition 'doFor'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:91:44: note: Function 'sim4command' argument 7 names different: declaration 'doForward' definition 'doFor'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:92:44: style:inconclusive: Function 'sim4command' argument 8 names different: declaration 'doReverse' definition 'doRev'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4command.H:52:33: note: Function 'sim4command' argument 8 names different: declaration 'doReverse' definition 'doRev'.
kmer-code-2013-trunk/libsim4/sim4core/sim4command.C:92:44: note: Function 'sim4command' argument 8 names different: declaration 'doReverse' definition 'doRev'.
kmer-code-2013-trunk/libsim4/sim4core/sim4parameters.C:23:5: performance: Variable '_mspLimitAbsolute' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:248:8: performance:inconclusive: Technically the member function 'Sim4::S2A' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:794:7: note: Technically the member function 'Sim4::S2A' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:248:8: note: Technically the member function 'Sim4::S2A' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:274:9: performance:inconclusive: Technically the member function 'Sim4::checkExonsForOverlaps' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:587:7: note: Technically the member function 'Sim4::checkExonsForOverlaps' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:274:9: note: Technically the member function 'Sim4::checkExonsForOverlaps' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:275:9: performance:inconclusive: Technically the member function 'Sim4::appendExons' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:607:7: note: Technically the member function 'Sim4::appendExons' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:275:9: note: Technically the member function 'Sim4::appendExons' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:276:9: performance:inconclusive: Technically the member function 'Sim4::maskExonsFromSeeds' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:34:7: note: Technically the member function 'Sim4::maskExonsFromSeeds' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:276:9: note: Technically the member function 'Sim4::maskExonsFromSeeds' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:277:9: performance:inconclusive: Technically the member function 'Sim4::maskExonsFromGenomic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:52:7: note: Technically the member function 'Sim4::maskExonsFromGenomic' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:277:9: note: Technically the member function 'Sim4::maskExonsFromGenomic' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:35:32: style:inconclusive: Function 'maskExonsFromSeeds' argument 2 names different: declaration 'theExons' definition 'theExon'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:276:52: note: Function 'maskExonsFromSeeds' argument 2 names different: declaration 'theExons' definition 'theExon'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:35:32: note: Function 'maskExonsFromSeeds' argument 2 names different: declaration 'theExons' definition 'theExon'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:52:34: style:inconclusive: Function 'maskExonsFromGenomic' argument 1 names different: declaration 'theExons' definition 'theExon'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:277:36: note: Function 'maskExonsFromGenomic' argument 1 names different: declaration 'theExons' definition 'theExon'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:52:34: note: Function 'maskExonsFromGenomic' argument 1 names different: declaration 'theExons' definition 'theExon'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:607:47: style:inconclusive: Function 'appendExons' argument 2 names different: declaration 'theExon' definition 'theExons'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:275:49: note: Function 'appendExons' argument 2 names different: declaration 'theExon' definition 'theExons'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:607:47: note: Function 'appendExons' argument 2 names different: declaration 'theExon' definition 'theExons'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:819:30: style:inconclusive: Function 'appendAlignments' argument 2 names different: declaration 'seq1' definition 's1'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:292:34: note: Function 'appendAlignments' argument 2 names different: declaration 'seq1' definition 's1'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:819:30: note: Function 'appendAlignments' argument 2 names different: declaration 'seq1' definition 's1'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:820:30: style:inconclusive: Function 'appendAlignments' argument 3 names different: declaration 'seq2' definition 's2'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:293:34: note: Function 'appendAlignments' argument 3 names different: declaration 'seq2' definition 's2'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:820:30: note: Function 'appendAlignments' argument 3 names different: declaration 'seq2' definition 's2'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:821:28: style:inconclusive: Function 'appendAlignments' argument 4 names different: declaration 'len1' definition 'l1'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:294:32: note: Function 'appendAlignments' argument 4 names different: declaration 'len1' definition 'l1'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:821:28: note: Function 'appendAlignments' argument 4 names different: declaration 'len1' definition 'l1'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:822:28: style:inconclusive: Function 'appendAlignments' argument 5 names different: declaration 'len2' definition 'l2'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:295:32: note: Function 'appendAlignments' argument 5 names different: declaration 'len2' definition 'l2'.
kmer-code-2013-trunk/libsim4/sim4core/sim4string.C:822:28: note: Function 'appendAlignments' argument 5 names different: declaration 'len2' definition 'l2'.
kmer-code-2013-trunk/libsim4/sim4core/sites.C:182:3: warning: Assignment of function parameter has no effect outside the function. Did you forget dereferencing it? [uselessAssignmentPtrArg]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:457:11: performance:inconclusive: Technically the member function 'Sim4::ScoreAcceptor_GeneSplicer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sites.C:270:7: note: Technically the member function 'Sim4::ScoreAcceptor_GeneSplicer' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:457:11: note: Technically the member function 'Sim4::ScoreAcceptor_GeneSplicer' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:459:11: performance:inconclusive: Technically the member function 'Sim4::UnLoadSites_GeneSplicer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/sites.C:187:7: note: Technically the member function 'Sim4::UnLoadSites_GeneSplicer' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:459:11: note: Technically the member function 'Sim4::UnLoadSites_GeneSplicer' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sites.C:554:17: style: The scope of the variable 'poz' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/sites.C:758:15: style: The scope of the variable 'k' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/sites.C:456:5: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/sites.C:516:7: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/sites.C:607:6: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/sites.C:686:7: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:418:11: performance:inconclusive: Technically the member function 'Sim4::ScoreDonor_Glimmer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:95:7: note: Technically the member function 'Sim4::ScoreDonor_Glimmer' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:418:11: note: Technically the member function 'Sim4::ScoreDonor_Glimmer' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:419:11: performance:inconclusive: Technically the member function 'Sim4::ScoreAcceptor_Glimmer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:109:7: note: Technically the member function 'Sim4::ScoreAcceptor_Glimmer' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:419:11: note: Technically the member function 'Sim4::ScoreAcceptor_Glimmer' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:421:8: style:inconclusive: Technically the member function 'Sim4::splice_original' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:567:7: note: Technically the member function 'Sim4::splice_original' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:421:8: note: Technically the member function 'Sim4::splice_original' can be const.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:182:19: style: Condition 'spliceInit==1' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:142:8: note: Assuming that condition 'spliceInit' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/splice.C:172:42: note: Assuming condition is false
kmer-code-2013-trunk/libsim4/sim4core/splice.C:182:19: note: Condition 'spliceInit==1' is always false
kmer-code-2013-trunk/libsim4/sim4core/splice.C:130:18: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:212:23: style: The scope of the variable 'ss' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:212:27: style: The scope of the variable 'ssx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:212:32: style: The scope of the variable 'cx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:212:36: style: The scope of the variable 'c' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:213:11: style: The scope of the variable 's' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:271:13: style: The scope of the variable 'ss' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:271:17: style: The scope of the variable 'ssx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:271:22: style: The scope of the variable 'cx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:271:26: style: The scope of the variable 'c' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:272:9: style: The scope of the variable 's' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:320:19: style: The scope of the variable 'ss' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:320:23: style: The scope of the variable 'ssx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:320:28: style: The scope of the variable 'cx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:320:32: style: The scope of the variable 'c' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:321:13: style: The scope of the variable 's' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:376:19: style: The scope of the variable 'ss' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:376:23: style: The scope of the variable 'ssx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:376:28: style: The scope of the variable 'cx' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:376:32: style: The scope of the variable 'c' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:377:13: style: The scope of the variable 's' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:574:14: style: The scope of the variable 't' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:574:17: style: The scope of the variable 'ch' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:630:14: style: The scope of the variable 't' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:630:17: style: The scope of the variable 'ch' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:709:17: style: The scope of the variable 'ch' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:266:51: style:inconclusive: Function 'splice_donor_uni' argument 6 names different: declaration 'max_IF' definition 'max_If'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:407:52: note: Function 'splice_donor_uni' argument 6 names different: declaration 'max_IF' definition 'max_If'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:266:51: note: Function 'splice_donor_uni' argument 6 names different: declaration 'max_IF' definition 'max_If'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:266:65: style:inconclusive: Function 'splice_donor_uni' argument 7 names different: declaration 'end_Ii' definition 'start_Ii'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:407:66: note: Function 'splice_donor_uni' argument 7 names different: declaration 'end_Ii' definition 'start_Ii'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:266:65: note: Function 'splice_donor_uni' argument 7 names different: declaration 'end_Ii' definition 'start_Ii'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:571:29: style:inconclusive: Function 'splice_original' argument 14 names different: declaration 'nsgemnetL' definition 'nsegmentL'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:425:30: note: Function 'splice_original' argument 14 names different: declaration 'nsgemnetL' definition 'nsegmentL'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:571:29: note: Function 'splice_original' argument 14 names different: declaration 'nsgemnetL' definition 'nsegmentL'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:627:32: style:inconclusive: Function 'splice_GeneSplicer' argument 14 names different: declaration 'nsgemnetL' definition 'nsegmentL'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:430:30: note: Function 'splice_GeneSplicer' argument 14 names different: declaration 'nsgemnetL' definition 'nsegmentL'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:627:32: note: Function 'splice_GeneSplicer' argument 14 names different: declaration 'nsgemnetL' definition 'nsegmentL'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:706:28: style:inconclusive: Function 'splice_Glimmer' argument 14 names different: declaration 'nsgementL' definition 'nsegmentL'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:435:30: note: Function 'splice_Glimmer' argument 14 names different: declaration 'nsgementL' definition 'nsegmentL'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:706:28: note: Function 'splice_Glimmer' argument 14 names different: declaration 'nsgementL' definition 'nsegmentL'.
kmer-code-2013-trunk/libsim4/sim4core/splice.C:205:66: style: Parameter 'gt_score' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:206:28: style: Parameter 'ct_score' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:266:32: style: Parameter 'It_score' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:314:31: style: Parameter 'ag_score' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:314:49: style: Parameter 'ac_score' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/splice.C:371:35: style: Parameter 'aI_score' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:309:7: style:inconclusive: Technically the member function 'Sim4::good_ratio' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/util.C:169:7: note: Technically the member function 'Sim4::good_ratio' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:309:7: note: Technically the member function 'Sim4::good_ratio' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:310:8: performance:inconclusive: Technically the member function 'Sim4::flip_list' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/util.C:118:7: note: Technically the member function 'Sim4::flip_list' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:310:8: note: Technically the member function 'Sim4::flip_list' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:341:10: style:inconclusive: Technically the member function 'Sim4::merge' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/util.C:178:7: note: Technically the member function 'Sim4::merge' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:341:10: note: Technically the member function 'Sim4::merge' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:342:10: performance:inconclusive: Technically the member function 'Sim4::get_sync_flag' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/util.C:299:7: note: Technically the member function 'Sim4::get_sync_flag' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:342:10: note: Technically the member function 'Sim4::get_sync_flag' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:345:10: performance:inconclusive: Technically the member function 'Sim4::filter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/util.C:695:7: note: Technically the member function 'Sim4::filter' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:345:10: note: Technically the member function 'Sim4::filter' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:346:10: performance:inconclusive: Technically the member function 'Sim4::wobble' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/util.C:505:7: note: Technically the member function 'Sim4::wobble' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:346:10: note: Technically the member function 'Sim4::wobble' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:349:10: style:inconclusive: Technically the member function 'Sim4::compact_list' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/util.C:138:7: note: Technically the member function 'Sim4::compact_list' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:349:10: note: Technically the member function 'Sim4::compact_list' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:370:10: style:inconclusive: Technically the member function 'Sim4::get_stats' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4core/util.C:77:7: note: Technically the member function 'Sim4::get_stats' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:370:10: note: Technically the member function 'Sim4::get_stats' can be const.
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:384:10: performance:inconclusive: Technically the member function 'Sim4::get_match_quality' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4core/util.C:800:7: note: Technically the member function 'Sim4::get_match_quality' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:384:10: note: Technically the member function 'Sim4::get_match_quality' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4core/util.C:394:28: style: Condition 'c->score==g->score' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/libsim4/sim4core/util.C:392:28: note: Assuming that condition 'c->score>g->score' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/util.C:394:28: note: Condition 'c->score==g->score' is always true
kmer-code-2013-trunk/libsim4/sim4core/util.C:346:10: warning: Either the condition 'Glist==0L' is redundant or there is possible null pointer dereference: Glist. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/util.C:350:14: note: Assuming that condition 'Glist==0L' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/util.C:346:10: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/util.C:347:10: warning: Either the condition 'Clist==0L' is redundant or there is possible null pointer dereference: Clist. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/util.C:350:31: note: Assuming that condition 'Clist==0L' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/util.C:347:10: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/util.C:348:10: warning: Either the condition 'oris==0L' is redundant or there is possible null pointer dereference: oris. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/util.C:350:47: note: Assuming that condition 'oris==0L' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/util.C:348:10: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/util.C:750:14: warning: Either the condition 't1' is redundant or there is possible null pointer dereference: t1. [nullPointerRedundantCheck]
kmer-code-2013-trunk/libsim4/sim4core/util.C:747:17: note: Assuming that condition 't1' is not redundant
kmer-code-2013-trunk/libsim4/sim4core/util.C:750:14: note: Null pointer dereference
kmer-code-2013-trunk/libsim4/sim4core/util.C:226:15: style: Variable 'head' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libsim4/sim4core/util.C:224:8: note: head is assigned
kmer-code-2013-trunk/libsim4/sim4core/util.C:226:15: note: head is overwritten
kmer-code-2013-trunk/libsim4/sim4core/util.C:756:10: style: Variable 't0' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libsim4/sim4core/util.C:748:16: note: t0 is assigned
kmer-code-2013-trunk/libsim4/sim4core/util.C:756:10: note: t0 is overwritten
kmer-code-2013-trunk/libsim4/sim4core/util.C:775:45: style: Variable 't1' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libsim4/sim4core/util.C:767:13: note: t1 is assigned
kmer-code-2013-trunk/libsim4/sim4core/util.C:775:45: note: t1 is overwritten
kmer-code-2013-trunk/libsim4/sim4core/util.C:141:7: style: The scope of the variable 'diff' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4core/util.C:323:29: style:inconclusive: Function 'sync_slide_intron' argument 1 names different: declaration 'w' definition 'in_w'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:344:32: note: Function 'sync_slide_intron' argument 1 names different: declaration 'w' definition 'in_w'.
kmer-code-2013-trunk/libsim4/sim4core/util.C:323:29: note: Function 'sync_slide_intron' argument 1 names different: declaration 'w' definition 'in_w'.
kmer-code-2013-trunk/libsim4/sim4core/util.C:509:20: style:inconclusive: Function 'wobble' argument 5 names different: declaration 'seq1' definition 'seq'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:346:67: note: Function 'wobble' argument 5 names different: declaration 'seq1' definition 'seq'.
kmer-code-2013-trunk/libsim4/sim4core/util.C:509:20: note: Function 'wobble' argument 5 names different: declaration 'seq1' definition 'seq'.
kmer-code-2013-trunk/libsim4/sim4core/util.C:573:24: style:inconclusive: Function 'slide_intron' argument 1 names different: declaration 'w' definition 'in_w'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4core/sim4.H:343:27: note: Function 'slide_intron' argument 1 names different: declaration 'w' definition 'in_w'.
kmer-code-2013-trunk/libsim4/sim4core/util.C:573:24: note: Function 'slide_intron' argument 1 names different: declaration 'w' definition 'in_w'.
kmer-code-2013-trunk/libsim4/sim4core/util.C:138:27: style: Parameter 'Lblock' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/util.C:299:41: style: Parameter 'rblock' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/util.C:573:49: style: Parameter 'last' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4core/util.C:323:54: style: Parameter 'last' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:231:38: style:inconclusive: Function 's4p_compareExons_Overlap' argument 5 names different: declaration 'numAOnly' definition 'numAMissed'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:277:43: note: Function 's4p_compareExons_Overlap' argument 5 names different: declaration 'numAOnly' definition 'numAMissed'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:231:38: note: Function 's4p_compareExons_Overlap' argument 5 names different: declaration 'numAOnly' definition 'numAMissed'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:232:38: style:inconclusive: Function 's4p_compareExons_Overlap' argument 6 names different: declaration 'numBOnly' definition 'numBMissed'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:278:43: note: Function 's4p_compareExons_Overlap' argument 6 names different: declaration 'numBOnly' definition 'numBMissed'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:232:38: note: Function 's4p_compareExons_Overlap' argument 6 names different: declaration 'numBOnly' definition 'numBMissed'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:350:35: style:inconclusive: Function 's4p_compareExons_Ends' argument 5 names different: declaration 'numAOnly' definition 'numAMissed'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:284:40: note: Function 's4p_compareExons_Ends' argument 5 names different: declaration 'numAOnly' definition 'numAMissed'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:350:35: note: Function 's4p_compareExons_Ends' argument 5 names different: declaration 'numAOnly' definition 'numAMissed'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:351:35: style:inconclusive: Function 's4p_compareExons_Ends' argument 6 names different: declaration 'numBOnly' definition 'numBMissed'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:285:40: note: Function 's4p_compareExons_Ends' argument 6 names different: declaration 'numBOnly' definition 'numBMissed'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:351:35: note: Function 's4p_compareExons_Ends' argument 6 names different: declaration 'numBOnly' definition 'numBMissed'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-compare.C:237:21: style: Variable 'overlap' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-deleteexon.C:10:10: style: The scope of the variable 'ed' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-deleteexon.C:10:15: style: The scope of the variable 'gd' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:181:10: performance:inconclusive: Technically the member function 'sim4polish::s4p_readPolishATAC' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-read.C:180:13: note: Technically the member function 'sim4polish::s4p_readPolishATAC' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:181:10: note: Technically the member function 'sim4polish::s4p_readPolishATAC' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:270:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:272:14: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:308:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:361:13: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:363:16: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:397:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:370:15: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:383:15: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:12:42: style:inconclusive: Function 's4p_linesToPolishS4DB' argument 1 names different: declaration 'lineNumber' definition 'startPosition'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:183:39: note: Function 's4p_linesToPolishS4DB' argument 1 names different: declaration 'lineNumber' definition 'startPosition'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:12:42: note: Function 's4p_linesToPolishS4DB' argument 1 names different: declaration 'lineNumber' definition 'startPosition'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:196:42: style:inconclusive: Function 's4p_linesToPolishGFF3' argument 1 names different: declaration 'lineNumber' definition 'startPosition'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:184:39: note: Function 's4p_linesToPolishGFF3' argument 1 names different: declaration 'lineNumber' definition 'startPosition'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:196:42: note: Function 's4p_linesToPolishGFF3' argument 1 names different: declaration 'lineNumber' definition 'startPosition'.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:15:43: style: Parameter 'lengths' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:199:43: style: Parameter 'lengths' can be declared with const [constParameter]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:223:10: performance:inconclusive: Technically the member function 'sim4polish::s4p_percentIdentityApprox' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:117:13: note: Technically the member function 'sim4polish::s4p_percentIdentityApprox' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:223:10: note: Technically the member function 'sim4polish::s4p_percentIdentityApprox' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:228:10: style:inconclusive: Technically the member function 'sim4polish::s4p_percentIdentityExact' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:137:13: note: Technically the member function 'sim4polish::s4p_percentIdentityExact' can be const.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:228:10: note: Technically the member function 'sim4polish::s4p_percentIdentityExact' can be const.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:229:10: style:inconclusive: Technically the member function 'sim4polish::s4p_percentCoverageExact' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-updatescores.C:131:13: note: Technically the member function 'sim4polish::s4p_percentCoverageExact' can be const.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polish.H:229:10: note: Technically the member function 'sim4polish::s4p_percentCoverageExact' can be const.
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:13:3: performance: Variable 'exPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:14:3: performance: Variable 'exMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:15:3: performance: Variable 'exAli' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:16:3: warning: Class 'sim4polishBuilder' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishBuilder.C:16:3: warning: Class 'sim4polishBuilder' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishFile.H:40:13: style:inconclusive: Technically the member function 'sim4polishFile::maxIID' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishFile.C:39:3: warning: Class 'sim4polishFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishFile.C:39:3: warning: Class 'sim4polishFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishFile.C:77:19: style: The scope of the variable 'p' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishFile.C:129:10: style: The scope of the variable 'cigam' can be reduced. [variableScope]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:12:3: performance: Variable 'len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:13:3: performance: Variable 'max' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:18:3: performance: Variable 'len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:19:3: performance: Variable 'max' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.H:22:19: style:inconclusive: Technically the member function 'sim4polishReader::getsim4polishStyle' can be const. [functionConst]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:20:3: warning: Class 'sim4polishList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishList.C:20:3: warning: Class 'sim4polishList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.H:14:3: style: Class 'sim4polishReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:18:5: warning: Class 'sim4polishReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishReader.C:18:5: warning: Class 'sim4polishReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.H:21:8: performance:inconclusive: Technically the member function 'sim4polishWriter::s4p_putHeaderS4DB' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:81:19: note: Technically the member function 'sim4polishWriter::s4p_putHeaderS4DB' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.H:21:8: note: Technically the member function 'sim4polishWriter::s4p_putHeaderS4DB' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.H:23:8: performance:inconclusive: Technically the member function 'sim4polishWriter::s4p_putHeaderATAC' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:86:19: note: Technically the member function 'sim4polishWriter::s4p_putHeaderATAC' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.H:23:8: note: Technically the member function 'sim4polishWriter::s4p_putHeaderATAC' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:36:5: warning: Class 'sim4polishWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libsim4/sim4polish/sim4polishWriter.C:36:5: warning: Class 'sim4polishWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/unaryEncoding.h:43:3: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
kmer-code-2013-trunk/libutil/bigQueue.H:44:3: warning: Member variable 'bigQueue::_inputFile' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libutil/bigQueue.H:56:3: warning: Member variable 'bigQueue::_inputFile' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libutil/bigQueue.H:68:3: warning: Member variable 'bigQueue::_inputFile' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libutil/uint32List.H:47:11: style:inconclusive: Technically the member function 'uint32List::length' can be const. [functionConst]
kmer-code-2013-trunk/libutil/readBuffer.H:11:20: style:inconclusive: Technically the member function 'readBuffer::eof' can be const. [functionConst]
kmer-code-2013-trunk/libutil/readBuffer.H:20:20: style:inconclusive: Technically the member function 'readBuffer::tell' can be const. [functionConst]
kmer-code-2013-trunk/libutil/readBuffer.H:22:20: style:inconclusive: Technically the member function 'readBuffer::filename' can be const. [functionConst]
kmer-code-2013-trunk/libutil/splitToWords.H:104:11: style:inconclusive: Technically the member function 'splitToWords::numWords' can be const. [functionConst]
kmer-code-2013-trunk/libutil/bitPackedArray.H:61:12: style:inconclusive: Technically the member function 'bitArray::get' can be const. [functionConst]
kmer-code-2013-trunk/libutil/bitPackedArray.H:239:11: note: Technically the member function 'bitArray::get' can be const.
kmer-code-2013-trunk/libutil/bitPackedArray.H:61:12: note: Technically the member function 'bitArray::get' can be const.
kmer-code-2013-trunk/libutil/recordFile.H:25:14: style:inconclusive: Technically the member function 'recordFile::numRecords' can be const. [functionConst]
kmer-code-2013-trunk/libutil/intervalList.H:109:13: style:inconclusive: Technically the member function 'intervalList::overlapping' can be const. [functionConst]
kmer-code-2013-trunk/libutil/intervalList.H:460:27: note: Technically the member function 'intervalList::overlapping' can be const.
kmer-code-2013-trunk/libutil/intervalList.H:109:13: note: Technically the member function 'intervalList::overlapping' can be const.
kmer-code-2013-trunk/libutil/intervalList.H:127:13: style:inconclusive: Technically the member function 'intervalList::numberOfIntervals' can be const. [functionConst]
kmer-code-2013-trunk/libutil/bigQueue.H:102:11: performance:inconclusive: Technically the member function 'bigQueue::save' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/libutil/bigQueue.C:330:11: note: Technically the member function 'bigQueue::save' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libutil/bigQueue.H:102:11: note: Technically the member function 'bigQueue::save' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/libutil/uint32List.H:17:5: warning: Class 'uint32List' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libutil/uint32List.H:17:5: warning: Class 'uint32List' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/bitPackedArray.H:88:5: warning: Class 'bitPackedHeap' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libutil/bitPackedArray.H:88:5: warning: Class 'bitPackedHeap' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/logMsg.H:20:5: warning: Class 'logMsg' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libutil/logMsg.H:20:5: warning: Class 'logMsg' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/readBuffer.H:7:3: style: Class 'readBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libutil/readBuffer.H:8:3: style: Class 'readBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libutil/splitToWords.H:14:3: style: Class 'splitToWords' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libutil/bitPackedArray.H:26:3: style: Class 'bitPackedArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libutil/bitPackedArray.H:87:3: style: Class 'bitPackedHeap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libutil/bitPackedFile.H:17:3: style: Class 'bitPackedFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libutil/bitPacking.h:193:10: style: The scope of the variable 'b1' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/bitPacking.h:245:10: style: The scope of the variable 'b1' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/bitPackedArray.H:116:13: style: The scope of the variable 'cval' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/bitPackedArray.H:167:13: style: The scope of the variable 'pidx' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/bitPackedArray.H:168:13: style: The scope of the variable 'pval' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/bitPackedFile.H:87:31: style:inconclusive: Function 'getBits' argument 1 names different: declaration 'size' definition 'siz'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/bitPackedFile.H:20:29: note: Function 'getBits' argument 1 names different: declaration 'size' definition 'siz'.
kmer-code-2013-trunk/libutil/bitPackedFile.H:87:31: note: Function 'getBits' argument 1 names different: declaration 'size' definition 'siz'.
kmer-code-2013-trunk/libutil/bitPackedFile.H:107:44: style:inconclusive: Function 'putBits' argument 2 names different: declaration 'size' definition 'siz'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/bitPackedFile.H:23:42: note: Function 'putBits' argument 2 names different: declaration 'size' definition 'siz'.
kmer-code-2013-trunk/libutil/bitPackedFile.H:107:44: note: Function 'putBits' argument 2 names different: declaration 'size' definition 'siz'.
kmer-code-2013-trunk/libutil/intervalList.H:187:64: style:inconclusive: Function 'add' argument 3 names different: declaration 'value' definition 'val'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/intervalList.H:101:50: note: Function 'add' argument 3 names different: declaration 'value' definition 'val'.
kmer-code-2013-trunk/libutil/intervalList.H:187:64: note: Function 'add' argument 3 names different: declaration 'value' definition 'val'.
kmer-code-2013-trunk/libutil/intervalList.H:341:39: style:inconclusive: Function 'invert' argument 1 names different: declaration 'lo' definition 'invlo'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/intervalList.H:123:25: note: Function 'invert' argument 1 names different: declaration 'lo' definition 'invlo'.
kmer-code-2013-trunk/libutil/intervalList.H:341:39: note: Function 'invert' argument 1 names different: declaration 'lo' definition 'invlo'.
kmer-code-2013-trunk/libutil/intervalList.H:341:51: style:inconclusive: Function 'invert' argument 2 names different: declaration 'hi' definition 'invhi'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/intervalList.H:123:34: note: Function 'invert' argument 2 names different: declaration 'hi' definition 'invhi'.
kmer-code-2013-trunk/libutil/intervalList.H:341:51: note: Function 'invert' argument 2 names different: declaration 'hi' definition 'invhi'.
kmer-code-2013-trunk/libutil/intervalList.H:460:49: style:inconclusive: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/intervalList.H:109:35: note: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'.
kmer-code-2013-trunk/libutil/intervalList.H:460:49: note: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'.
kmer-code-2013-trunk/libutil/intervalList.H:461:49: style:inconclusive: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/intervalList.H:110:35: note: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'.
kmer-code-2013-trunk/libutil/intervalList.H:461:49: note: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'.
kmer-code-2013-trunk/libutil/intervalList.H:544:59: style:inconclusive: Function 'depth' argument 1 names different: declaration 'A' definition 'IL'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/intervalList.H:125:45: note: Function 'depth' argument 1 names different: declaration 'A' definition 'IL'.
kmer-code-2013-trunk/libutil/intervalList.H:544:59: note: Function 'depth' argument 1 names different: declaration 'A' definition 'IL'.
kmer-code-2013-trunk/libutil/fibonacciEncoding.h:121:35: style: Parameter 'ptr' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/bitPacking.h:181:26: style: Parameter 'ptr' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/bitPacking.h:184:26: style: Parameter 'sizs' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/bitPacking.h:241:26: style: Parameter 'sizs' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/bitPacking.h:107:25: style: Parameter 'ptr' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/bitPacking.h:193:14: style: Variable 'b1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/bitPacking.h:245:14: style: Variable 'b1' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/unaryEncoding.h:39:9: style: Variable 'siz' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/unaryEncoding.h:43:7: style: Variable 'pos' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/bitPackedArray.H:116:18: style: Variable 'cval' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/bitPackedArray.H:167:18: style: Variable 'pidx' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/bitPackedArray.H:168:18: style: Variable 'pval' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/bitPackedArray.C:73:5: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled]
kmer-code-2013-trunk/libutil/bitPackedArray.C:99:5: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled]
kmer-code-2013-trunk/libutil/bitPackedArray.C:18:3: warning: Class 'bitPackedArray' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libutil/bitPackedArray.C:18:3: warning: Class 'bitPackedArray' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/bitPackedArray.C:85:3: warning: Class 'bitArray' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libutil/bitPackedArray.C:85:3: warning: Class 'bitArray' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/bitPackedFile.C:16:3: warning: Class 'bitPackedFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libutil/bitPackedFile.C:16:3: warning: Class 'bitPackedFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/bitPackedFile.C:403:28: style:inconclusive: Function 'seek' argument 1 names different: declaration 'pos' definition 'bitpos'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/bitPackedFile.H:27:26: note: Function 'seek' argument 1 names different: declaration 'pos' definition 'bitpos'.
kmer-code-2013-trunk/libutil/bitPackedFile.C:403:28: note: Function 'seek' argument 1 names different: declaration 'pos' definition 'bitpos'.
kmer-code-2013-trunk/libutil/file.c:174:22: style: Variable 'bytesRead' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/file.c:300:20: style: Variable 'towrite' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/file.c:301:20: style: Variable 'written' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/file.c:325:20: style: Variable 'toread' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/file.c:326:20: style: Variable 'written' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/file.c:327:20: style: Variable 'failed' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/file.c:382:19: style: Variable 'isRW' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/file.c:398:14: style: Variable 'isRW' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/file.c:403:14: style: Variable 'isRW' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/kazlib/except.c:206:5: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/kazlib/except.c:206:5: warning: %ld in format string (no. 3) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/kazlib/hash.c:813:26: style: Variable 'randbox' can be declared with const [constVariable]
kmer-code-2013-trunk/libutil/kazlib/list.c:306:51: style: Parameter 'node' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/kazlib/list.c:368:42: style: Parameter 'node' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/kazlib/sfx.c:1121:2: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/kazlib/sfx.c:1124:2: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/kazlib/sfx.c:1127:2: warning: %ld in format string (no. 2) requires 'long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/kazlib/sfx.c:1099:12: style: Variable 'result' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libutil/kazlib/sfx.c:1096:9: note: result is assigned
kmer-code-2013-trunk/libutil/kazlib/sfx.c:1099:12: note: result is overwritten
kmer-code-2013-trunk/libutil/kazlib/sfx.c:76:56: style: Parameter 'orig' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/md5.c:267:52: style: Parameter 'input' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:129:18: style:inconclusive: Function 'mtRandom32' argument 1 names different: declaration 'mt' definition 'ctx'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/util.h:283:33: note: Function 'mtRandom32' argument 1 names different: declaration 'mt' definition 'ctx'.
kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:129:18: note: Function 'mtRandom32' argument 1 names different: declaration 'mt' definition 'ctx'.
kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:94:21: style: Parameter 'init_key' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:186:6: style: Variable 'y2' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/mt19937ar/tt800.c:29:26: style: Variable 'mag01' can be declared with const [constVariable]
kmer-code-2013-trunk/libutil/palloc.c:37:5: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:100:5: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:100:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:136:7: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:171:7: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:189:7: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:189:7: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:189:7: portability: %zd in format string (no. 4) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:208:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:208:5: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:229:3: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/palloc.c:231:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/readBuffer.C:69:3: warning: Class 'readBuffer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libutil/readBuffer.C:69:3: warning: Class 'readBuffer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/readBuffer.C:218:12: style: The scope of the variable 'bAct' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/readBuffer.C:64:30: style:inconclusive: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'. [funcArgNamesDifferent]
kmer-code-2013-trunk/libutil/readBuffer.H:8:20: note: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'.
kmer-code-2013-trunk/libutil/readBuffer.C:64:30: note: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'.
kmer-code-2013-trunk/libutil/readBuffer.C:218:20: style: Variable 'bAct' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/recordFile.C:22:3: warning: Class 'recordFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/libutil/recordFile.C:22:3: warning: Class 'recordFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/libutil/recordFile.C:249:13: style: The scope of the variable 'len' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/recordFile.C:298:13: style: The scope of the variable 'len' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/recordFile.C:249:17: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/recordFile.C:298:17: style: Variable 'len' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/sweatShop.C:81:12: warning: Member variable 'sweatShop::_stateMutex' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libutil/sweatShop.C:16:3: warning: Member variable 'sweatShopWorker::threadID' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/libutil/sweatShop.H:43:11: style: Unused private function: 'sweatShop::loader' [unusedPrivateFunction]
kmer-code-2013-trunk/libutil/sweatShop.H:44:11: style: Unused private function: 'sweatShop::worker' [unusedPrivateFunction]
kmer-code-2013-trunk/libutil/sweatShop.H:45:11: style: Unused private function: 'sweatShop::writer' [unusedPrivateFunction]
kmer-code-2013-trunk/libutil/sweatShop.H:46:11: style: Unused private function: 'sweatShop::status' [unusedPrivateFunction]
kmer-code-2013-trunk/libutil/sweatShop.C:38:3: style: Class 'sweatShopState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/libutil/sweatShop.C:57:19: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libutil/sweatShop.C:63:25: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libutil/sweatShop.C:69:19: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libutil/sweatShop.C:75:19: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libutil/sweatShop.C:171:19: style: Variable '_loaderP' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libutil/sweatShop.C:167:19: note: _loaderP is assigned
kmer-code-2013-trunk/libutil/sweatShop.C:171:19: note: _loaderP is overwritten
kmer-code-2013-trunk/libutil/sweatShop.C:242:11: style: The scope of the variable 'err' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/sweatShop.C:363:21: style: Variable 'thisTime' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/sweatShop.C:368:21: style: Variable 'cpuPerSec' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/test/atomic.C:55:5: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/test/atomic.C:59:3: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/test/endianess.c:12:10: error: No pair for character ("). Can't process file. File is either invalid or unicode, which is currently not supported. [syntaxError]
kmer-code-2013-trunk/libutil/test/tcat.C:40:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libutil/test/test-bigQueue.C:64:18: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:267:12: style: Variable 'testSize' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:262:12: note: testSize is assigned
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:267:12: note: testSize is overwritten
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:268:12: style: Variable 'testIter' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:263:12: note: testIter is assigned
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:268:12: note: testIter is overwritten
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:114:15: style: Local variable 'i' shadows outer variable [shadowVariable]
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:94:18: note: Shadowed declaration
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:114:15: note: Shadow variable
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:128:17: style: Local variable 'i' shadows outer variable [shadowVariable]
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:94:18: note: Shadowed declaration
kmer-code-2013-trunk/libutil/test/test-bitPackedFile.C:128:17: note: Shadow variable
kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:89:3: style:inconclusive: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode]
kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:34:12: style: The scope of the variable 'bufferLen' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:59:23: style: Parameter 'argv' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:34:26: style: Variable 'bufferLen' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/test/test-intervalList.C:209:26: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/libutil/test/test-readBuffer.C:86:3: portability: %d in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/test/test-readBuffer.C:86:3: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/test/test-readBuffer.C:86:3: portability: %d in format string (no. 3) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
kmer-code-2013-trunk/libutil/test/test-readBuffer.C:42:12: style: The scope of the variable 'bufferLen' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/test/test-readBuffer.C:70:23: style: Parameter 'argv' can be declared with const [constParameter]
kmer-code-2013-trunk/libutil/test/test-readBuffer.C:42:26: style: Variable 'bufferLen' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/test/test-recordFile.C:51:18: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/libutil/test/test-types.c:19:10: style: Condition 'u3<0' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/libutil/test/test-types.c:8:18: note: Assignment 'u3=-1', assigned value is -1
kmer-code-2013-trunk/libutil/test/test-types.c:19:10: note: Condition 'u3<0' is always true
kmer-code-2013-trunk/libutil/test/test-types.c:22:10: style: Condition 's3>0' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/libutil/test/test-types.c:9:17: note: Assignment 's3=-1', assigned value is -1
kmer-code-2013-trunk/libutil/test/test-types.c:22:10: note: Condition 's3>0' is always false
kmer-code-2013-trunk/libutil/test/test-types.c:25:10: style: Condition 'u6<0' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/libutil/test/test-types.c:10:18: note: Assignment 'u6=-1', assigned value is -1
kmer-code-2013-trunk/libutil/test/test-types.c:25:10: note: Condition 'u6<0' is always true
kmer-code-2013-trunk/libutil/test/test-types.c:28:10: style: Condition 's6>0' is always false [knownConditionTrueFalse]
kmer-code-2013-trunk/libutil/test/test-types.c:11:17: note: Assignment 's6=-1', assigned value is -1
kmer-code-2013-trunk/libutil/test/test-types.c:28:10: note: Condition 's6>0' is always false
kmer-code-2013-trunk/libutil/unaryEncodingTester.C:18:11: style: The scope of the variable 'val' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/unaryEncodingTester.C:52:11: style: The scope of the variable 'val' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/unaryEncodingTester.C:87:11: style: The scope of the variable 'val' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/unaryEncodingTester.C:121:11: style: The scope of the variable 'val' can be reduced. [variableScope]
kmer-code-2013-trunk/libutil/unaryEncodingTester.C:18:15: style: Variable 'val' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/unaryEncodingTester.C:52:15: style: Variable 'val' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/unaryEncodingTester.C:87:15: style: Variable 'val' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/libutil/unaryEncodingTester.C:121:15: style: Variable 'val' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/args.C:266:12: warning: Member variable 'merylArgs::includeDefLine' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/meryl/args.C:266:12: warning: Member variable 'merylArgs::includeMer' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/meryl/args.C:290:3: warning: Class 'merylArgs' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/meryl/args.C:290:3: warning: Class 'merylArgs' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/meryl/meryl.H:28:3: style: Class 'merylArgs' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:279:15: warning: 'operator=' should check for assignment to self to avoid problems with dynamic memory. [operatorEqToSelf]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:128:11: style:inconclusive: Technically the member function 'splitToWords::numWords' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:182:15: style:inconclusive: Technically the member function 'intervalList::numberOfIntervals' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:201:15: style:inconclusive: Technically the member function 'intervalList::overlapping' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:484:15: note: Technically the member function 'intervalList::overlapping' can be const.
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:201:15: note: Technically the member function 'intervalList::overlapping' can be const.
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:224:23: style:inconclusive: Technically the member function 'intervalList::lo' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:225:23: style:inconclusive: Technically the member function 'intervalList::hi' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:249:15: style:inconclusive: Technically the member function 'intervalDepth::numberOfIntervals' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:253:23: style:inconclusive: Technically the member function 'intervalDepth::lo' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:254:23: style:inconclusive: Technically the member function 'intervalDepth::hi' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:255:23: style:inconclusive: Technically the member function 'intervalDepth::de' can be const. [functionConst]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:269:3: warning: Class 'intervalList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:656:3: warning: Class 'intervalDepth' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:656:3: warning: Class 'intervalDepth' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:38:3: style: Class 'splitToWords' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:245:3: style: Class 'intervalDepth' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:955:13: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:955:13: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:955:13: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:955:13: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:958:15: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:958:15: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:958:15: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:958:15: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:982:13: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:982:13: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:982:13: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:982:13: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:985:15: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:985:15: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:985:15: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:985:15: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:994:9: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:994:9: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'unsigned long'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:337:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:338:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:620:23: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:621:23: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:847:9: style: The scope of the variable 'showDepthIntersect' can be reduced. [variableScope]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:848:9: style: The scope of the variable 'showVariantIntersect' can be reduced. [variableScope]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:849:9: style: The scope of the variable 'showVarDepthIntersect' can be reduced. [variableScope]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:484:45: style:inconclusive: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'. [funcArgNamesDifferent]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:201:45: note: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'.
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:484:45: note: Function 'overlapping' argument 1 names different: declaration 'lo' definition 'rangelo'.
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:485:45: style:inconclusive: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'. [funcArgNamesDifferent]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:202:45: note: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'.
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:485:45: note: Function 'overlapping' argument 2 names different: declaration 'hi' definition 'rangehi'.
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:279:39: style: Parameter 'src' can be declared with const [constParameter]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:847:31: style: Variable 'showDepthIntersect' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:848:31: style: Variable 'showVariantIntersect' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:849:31: style: Variable 'showVarDepthIntersect' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:856:26: style: Variable 'showDepthIntersect' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:858:28: style: Variable 'showVariantIntersect' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:860:29: style: Variable 'showVarDepthIntersect' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:760:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:1004:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
kmer-code-2013-trunk/meryl/build-threads.C:23:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/build.C:585:5: style: Obsolescent function 'bzero' called. It is recommended to use 'memset' instead. [prohibitedbzeroCalled]
kmer-code-2013-trunk/meryl/build.C:53:8: style:inconclusive: Technically the member function 'sortedList_t::operator<' can be const. [functionConst]
kmer-code-2013-trunk/meryl/build.C:61:8: style:inconclusive: Technically the member function 'sortedList_t::operator>=' can be const. [functionConst]
kmer-code-2013-trunk/meryl/build.C:53:32: style: Parameter 'that' can be declared with const [constParameter]
kmer-code-2013-trunk/meryl/build.C:61:33: style: Parameter 'that' can be declared with const [constParameter]
kmer-code-2013-trunk/meryl/build.C:69:41: style: Parameter 'that' can be declared with const [constParameter]
kmer-code-2013-trunk/meryl/build.C:412:8: style: Unused variable: mstring [unusedVariable]
kmer-code-2013-trunk/meryl/dump.C:29:24: style: The scope of the variable 'str' can be reduced. [variableScope]
kmer-code-2013-trunk/meryl/kmer-mask.C:754:32: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/meryl/mapMers.C:21:13: style: The scope of the variable 'beVerbose' can be reduced. [variableScope]
kmer-code-2013-trunk/meryl/mapMers.C:21:24: style: Variable 'beVerbose' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/mapMers.C:44:17: style: Variable 'beVerbose' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/maskMers.C:364:44: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/meryl/merge.listmerge.C:25:5: performance: Variable '_posLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.listmerge.C:26:5: performance: Variable '_posMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.listmerge.C:29:5: performance: Variable '_mmmLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.listmerge.C:30:5: performance: Variable '_mmmMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.listmerge.C:33:5: performance: Variable '_tip' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.listmerge.C:34:5: performance: Variable '_fre' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.listmerge.C:50:11: style:inconclusive: Technically the member function 'mMerList::loadMore' can be const. [functionConst]
kmer-code-2013-trunk/meryl/merge.listmerge.C:52:11: style:inconclusive: Technically the member function 'mMerList::length' can be const. [functionConst]
kmer-code-2013-trunk/meryl/merge.listmerge.C:27:5: warning: Class 'mMerList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/meryl/merge.listmerge.C:27:5: warning: Class 'mMerList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/meryl/merge.listmerge.C:24:3: style: Class 'mMerList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/meryl/merge.listmerge.C:295:12: style: The scope of the variable 'thisMer' can be reduced. [variableScope]
kmer-code-2013-trunk/meryl/merge.qsort.C:31:3: warning: Member variable 'mMerList::_sorted' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/meryl/merge.qsort.C:32:5: performance: Variable '_posLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.qsort.C:33:5: performance: Variable '_posMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.qsort.C:36:5: performance: Variable '_mmmLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.qsort.C:37:5: performance: Variable '_mmmMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/merge.qsort.C:45:11: style:inconclusive: Technically the member function 'mMerList::length' can be const. [functionConst]
kmer-code-2013-trunk/meryl/merge.qsort.C:34:5: warning: Class 'mMerList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/meryl/merge.qsort.C:34:5: warning: Class 'mMerList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/meryl/merge.qsort.C:31:3: style: Class 'mMerList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/meryl/merge.qsort.C:22:0: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/merge.qsort.C:23:0: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/merge.qsort.C:285:12: style: The scope of the variable 'thisMer' can be reduced. [variableScope]
kmer-code-2013-trunk/meryl/merge.qsort.C:185:9: style: Unused variable: debugstring2 [unusedVariable]
kmer-code-2013-trunk/meryl/mervin.C:260:3: warning: Member variable 'kmerGlobal::inBuffer' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/meryl/mervin.C:260:3: warning: Member variable 'kmerGlobal::naptime' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/meryl/mervin.C:34:5: performance: Variable 'pileLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:35:5: performance: Variable 'pilePrefix' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:65:5: performance: Variable 'sorterLocked' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:66:5: performance: Variable 'sorterLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:67:5: performance: Variable 'sorterMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:271:5: performance: Variable 'inputBufferMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:272:5: performance: Variable 'inputBufferLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:273:5: performance: Variable 'inputBufferPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:279:5: performance: Variable 'fkPre' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:280:5: performance: Variable 'fkMer' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:282:5: performance: Variable 'rkPre' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:283:5: performance: Variable 'rkMer' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:285:5: performance: Variable 'kLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:287:5: performance: Variable 'pilesFreeLock' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:288:5: performance: Variable 'pilesFreeLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:289:5: performance: Variable 'pilesFreeMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/meryl/mervin.C:68:5: warning: Class 'kmerSorter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/meryl/mervin.C:68:5: warning: Class 'kmerSorter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/meryl/mervin.C:290:5: warning: Class 'kmerGlobal' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/meryl/mervin.C:290:5: warning: Class 'kmerGlobal' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/meryl/mervin.C:33:3: style: Class 'kmerPile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/meryl/mervin.C:593:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/mervin.C:673:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/mervin.C:674:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/mervin.C:734:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/mervin.C:735:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/meryl/mervin.C:329:25: style: Variable 'naptime.tv_nsec' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/meryl/mervin.C:328:25: note: naptime.tv_nsec is assigned
kmer-code-2013-trunk/meryl/mervin.C:329:25: note: naptime.tv_nsec is overwritten
kmer-code-2013-trunk/meryl/mervin.C:679:23: style: Variable 'naptime.tv_nsec' is reassigned a value before the old one has been used. [redundantAssignment]
kmer-code-2013-trunk/meryl/mervin.C:678:23: note: naptime.tv_nsec is assigned
kmer-code-2013-trunk/meryl/mervin.C:679:23: note: naptime.tv_nsec is overwritten
kmer-code-2013-trunk/meryl/mervin.C:200:10: style: The scope of the variable 'broken' can be reduced. [variableScope]
kmer-code-2013-trunk/meryl/mervin.C:76:23: style: Parameter 'pileDat' can be declared with const [constParameter]
kmer-code-2013-trunk/meryl/mervin.C:200:17: style: Variable 'broken' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/mervin.C:205:16: style: Variable 'broken' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/meryl/test/kmerlite.H:20:34: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/seagen/configuration.C:84:25: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/seagen/encodedQuery.C:152:53: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/seagen/hitReader.H:52:10: style:inconclusive: Technically the member function 'hitReader::bestScore' can be const. [functionConst]
kmer-code-2013-trunk/seagen/hitReader.H:53:10: style:inconclusive: Technically the member function 'hitReader::worstScore' can be const. [functionConst]
kmer-code-2013-trunk/seagen/hitReader.H:54:10: style:inconclusive: Technically the member function 'hitReader::iid' can be const. [functionConst]
kmer-code-2013-trunk/seagen/hitReader.H:55:10: style:inconclusive: Technically the member function 'hitReader::numHits' can be const. [functionConst]
kmer-code-2013-trunk/seagen/hitReader.H:44:3: style: Class 'hitReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/seagen/filterEST.C:76:26: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/seagen/filterMRNA.C:59:13: style:inconclusive: Same expression used in consecutive assignments of 'hiCov' and 'loCov'. [duplicateAssignExpression]
kmer-code-2013-trunk/seagen/filterMRNA.C:60:13: note: Same expression used in consecutive assignments of 'hiCov' and 'loCov'.
kmer-code-2013-trunk/seagen/filterMRNA.C:59:13: note: Same expression used in consecutive assignments of 'hiCov' and 'loCov'.
kmer-code-2013-trunk/seagen/filtertest.C:128:21: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seagen/filtertest.C:129:21: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seagen/filtertest.C:139:21: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seagen/filtertest.C:140:21: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seagen/filtertest.C:211:13: style: Variable 'L' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/seagen/filtertest.C:212:13: style: Variable 'H' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/seagen/filtertest.C:213:13: style: Variable 'V' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/seagen/hitMatrix.H:51:5: performance: Variable '_qsLo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitMatrix.H:52:5: performance: Variable '_qsHi' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitMatrix.H:53:5: performance: Variable '_dsLo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitMatrix.H:54:5: performance: Variable '_dsHi' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/encodedQuery.H:17:20: style:inconclusive: Technically the member function 'encodedQuery::IID' can be const. [functionConst]
kmer-code-2013-trunk/seagen/encodedQuery.H:19:20: style:inconclusive: Technically the member function 'encodedQuery::numberOfMers' can be const. [functionConst]
kmer-code-2013-trunk/seagen/encodedQuery.H:20:20: style:inconclusive: Technically the member function 'encodedQuery::numberOfValidMers' can be const. [functionConst]
kmer-code-2013-trunk/seagen/encodedQuery.H:25:20: style:inconclusive: Technically the member function 'encodedQuery::bpTotal' can be const. [functionConst]
kmer-code-2013-trunk/seagen/encodedQuery.H:76:15: note: Technically the member function 'encodedQuery::bpTotal' can be const.
kmer-code-2013-trunk/seagen/encodedQuery.H:25:20: note: Technically the member function 'encodedQuery::bpTotal' can be const.
kmer-code-2013-trunk/seagen/encodedQuery.H:28:20: style:inconclusive: Technically the member function 'encodedQuery::getSkip' can be const. [functionConst]
kmer-code-2013-trunk/seagen/encodedQuery.H:98:15: note: Technically the member function 'encodedQuery::getSkip' can be const.
kmer-code-2013-trunk/seagen/encodedQuery.H:28:20: note: Technically the member function 'encodedQuery::getSkip' can be const.
kmer-code-2013-trunk/seagen/encodedQuery.H:34:20: style:inconclusive: Technically the member function 'encodedQuery::theOutputLength' can be const. [functionConst]
kmer-code-2013-trunk/seagen/encodedQuery.H:35:20: style:inconclusive: Technically the member function 'encodedQuery::numberOfResults' can be const. [functionConst]
kmer-code-2013-trunk/seagen/searcherState.H:18:5: performance: Variable 'posnMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/searcherState.H:19:5: performance: Variable 'posnLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitMatrix.C:7:3: performance: Variable '_qsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitMatrix.C:8:3: performance: Variable '_qsMers' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitMatrix.C:9:3: performance: Variable '_qsIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitMatrix.C:11:3: performance: Variable '_hitsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitMatrix.C:12:3: performance: Variable '_hitsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/configuration.H:96:9: performance:inconclusive: Technically the member function 'configuration::setTime' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/seagen/hitMatrix.C:13:3: warning: Class 'hitMatrix' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seagen/hitMatrix.C:13:3: warning: Class 'hitMatrix' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seagen/searcherState.H:20:5: warning: Class 'searcherState' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seagen/searcherState.H:20:5: warning: Class 'searcherState' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seagen/hitMatrix.C:567:20: style: The scope of the variable 'n' can be reduced. [variableScope]
kmer-code-2013-trunk/seagen/hitReader.C:47:3: performance: Variable '_filesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitReader.C:48:3: performance: Variable '_filesLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitReader.C:51:3: performance: Variable '_listLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitReader.C:52:3: performance: Variable '_listMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitReader.C:55:3: performance: Variable '_iid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seagen/hitReader.H:49:10: performance:inconclusive: Technically the member function 'hitReader::loadHit' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/seagen/hitReader.C:89:12: note: Technically the member function 'hitReader::loadHit' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/seagen/hitReader.H:49:10: note: Technically the member function 'hitReader::loadHit' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/seagen/hitReader.C:49:3: warning: Class 'hitReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seagen/hitReader.C:49:3: warning: Class 'hitReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seagen/misc/dumpCrapSeqs.C:15:18: style: The scope of the variable 'Q' can be reduced. [variableScope]
kmer-code-2013-trunk/seagen/misc/dumpCrapSeqs.C:15:20: style: Variable 'Q' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/seagen/misc/f.C:33:12: style: The scope of the variable 'file' can be reduced. [variableScope]
kmer-code-2013-trunk/seagen/misc/f.C:36:12: style: The scope of the variable 'isBINARY' can be reduced. [variableScope]
kmer-code-2013-trunk/seagen/misc/h.C:32:12: style: The scope of the variable 'file' can be reduced. [variableScope]
kmer-code-2013-trunk/seagen/misc/h.C:35:12: style: The scope of the variable 'isBINARY' can be reduced. [variableScope]
kmer-code-2013-trunk/seagen/sortHits.C:28:5: warning: Class 'aHitReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seagen/sortHits.C:28:5: warning: Class 'aHitReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seagen/sortHits.C:26:3: style: Class 'aHitReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/seagen/sortHits.C:153:14: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seagen/sortHits.C:154:14: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seagen/thr-output.C:42:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seagen/thr-search.C:48:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seagen/thr-search.C:49:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/configuration.C:10:16: warning: Member variable 'configuration::_genome' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/filterObj.H:72:3: performance: Variable 'theOutputPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/filterObj.H:73:3: performance: Variable 'theOutputMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:14:3: performance: Variable '_merSize' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:15:3: performance: Variable '_merSkip' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:16:3: performance: Variable '_numSearchThreads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:21:3: performance: Variable '_maxDiagonal' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:22:3: performance: Variable '_maxGap' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:23:3: performance: Variable '_qsOverlap' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:24:3: performance: Variable '_dsOverlap' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:26:3: performance: Variable '_minLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:48:3: performance: Variable '_loaderHighWaterMark' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/configuration.C:56:3: performance: Variable '_writerHighWaterMark' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/seatac.H:127:9: performance:inconclusive: Technically the member function 'configuration::usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/seatac/configuration.C:116:16: note: Technically the member function 'configuration::usage' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/seatac/seatac.H:127:9: note: Technically the member function 'configuration::usage' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/seatac/seatac.H:131:9: performance:inconclusive: Technically the member function 'configuration::setTime' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/seatac/sharedObj.H:19:5: warning: Class 'sharedObj' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seatac/sharedObj.H:19:5: warning: Class 'sharedObj' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seatac/filterObj.H:80:5: warning: Class 'filterObj' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seatac/filterObj.H:80:5: warning: Class 'filterObj' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seatac/statObj.H:50:5: warning: Class 'statObj' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seatac/statObj.H:50:5: warning: Class 'statObj' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seatac/sharedObj.H:18:3: style: Class 'sharedObj' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/seatac/filterObj.H:60:33: style:inconclusive: Function 'filterObj' argument 1 names different: declaration 'so' definition 'so_'. [funcArgNamesDifferent]
kmer-code-2013-trunk/seatac/filterObj.H:21:24: note: Function 'filterObj' argument 1 names different: declaration 'so' definition 'so_'.
kmer-code-2013-trunk/seatac/filterObj.H:60:33: note: Function 'filterObj' argument 1 names different: declaration 'so' definition 'so_'.
kmer-code-2013-trunk/seatac/filterObj.H:60:44: style:inconclusive: Function 'filterObj' argument 2 names different: declaration 'soOpts' definition 'op_'. [funcArgNamesDifferent]
kmer-code-2013-trunk/seatac/filterObj.H:21:34: note: Function 'filterObj' argument 2 names different: declaration 'soOpts' definition 'op_'.
kmer-code-2013-trunk/seatac/filterObj.H:60:44: note: Function 'filterObj' argument 2 names different: declaration 'soOpts' definition 'op_'.
kmer-code-2013-trunk/seatac/filterObj.H:129:26: style:inconclusive: Function 'addHit' argument 1 names different: declaration 'direction' definition 'orientation'. [funcArgNamesDifferent]
kmer-code-2013-trunk/seatac/filterObj.H:24:24: note: Function 'addHit' argument 1 names different: declaration 'direction' definition 'orientation'.
kmer-code-2013-trunk/seatac/filterObj.H:129:26: note: Function 'addHit' argument 1 names different: declaration 'direction' definition 'orientation'.
kmer-code-2013-trunk/seatac/statObj.H:38:29: style:inconclusive: Function 'statObj' argument 1 names different: declaration 'so' definition 'so_'. [funcArgNamesDifferent]
kmer-code-2013-trunk/seatac/statObj.H:11:22: note: Function 'statObj' argument 1 names different: declaration 'so' definition 'so_'.
kmer-code-2013-trunk/seatac/statObj.H:38:29: note: Function 'statObj' argument 1 names different: declaration 'so' definition 'so_'.
kmer-code-2013-trunk/seatac/statObj.H:38:40: style:inconclusive: Function 'statObj' argument 2 names different: declaration 'soOpts' definition 'op_'. [funcArgNamesDifferent]
kmer-code-2013-trunk/seatac/statObj.H:11:32: note: Function 'statObj' argument 2 names different: declaration 'soOpts' definition 'op_'.
kmer-code-2013-trunk/seatac/statObj.H:38:40: note: Function 'statObj' argument 2 names different: declaration 'soOpts' definition 'op_'.
kmer-code-2013-trunk/seatac/encodedQuery.C:11:3: performance: Variable '_seqLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/encodedQuery.C:12:3: performance: Variable '_merSize' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/encodedQuery.C:15:3: performance: Variable '_seqPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/encodedQuery.C:17:3: performance: Variable '_substring' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/heavychains.H:229:3: warning: Member variable 'Interval::lo' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/heavychains.H:229:3: warning: Member variable 'Interval::hi' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/heavychains.H:229:3: warning: Member variable 'Interval::S' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/heavychains.H:304:3: warning: Member variable 'DPTree::MaxJump' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/heavychains.H:249:5: warning: Member variable 'kd_node::Xy' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/heavychains.H:249:5: warning: Member variable 'kd_node::start' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/heavychains.H:249:5: warning: Member variable 'kd_node::stop' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/heavychains.H:249:5: warning: Member variable 'kd_node::intv' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/heavychains.H:52:5: performance: Variable 'beVerbose' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/heavychains.H:107:16: style:inconclusive: Technically the member function 'StrandPair::sequenceIID1' can be const. [functionConst]
kmer-code-2013-trunk/seatac/filter-heavychains.C:173:8: style:inconclusive: Technically the member function 'StrandPairManager::process' can be const. [functionConst]
kmer-code-2013-trunk/seatac/filter-heavychains.C:178:10: style:inconclusive: Technically the member function 'StrandPairManager::print' can be const. [functionConst]
kmer-code-2013-trunk/seatac/filter-heavychains.C:184:8: style:inconclusive: Technically the member function 'StrandPairManager::addStats' can be const. [functionConst]
kmer-code-2013-trunk/seatac/heavychains.H:60:5: warning: Class 'StrandPair' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seatac/heavychains.H:60:5: warning: Class 'StrandPair' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seatac/heavychains.H:308:5: warning: Class 'DPTree' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seatac/heavychains.H:308:5: warning: Class 'DPTree' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seatac/filter-heavychains.C:232:10: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-heavychains.C:245:4: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-heavychains.C:250:4: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-heavychains.C:256:11: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-heavychains.C:299:10: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-heavychains.C:309:4: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-heavychains.C:314:4: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/heavychains.H:372:12: style: The scope of the variable 'score' can be reduced. [variableScope]
kmer-code-2013-trunk/seatac/heavychains.H:372:18: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/seatac/filter-nop.C:37:3: warning: Member variable 'filterLongest::outstring' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/seatac/filter-nop.C:72:8: performance:inconclusive: Technically the member function 'filterLongest::filter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/seatac/filter-nop.C:139:10: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-nop.C:152:4: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-nop.C:157:4: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-nop.C:162:11: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-nop.C:175:10: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-nop.C:180:4: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-nop.C:185:4: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/seatac/filter-nop.C:115:17: style:inconclusive: Function 'construct' argument 1 names different: declaration 'options' definition 'opts'. [funcArgNamesDifferent]
kmer-code-2013-trunk/seatac/filter-nop.C:13:28: note: Function 'construct' argument 1 names different: declaration 'options' definition 'opts'.
kmer-code-2013-trunk/seatac/filter-nop.C:115:17: note: Function 'construct' argument 1 names different: declaration 'options' definition 'opts'.
kmer-code-2013-trunk/seatac/heavychains-driver.C:98:19: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
kmer-code-2013-trunk/seatac/heavychains-driver.C:58:22: warning: Possible null pointer dereference: inFileName [nullPointer]
kmer-code-2013-trunk/seatac/heavychains-driver.C:34:25: note: Assignment 'inFileName=0L', assigned value is 0
kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false
kmer-code-2013-trunk/seatac/heavychains-driver.C:58:22: note: Null pointer dereference
kmer-code-2013-trunk/seatac/heavychains-driver.C:59:22: warning: Possible null pointer dereference: outFileName [nullPointer]
kmer-code-2013-trunk/seatac/heavychains-driver.C:35:25: note: Assignment 'outFileName=0L', assigned value is 0
kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false
kmer-code-2013-trunk/seatac/heavychains-driver.C:59:22: note: Null pointer dereference
kmer-code-2013-trunk/seatac/heavychains-driver.C:82:11: style: The scope of the variable 'tmp_filled' can be reduced. [variableScope]
kmer-code-2013-trunk/seatac/heavychains.C:164:44: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/seatac/hitMatrix.C:5:3: performance: Variable '_qsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/hitMatrix.C:6:3: performance: Variable '_qsIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/hitMatrix.C:15:3: performance: Variable '_hitsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/hitMatrix.C:16:3: performance: Variable '_hitsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/seatac/hitMatrix.C:17:3: warning: Class 'hitMatrix' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/seatac/hitMatrix.C:17:3: warning: Class 'hitMatrix' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/seatac/hitMatrix.C:285:20: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition]
kmer-code-2013-trunk/seatac/hitMatrix.C:283:18: note: outer condition: qsLow<=_hits[i]._qsPos
kmer-code-2013-trunk/seatac/hitMatrix.C:285:20: note: opposite inner condition: qsLow>_hits[i]._qsPos
kmer-code-2013-trunk/seatac/seatac.C:201:21: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/seatac/thr-search.C:3:42: error: There is an unknown macro here somewhere. Configuration is required. If uint64FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4db/sim4th.C:298:20: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/sim4db/sim4th.C:308:20: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:77:16: style: The scope of the variable 'splitFile' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:78:16: style: The scope of the variable 'intronLimit' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:135:9: style: The scope of the variable 'exA' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:136:9: style: The scope of the variable 'exB' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:77:26: style: Variable 'splitFile' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:78:28: style: Variable 'intronLimit' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:100:17: style: Variable 'splitFile' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:106:19: style: Variable 'intronLimit' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/comparePolishes.C:484:29: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4dbutils/convertPolishes.C:37:12: style: The comparison 'GOOD == 0L' is always true. [knownConditionTrueFalse]
kmer-code-2013-trunk/sim4dbutils/convertPolishes.C:12:36: note: 'GOOD' is assigned value '0L' here.
kmer-code-2013-trunk/sim4dbutils/convertPolishes.C:37:12: note: The comparison 'GOOD == 0L' is always true.
kmer-code-2013-trunk/sim4dbutils/convertToExtent.C:59:8: style: The scope of the variable 'beVerbose' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/convertToExtent.C:59:22: style: Variable 'beVerbose' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/convertToExtent.C:68:17: style: Variable 'beVerbose' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/coveragehack.C:120:21: style: The scope of the variable 'includeGapsAsContamination' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/coveragehack.C:166:29: style: Local variable 'gaps' shadows outer variable [shadowVariable]
kmer-code-2013-trunk/sim4dbutils/coveragehack.C:116:21: note: Shadowed declaration
kmer-code-2013-trunk/sim4dbutils/coveragehack.C:166:29: note: Shadow variable
kmer-code-2013-trunk/sim4dbutils/coveragehack.C:116:30: style: Variable 'gaps' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/coveragehack.C:120:48: style: Variable 'includeGapsAsContamination' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/coveragehack.C:144:34: style: Variable 'includeGapsAsContamination' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/sim4dbutils/detectChimera.C:129:43: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4dbutils/filterPolishes.C:180:31: style: Same expression on both sides of '&&'. [duplicateExpression]
kmer-code-2013-trunk/sim4dbutils/headPolishes.C:47:9: style: The comparison 'W == 0L' is always true. [knownConditionTrueFalse]
kmer-code-2013-trunk/sim4dbutils/headPolishes.C:14:27: note: 'W' is assigned value '0L' here.
kmer-code-2013-trunk/sim4dbutils/headPolishes.C:47:9: note: The comparison 'W == 0L' is always true.
kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:119:21: style: Array index 'first' is used before limits check. [arrayIndexThenCheck]
kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:16:81: style: Parameter 'numSeqs' can be declared with const [constParameter]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:471:13: style: Array index 'mr1bgn' is used before limits check. [arrayIndexThenCheck]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:474:13: style: Array index 'mr2bgn' is used before limits check. [arrayIndexThenCheck]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:31:5: performance: Variable 'cloneIndex' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:32:5: performance: Variable 'isFirstMate' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:35:5: performance: Variable 'cloneIndex' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:36:5: performance: Variable 'isFirstMate' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:471:62: style: Condition 'mr1bgn<mr1END' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:469:18: note: Assuming that condition 'mr1bgn<mr1END' is not redundant
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:471:62: note: Condition 'mr1bgn<mr1END' is always true
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:474:62: style: Condition 'mr2bgn<mr2END' is always true [knownConditionTrueFalse]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:469:39: note: Assuming that condition 'mr2bgn<mr2END' is not redundant
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:474:62: note: Condition 'mr2bgn<mr2END' is always true
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:444:3: portability: %lu in format string (no. 1) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:445:3: portability: %lu in format string (no. 1) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:266:19: style: The scope of the variable 'minIdent' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:267:19: style: The scope of the variable 'minLength' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:268:19: style: The scope of the variable 'minCoverage' can be reduced. [variableScope]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:146:35: performance: Searching before insertion is not necessary. [stlFindInsert]
kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:212:35: performance: Searching before insertion is not necessary. [stlFindInsert]
kmer-code-2013-trunk/sim4dbutils/pickBestPolish.C:35:30: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4dbutils/pickUniquePolish-nhgri.C:703:25: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4dbutils/plotIntronSize.C:101:13: error: Uninitialized variable: hist [uninitvar]
kmer-code-2013-trunk/sim4dbutils/realignPolishes.C:160:30: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4dbutils/removeRedundant.C:107:29: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4dbutils/sortPolishes.C:87:29: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4dbutils/summarizePolishes.C:247:41: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/sim4dbutils/trimSequencesBasedOnMatches.C:34:7: error: fprintf format string requires 2 parameters but only 1 is given. [wrongPrintfScanfArgNum]
kmer-code-2013-trunk/sim4dbutils/vennPolishes.C:175:28: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/snapper/snapper2.H:228:5: performance: Variable 'theHitsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:229:5: performance: Variable 'theHitsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:279:5: performance: Variable 'threadID' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:281:5: performance: Variable 'posnMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:282:5: performance: Variable 'posnLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:331:5: performance: Variable '_unique' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:332:5: performance: Variable '_qsLo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:333:5: performance: Variable '_qsHi' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:334:5: performance: Variable '_dsLo' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:335:5: performance: Variable '_dsHi' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:8:3: performance: Variable '_KBmerSize' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:9:3: performance: Variable '_KBcompression' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:12:3: performance: Variable '_merSkip' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:14:3: performance: Variable '_numSearchThreads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:27:3: performance: Variable '_maxDiagonal' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:31:3: performance: Variable '_extendMinimum' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:32:3: performance: Variable '_extendMaximum' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:34:3: performance: Variable '_repeatThreshold' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:36:3: performance: Variable '_minHitLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:39:3: performance: Variable '_minMatchIdentity' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:40:3: performance: Variable '_minMatchCoverage' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:44:3: performance: Variable '_afLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:45:3: performance: Variable '_afInit' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:47:3: performance: Variable '_discardExonLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:48:3: performance: Variable '_discardExonQuality' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:59:3: performance: Variable '_ignoreThreshold' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:62:3: performance: Variable '_maskThreshold' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/configuration.C:64:3: performance: Variable '_onlyThreshold' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/snapper2.H:87:9: performance:inconclusive: Technically the member function 'configuration::setTime' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/snapper/snapper2.H:230:5: warning: Class 'query' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/snapper/snapper2.H:230:5: warning: Class 'query' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/snapper/snapper2.H:278:3: style: Class 'searcherState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/snapper/snapper2.H:409:28: style: Parameter 'ps' can be declared with const [constParameter]
kmer-code-2013-trunk/snapper/hitMatrix.C:6:3: performance: Variable '_qsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/hitMatrix.C:7:3: performance: Variable '_qsMers' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/hitMatrix.C:8:3: performance: Variable '_qsIdx' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/hitMatrix.C:10:3: performance: Variable '_hitsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/hitMatrix.C:11:3: performance: Variable '_hitsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/snapper/hitMatrix.C:12:3: warning: Class 'hitMatrix' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/snapper/hitMatrix.C:12:3: warning: Class 'hitMatrix' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/snapper/hitMatrix.C:5:43: style:inconclusive: Function 'hitMatrix' argument 2 names different: declaration 'q' definition 'qsMers'. [funcArgNamesDifferent]
kmer-code-2013-trunk/snapper/snapper2.H:347:34: note: Function 'hitMatrix' argument 2 names different: declaration 'q' definition 'qsMers'.
kmer-code-2013-trunk/snapper/hitMatrix.C:5:43: note: Function 'hitMatrix' argument 2 names different: declaration 'q' definition 'qsMers'.
kmer-code-2013-trunk/snapper/hitMatrix.C:151:29: style:inconclusive: Function 'filter' argument 4 names different: declaration 'theOutput' definition 'theHits'. [funcArgNamesDifferent]
kmer-code-2013-trunk/snapper/snapper2.H:361:28: note: Function 'filter' argument 4 names different: declaration 'theOutput' definition 'theHits'.
kmer-code-2013-trunk/snapper/hitMatrix.C:151:29: note: Function 'filter' argument 4 names different: declaration 'theOutput' definition 'theHits'.
kmer-code-2013-trunk/snapper/hitMatrix.C:152:29: style:inconclusive: Function 'filter' argument 5 names different: declaration 'theOutputPos' definition 'theHitsPos'. [funcArgNamesDifferent]
kmer-code-2013-trunk/snapper/snapper2.H:362:28: note: Function 'filter' argument 5 names different: declaration 'theOutputPos' definition 'theHitsPos'.
kmer-code-2013-trunk/snapper/hitMatrix.C:152:29: note: Function 'filter' argument 5 names different: declaration 'theOutputPos' definition 'theHitsPos'.
kmer-code-2013-trunk/snapper/hitMatrix.C:153:29: style:inconclusive: Function 'filter' argument 6 names different: declaration 'theOutputMax' definition 'theHitsMax'. [funcArgNamesDifferent]
kmer-code-2013-trunk/snapper/snapper2.H:363:28: note: Function 'filter' argument 6 names different: declaration 'theOutputMax' definition 'theHitsMax'.
kmer-code-2013-trunk/snapper/hitMatrix.C:153:29: note: Function 'filter' argument 6 names different: declaration 'theOutputMax' definition 'theHitsMax'.
kmer-code-2013-trunk/snapper/snapper2.C:59:52: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/snapper/thr-filter.C:58:21: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/snapper/thr-filter.C:59:21: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:35:3: warning: Member variable 'dpMatch::alignA' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:35:3: warning: Member variable 'dpMatch::alignB' is not initialized in the constructor. [uninitMemberVar]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:112:10: style:inconclusive: Technically the member function 'dpMatrix::dpMatrixCellGetScore' can be const. [functionConst]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:116:10: style:inconclusive: Technically the member function 'dpMatrix::dpMatrixCellGetAction' can be const. [functionConst]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:293:22: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:16:10: style: The scope of the variable 'c' can be reduced. [variableScope]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:141:29: style: Parameter 'stringA' can be declared with const [constParameter]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:142:29: style: Parameter 'stringB' can be declared with const [constParameter]
kmer-code-2013-trunk/snapper/thr-polish-dp.C:16:11: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/snapper/thr-search.C:108:20: style:inconclusive: Technically the member function 'encodedQuery::numberOfMersActive' can be const. [functionConst]
kmer-code-2013-trunk/snapper/thr-search.C:109:20: style:inconclusive: Technically the member function 'encodedQuery::numberOfMersInQuery' can be const. [functionConst]
kmer-code-2013-trunk/snapper/thr-search.C:111:20: style:inconclusive: Technically the member function 'encodedQuery::getMer' can be const. [functionConst]
kmer-code-2013-trunk/snapper/thr-search.C:112:20: style:inconclusive: Technically the member function 'encodedQuery::getPosn' can be const. [functionConst]
kmer-code-2013-trunk/snapper/thr-search.C:113:20: style:inconclusive: Technically the member function 'encodedQuery::getSpan' can be const. [functionConst]
kmer-code-2013-trunk/snapper/thr-search.C:20:5: warning: Class 'encodedQuery' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/snapper/thr-search.C:20:5: warning: Class 'encodedQuery' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/tapper/tapperTag.H:147:12: style:inconclusive: Technically the member function 'tapperTagFileMetaData::tagSize' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperTag.H:148:12: style:inconclusive: Technically the member function 'tapperTagFileMetaData::isPairedTagFile' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperTag.H:149:12: style:inconclusive: Technically the member function 'tapperTagFileMetaData::mean' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperTag.H:150:12: style:inconclusive: Technically the member function 'tapperTagFileMetaData::stddev' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperHit.H:11:13: style:inconclusive: Technically the member function 'tapperHit::numberOfBaseMismatches' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperHit.H:12:13: style:inconclusive: Technically the member function 'tapperHit::numberOfColorMismatches' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperHit.H:13:13: style:inconclusive: Technically the member function 'tapperHit::numberOfColorInconsistencies' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperHit.H:35:10: style:inconclusive: Technically the member function 'tapperHit::happyNearEnd' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperHit.H:68:10: style:inconclusive: Technically the member function 'tapperHit::mateTooFarBefore' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperHit.H:122:10: style:inconclusive: Technically the member function 'tapperHit::mateTooFarAfter' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperHit.H:161:10: style:inconclusive: Technically the member function 'tapperHit::happy' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tapperTag.H:190:5: warning: Class 'tapperTagFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/tapper/tapperTag.H:190:5: warning: Class 'tapperTagFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/tapper/tapperResult.H:414:5: warning: Class 'tapperResultFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/tapper/tapperResult.H:414:5: warning: Class 'tapperResultFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/tapper/tapperTag.H:191:17: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tagger.C:27:0: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tagger.C:28:0: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tapperHit.H:174:12: style: Redundant initialization for 'dist'. The initialized value is overwritten before it is read. [redundantInitialization]
kmer-code-2013-trunk/tapper/tapperHit.H:162:25: note: dist is initialized
kmer-code-2013-trunk/tapper/tapperHit.H:174:12: note: dist is overwritten
kmer-code-2013-trunk/tapper/tagger.C:169:30: style: The scope of the variable 'seqb' can be reduced. [variableScope]
kmer-code-2013-trunk/tapper/tagger.C:170:30: style: The scope of the variable 'quab' can be reduced. [variableScope]
kmer-code-2013-trunk/tapper/tapperHit.H:236:35: performance: Function parameter 'a' should be passed by const reference. [passedByValue]
kmer-code-2013-trunk/tapper/tapperHit.H:236:54: performance: Function parameter 'b' should be passed by const reference. [passedByValue]
kmer-code-2013-trunk/tapper/tapperHit.H:68:38: style: Parameter 'that' can be declared with const [constParameter]
kmer-code-2013-trunk/tapper/tapperHit.H:122:37: style: Parameter 'that' can be declared with const [constParameter]
kmer-code-2013-trunk/tapper/tapperHit.H:161:27: style: Parameter 'b' can be declared with const [constParameter]
kmer-code-2013-trunk/tapper/tagger.C:301:13: style: Variable 'acgt' can be declared with const [constVariable]
kmer-code-2013-trunk/tapper/tapperTag.H:33:20: style: Parameter 'id' can be declared with const [constParameter]
kmer-code-2013-trunk/tapper/tapperResult.H:355:12: style: Variable 'bmmin' can be declared with const [constVariable]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:62:3: performance: Variable 'bgnRead' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:63:3: performance: Variable 'endRead' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:65:3: performance: Variable 'thisPartition' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:66:3: performance: Variable 'numPartitions' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:68:3: performance: Variable 'repeatThreshold' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:70:3: performance: Variable 'maxMemory' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:71:3: performance: Variable 'numThreads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:74:3: performance: Variable 'maxColorError' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:75:3: performance: Variable 'maxBaseError' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:4:5: performance: Variable 'posn1fMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:5:5: performance: Variable 'posn1fLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:8:5: performance: Variable 'posn1rMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:9:5: performance: Variable 'posn1rLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:12:5: performance: Variable 'posn2fMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:13:5: performance: Variable 'posn2fLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:16:5: performance: Variable 'posn2rMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:17:5: performance: Variable 'posn2rLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperThreadData.H:20:5: performance: Variable 'numHappiesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:18:12: performance:inconclusive: Technically the member function 'tapperGlobalData::convertACGTtoColor' can be static (but you may consider moving to unnamed namespace). [functionStatic]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:177:19: note: Technically the member function 'tapperGlobalData::convertACGTtoColor' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/tapper/tapperGlobalData.H:18:12: note: Technically the member function 'tapperGlobalData::convertACGTtoColor' can be static (but you may consider moving to unnamed namespace).
kmer-code-2013-trunk/tapper/tapperThreadData.H:6:5: warning: Class 'tapperThreadData' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/tapper/tapperThreadData.H:6:5: warning: Class 'tapperThreadData' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/tapper/tapperComputation.H:92:5: warning: Class 'tapperComputation' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/tapper/tapperComputation.H:92:5: warning: Class 'tapperComputation' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/tapper/tapperThreadData.H:3:3: style: Class 'tapperThreadData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/tapper/tapper.C:19:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tapper.C:38:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tapper.C:39:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tapper.C:523:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tapper.C:524:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tapper.C:525:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:179:14: style: The scope of the variable 'n' can be reduced. [variableScope]
kmer-code-2013-trunk/tapper/tapper.C:127:37: style:inconclusive: Function 'alignToReference' argument 2 names different: declaration 'so' definition 'so_in'. [funcArgNamesDifferent]
kmer-code-2013-trunk/tapper/tapperHit.H:30:34: note: Function 'alignToReference' argument 2 names different: declaration 'so' definition 'so_in'.
kmer-code-2013-trunk/tapper/tapper.C:127:37: note: Function 'alignToReference' argument 2 names different: declaration 'so' definition 'so_in'.
kmer-code-2013-trunk/tapper/tapper.C:128:37: style:inconclusive: Function 'alignToReference' argument 3 names different: declaration 'po' definition 'po_in'. [funcArgNamesDifferent]
kmer-code-2013-trunk/tapper/tapperHit.H:31:34: note: Function 'alignToReference' argument 3 names different: declaration 'po' definition 'po_in'.
kmer-code-2013-trunk/tapper/tapper.C:128:37: note: Function 'alignToReference' argument 3 names different: declaration 'po' definition 'po_in'.
kmer-code-2013-trunk/tapper/tapper.C:129:37: style:inconclusive: Function 'alignToReference' argument 4 names different: declaration 'tag' definition 'tag_in'. [funcArgNamesDifferent]
kmer-code-2013-trunk/tapper/tapperHit.H:32:34: note: Function 'alignToReference' argument 4 names different: declaration 'tag' definition 'tag_in'.
kmer-code-2013-trunk/tapper/tapper.C:129:37: note: Function 'alignToReference' argument 4 names different: declaration 'tag' definition 'tag_in'.
kmer-code-2013-trunk/tapper/tapper.C:129:52: style:inconclusive: Function 'alignToReference' argument 5 names different: declaration 'len' definition 'len_in'. [funcArgNamesDifferent]
kmer-code-2013-trunk/tapper/tapperHit.H:32:46: note: Function 'alignToReference' argument 5 names different: declaration 'len' definition 'len_in'.
kmer-code-2013-trunk/tapper/tapper.C:129:52: note: Function 'alignToReference' argument 5 names different: declaration 'len' definition 'len_in'.
kmer-code-2013-trunk/tapper/tapperGlobalData.H:177:57: style: Parameter 'acgt' can be declared with const [constParameter]
kmer-code-2013-trunk/tapper/tapper.C:129:37: style: Parameter 'tag_in' can be declared with const [constParameter]
kmer-code-2013-trunk/tapper/tapper.C:89:21: style: Parameter 'colors' can be declared with const [constParameter]
kmer-code-2013-trunk/tapper/tapper.C:484:33: style: Parameter 'posn' can be declared with const [constParameter]
kmer-code-2013-trunk/tapper/tapperGlobalData.H:179:16: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
kmer-code-2013-trunk/tapper/tappererrorcorrect.C:16:5: performance: Variable 'alignsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tappererrorcorrect.C:19:5: performance: Variable 'alignsPerBlock' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/tapper/tappererrorcorrect.C:78:8: style:inconclusive: Technically the member function 'alignmentList::empty' can be const. [functionConst]
kmer-code-2013-trunk/tapper/tappererrorcorrect.C:17:5: warning: Class 'alignmentList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
kmer-code-2013-trunk/tapper/tappererrorcorrect.C:17:5: warning: Class 'alignmentList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
kmer-code-2013-trunk/tapper/tappererrorcorrect.C:15:3: style: Class 'alignmentList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
kmer-code-2013-trunk/tapper/tappererrorcorrect.C:99:13: style: The scope of the variable 'outputName' can be reduced. [variableScope]
kmer-code-2013-trunk/tapper/tappererrorcorrect.C:220:54: debug: Wrong data detected by condition !tok->next()->astOperand2() [DacaWrongData]
kmer-code-2013-trunk/tapper/tappersort.C:148:26: error: There is an unknown macro here somewhere. Configuration is required. If uint32FMTW is a macro then please configure it. [unknownMacro]
kmer-code-2013-trunk/trie/trie.C:31:5: performance: Variable 'seqiid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/trie/trie.C:32:5: performance: Variable 'nodeiid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
kmer-code-2013-trunk/trie/trie.C:48:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/trie/trie.C:49:26: style: C-style pointer casting [cstyleCast]
kmer-code-2013-trunk/atac-driver/matchExtender/match.H:12:1: error: The one definition rule is violated, different classes/structs have the same name 'match_s' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/atac-driver/uniqueFilter/uniqueFilter.C:73:1: note: The one definition rule is violated, different classes/structs have the same name 'match_s'
kmer-code-2013-trunk/atac-driver/matchExtender/match.H:12:1: note: The one definition rule is violated, different classes/structs have the same name 'match_s'
kmer-code-2013-trunk/libutil/splitToWords.H:5:1: error: The one definition rule is violated, different classes/structs have the same name 'splitToWords' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:29:1: note: The one definition rule is violated, different classes/structs have the same name 'splitToWords'
kmer-code-2013-trunk/libutil/splitToWords.H:5:1: note: The one definition rule is violated, different classes/structs have the same name 'splitToWords'
kmer-code-2013-trunk/libutil/intervalList.H:12:1: error: The one definition rule is violated, different classes/structs have the same name '_intervalPair' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/meryl/asmMerQC-regions.C:144:1: note: The one definition rule is violated, different classes/structs have the same name '_intervalPair'
kmer-code-2013-trunk/libutil/intervalList.H:12:1: note: The one definition rule is violated, different classes/structs have the same name '_intervalPair'
kmer-code-2013-trunk/meryl/merge.listmerge.C:13:1: error: The one definition rule is violated, different classes/structs have the same name 'mMer' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/meryl/merge.qsort.C:13:1: note: The one definition rule is violated, different classes/structs have the same name 'mMer'
kmer-code-2013-trunk/meryl/merge.listmerge.C:13:1: note: The one definition rule is violated, different classes/structs have the same name 'mMer'
kmer-code-2013-trunk/meryl/merge.listmerge.C:22:1: error: The one definition rule is violated, different classes/structs have the same name 'mMerList' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/meryl/merge.qsort.C:29:1: note: The one definition rule is violated, different classes/structs have the same name 'mMerList'
kmer-code-2013-trunk/meryl/merge.listmerge.C:22:1: note: The one definition rule is violated, different classes/structs have the same name 'mMerList'
kmer-code-2013-trunk/seagen/aHit.H:8:1: error: The one definition rule is violated, different classes/structs have the same name 'aHit' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/seagen/filtertest.C:16:1: note: The one definition rule is violated, different classes/structs have the same name 'aHit'
kmer-code-2013-trunk/seagen/aHit.H:8:1: note: The one definition rule is violated, different classes/structs have the same name 'aHit'
kmer-code-2013-trunk/seagen/hitReader.H:29:9: error: The one definition rule is violated, different classes/structs have the same name 'hit_s' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/seagen/misc/f.C:11:9: note: The one definition rule is violated, different classes/structs have the same name 'hit_s'
kmer-code-2013-trunk/seagen/hitReader.H:29:9: note: The one definition rule is violated, different classes/structs have the same name 'hit_s'
kmer-code-2013-trunk/seagen/hitReader.H:29:9: error: The one definition rule is violated, different classes/structs have the same name 'hit_s' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/seagen/misc/h.C:11:9: note: The one definition rule is violated, different classes/structs have the same name 'hit_s'
kmer-code-2013-trunk/seagen/hitReader.H:29:9: note: The one definition rule is violated, different classes/structs have the same name 'hit_s'
kmer-code-2013-trunk/seatac/seatac.H:64:1: error: The one definition rule is violated, different classes/structs have the same name 'configuration' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/snapper/snapper2.H:80:1: note: The one definition rule is violated, different classes/structs have the same name 'configuration'
kmer-code-2013-trunk/seatac/seatac.H:64:1: note: The one definition rule is violated, different classes/structs have the same name 'configuration'
kmer-code-2013-trunk/seagen/aHit.H:8:1: error: The one definition rule is violated, different classes/structs have the same name 'aHit' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/snapper/snapper2.H:209:1: note: The one definition rule is violated, different classes/structs have the same name 'aHit'
kmer-code-2013-trunk/seagen/aHit.H:8:1: note: The one definition rule is violated, different classes/structs have the same name 'aHit'
kmer-code-2013-trunk/seagen/searcherState.H:2:1: error: The one definition rule is violated, different classes/structs have the same name 'searcherState' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/snapper/snapper2.H:267:1: note: The one definition rule is violated, different classes/structs have the same name 'searcherState'
kmer-code-2013-trunk/seagen/searcherState.H:2:1: note: The one definition rule is violated, different classes/structs have the same name 'searcherState'
kmer-code-2013-trunk/seagen/hitMatrix.H:31:1: error: The one definition rule is violated, different classes/structs have the same name 'diagonalLine' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/snapper/snapper2.H:298:1: note: The one definition rule is violated, different classes/structs have the same name 'diagonalLine'
kmer-code-2013-trunk/seagen/hitMatrix.H:31:1: note: The one definition rule is violated, different classes/structs have the same name 'diagonalLine'
kmer-code-2013-trunk/seagen/hitMatrix.H:39:1: error: The one definition rule is violated, different classes/structs have the same name 'trapMatch' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/snapper/snapper2.H:311:1: note: The one definition rule is violated, different classes/structs have the same name 'trapMatch'
kmer-code-2013-trunk/seagen/hitMatrix.H:39:1: note: The one definition rule is violated, different classes/structs have the same name 'trapMatch'
kmer-code-2013-trunk/seatac/seatac.H:32:1: error: The one definition rule is violated, different classes/structs have the same name 'encodedQuery' [ctuOneDefinitionRuleViolation]
kmer-code-2013-trunk/snapper/thr-search.C:8:1: note: The one definition rule is violated, different classes/structs have the same name 'encodedQuery'
kmer-code-2013-trunk/seatac/seatac.H:32:1: note: The one definition rule is violated, different classes/structs have the same name 'encodedQuery'
diff:
head kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:123:15: style: Condition 'beg==gap' is always false [knownConditionTrueFalse]
     kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:106:19: note: beg is assigned 'i-1' here.
     kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:107:21: note: Assignment 'gap=i', assigned value is symbolic=beg+1
     kmer-code-2013-trunk/atac-driver/alignOverlap/overlap-find.C:123:15: note: Condition 'beg==gap' is always false
head kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_overlap.C:118:44: style: Parameter 'x' can be declared with const [constParameter]
head kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:172:45: style: Parameter 'trace' can be declared with const [constParameter]
2.5 kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:50:9: warning: The address of local variable 'aseg' might be accessed at non-zero index. [objectIndex]
     kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:80:22: note: Address of variable taken here.
     kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:80:22: note: Calling function 'safe_substr', 1st argument '&aseg' value is lifetime=aseg
     kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:50:9: note: The address of local variable 'aseg' might be accessed at non-zero index.
2.5 kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:50:9: warning: The address of local variable 'bseg' might be accessed at non-zero index. [objectIndex]
     kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:87:22: note: Address of variable taken here.
     kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:87:22: note: Calling function 'safe_substr', 1st argument '&bseg' value is lifetime=bseg
     kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:50:9: note: The address of local variable 'bseg' might be accessed at non-zero index.
2.5 kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:84:43: warning: Possible null pointer dereference: bseg [nullPointer]
     kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:63:33: note: Assignment 'bseg=NULL', assigned value is 0
     kmer-code-2013-trunk/atac-driver/chainer/localalign/GF_ALN_pieceOlap.C:84:43: note: Null pointer dereference
head kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:29:16: style: Parameter 'inLine' can be declared with const [constParameter]
head kmer-code-2013-trunk/atac-driver/libatac/atacFile.C:84:34: style: Parameter 'type' can be declared with const [constParameter]
head kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender-func.C:355:31: style: Condition 'good_run_len>minEndRunLen' is always true [knownConditionTrueFalse]
     kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender-func.C:352:31: note: Assuming that condition 'good_run_len==minEndRunLen' is not redundant
     kmer-code-2013-trunk/atac-driver/matchExtender/matchExtender-func.C:355:31: note: Condition 'good_run_len>minEndRunLen' is always true
head kmer-code-2013-trunk/leaff/leaff.C:452:17: style: Variable 'bases' can be declared with const [constVariable]
head kmer-code-2013-trunk/libbio/test/test-bigmer-msf.C:41:10: style: Variable 'dna' can be declared with const [constVariable]
head kmer-code-2013-trunk/libkmer/driver-existDB.C:52:41: style: Condition 'ee!=eg' is always false [knownConditionTrueFalse]
     kmer-code-2013-trunk/libkmer/driver-existDB.C:52:27: note: Assuming that condition 'ef!=eg' is not redundant
     kmer-code-2013-trunk/libkmer/driver-existDB.C:52:13: note: Assuming that condition 'ee!=ef' is not redundant
     kmer-code-2013-trunk/libkmer/driver-existDB.C:52:41: note: Condition 'ee!=eg' is always false
head kmer-code-2013-trunk/libkmer/driver-existDB.C:55:41: style: Condition 'ce!=cg' is always false [knownConditionTrueFalse]
     kmer-code-2013-trunk/libkmer/driver-existDB.C:55:27: note: Assuming that condition 'cf!=cg' is not redundant
     kmer-code-2013-trunk/libkmer/driver-existDB.C:55:13: note: Assuming that condition 'ce!=cf' is not redundant
     kmer-code-2013-trunk/libkmer/driver-existDB.C:55:41: note: Condition 'ce!=cg' is always false
head kmer-code-2013-trunk/libkmer/positionDB-mismatch.C:93:12: style: Variable 'err' can be declared with const [constVariable]
head kmer-code-2013-trunk/libseq/test-correctSequence.H:25:13: style: Variable 'bases' can be declared with const [constVariable]
head kmer-code-2013-trunk/libseq/test-merStream.C:15:71: style: Parameter 'SP' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:311:24: style: Parameter 's1' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/Xtend1.C:43:24: style: Parameter 's1' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/align.C:619:29: style: Condition 'j2-i2<j1-i1' is always true [knownConditionTrueFalse]
     kmer-code-2013-trunk/libsim4/sim4core/align.C:593:22: note: Assuming that condition 'j2-i2==j1-i1' is not redundant
     kmer-code-2013-trunk/libsim4/sim4core/align.C:619:29: note: Condition 'j2-i2<j1-i1' is always true
head kmer-code-2013-trunk/libsim4/sim4core/extend.C:169:23: style: Parameter 's1' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/extend.C:169:33: style: Parameter 's2' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/extend.C:7:23: style: Parameter 's1' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/extend.C:7:33: style: Parameter 's2' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/glimmerSplice.C:221:38: style: Parameter 'perm' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/pluri_align.C:9:40: style: Parameter 'head' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/poly.C:531:7: style: Condition 'exons_head' is always true [knownConditionTrueFalse]
     kmer-code-2013-trunk/libsim4/sim4core/poly.C:521:17: note: Assuming that condition '!Exons->next_exon' is not redundant
     kmer-code-2013-trunk/libsim4/sim4core/poly.C:529:14: note: exons_head is assigned 'Exons->next_exon' here.
     kmer-code-2013-trunk/libsim4/sim4core/poly.C:531:7: note: Condition 'exons_head' is always true
2.5 kmer-code-2013-trunk/libsim4/sim4core/poly.C:531:7: style: Condition 'exons_head' is always true [knownConditionTrueFalse]
     kmer-code-2013-trunk/libsim4/sim4core/poly.C:521:17: note: Assuming that condition '!Exons->next_exon' is not redundant
     kmer-code-2013-trunk/libsim4/sim4core/poly.C:529:21: note: Assignment 'exons_head=Exons->next_exon', assigned value is never 0
     kmer-code-2013-trunk/libsim4/sim4core/poly.C:531:7: note: Condition 'exons_head' is always true
head kmer-code-2013-trunk/libsim4/sim4core/sim4.H:378:41: style: Parameter 'target' can be declared with const [constParameter]
2.5 kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:112:7: warning: Either the condition 'prev==0L' is redundant or there is possible null pointer dereference: tmp_block. [nullPointerRedundantCheck]
     kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:92:14: note: Assuming that condition 'prev==0L' is not redundant
     kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:109:17: note: Assignment 'tmp_block=prev', assigned value is 0
     kmer-code-2013-trunk/libsim4/sim4core/sim4b1-1.C:112:7: note: Null pointer dereference
head kmer-code-2013-trunk/libsim4/sim4core/splice.C:205:66: style: Parameter 'gt_score' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/splice.C:206:28: style: Parameter 'ct_score' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/splice.C:266:32: style: Parameter 'It_score' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/splice.C:314:31: style: Parameter 'ag_score' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/splice.C:314:49: style: Parameter 'ac_score' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/splice.C:371:35: style: Parameter 'aI_score' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/util.C:138:27: style: Parameter 'Lblock' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/util.C:299:41: style: Parameter 'rblock' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/util.C:323:54: style: Parameter 'last' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4core/util.C:394:28: style: Condition 'c->score==g->score' is always true [knownConditionTrueFalse]
     kmer-code-2013-trunk/libsim4/sim4core/util.C:392:28: note: Assuming that condition 'c->score>g->score' is not redundant
     kmer-code-2013-trunk/libsim4/sim4core/util.C:394:28: note: Condition 'c->score==g->score' is always true
head kmer-code-2013-trunk/libsim4/sim4core/util.C:573:49: style: Parameter 'last' can be declared with const [constParameter]
2.5 kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-read.C:78:16: style: Condition 'numLines>0' is always true [knownConditionTrueFalse]
     kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-read.C:33:24: note: Assignment 'numLines=10240', assigned value is 10240
     kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-read.C:78:16: note: Condition 'numLines>0' is always true
head kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:15:43: style: Parameter 'lengths' can be declared with const [constParameter]
head kmer-code-2013-trunk/libsim4/sim4polish/sim4polish-stringtopolish.C:199:43: style: Parameter 'lengths' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/bitPacking.h:107:25: style: Parameter 'ptr' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/bitPacking.h:181:26: style: Parameter 'ptr' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/bitPacking.h:184:26: style: Parameter 'sizs' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/bitPacking.h:241:26: style: Parameter 'sizs' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/fibonacciEncoding.h:121:35: style: Parameter 'ptr' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/kazlib/hash.c:813:26: style: Variable 'randbox' can be declared with const [constVariable]
head kmer-code-2013-trunk/libutil/kazlib/list.c:306:51: style: Parameter 'node' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/kazlib/list.c:368:42: style: Parameter 'node' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/kazlib/sfx.c:76:56: style: Parameter 'orig' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/md5.c:267:52: style: Parameter 'input' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/mt19937ar/mt19937ar.c:94:21: style: Parameter 'init_key' can be declared with const [constParameter]
head kmer-code-2013-trunk/libutil/mt19937ar/tt800.c:29:26: style: Variable 'mag01' can be declared with const [constVariable]
2.5 kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:18:8: warning:inconclusive: Possible null pointer dereference: testing [nullPointer]
     kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:11:31: note: Assignment 'testing=0L', assigned value is 0
     kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:13:10: note: Assuming condition is false
     kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:18:8: note: Null pointer dereference
2.5 kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:45:8: warning:inconclusive: Possible null pointer dereference: testing [nullPointer]
     kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:36:31: note: Assignment 'testing=0L', assigned value is 0
     kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:38:10: note: Assuming condition is false
     kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:45:8: note: Null pointer dereference
head kmer-code-2013-trunk/libutil/test/test-bzipBuffer.C:59:23: style: Parameter 'argv' can be declared with const [constParameter]
2.5 kmer-code-2013-trunk/libutil/test/test-readBuffer.C:25:8: warning:inconclusive: Possible null pointer dereference: testing [nullPointer]
     kmer-code-2013-trunk/libutil/test/test-readBuffer.C:13:31: note: Assignment 'testing=0L', assigned value is 0
     kmer-code-2013-trunk/libutil/test/test-readBuffer.C:18:28: note: Assuming condition is false
     kmer-code-2013-trunk/libutil/test/test-readBuffer.C:25:8: note: Null pointer dereference
2.5 kmer-code-2013-trunk/libutil/test/test-readBuffer.C:56:8: warning:inconclusive: Possible null pointer dereference: testing [nullPointer]
     kmer-code-2013-trunk/libutil/test/test-readBuffer.C:44:31: note: Assignment 'testing=0L', assigned value is 0
     kmer-code-2013-trunk/libutil/test/test-readBuffer.C:48:10: note: Assuming condition is false
     kmer-code-2013-trunk/libutil/test/test-readBuffer.C:56:8: note: Null pointer dereference
head kmer-code-2013-trunk/libutil/test/test-readBuffer.C:70:23: style: Parameter 'argv' can be declared with const [constParameter]
head kmer-code-2013-trunk/meryl/mervin.C:76:23: style: Parameter 'pileDat' can be declared with const [constParameter]
head kmer-code-2013-trunk/seatac/heavychains-driver.C:58:22: warning: Possible null pointer dereference: inFileName [nullPointer]
     kmer-code-2013-trunk/seatac/heavychains-driver.C:34:25: note: Assignment 'inFileName=0L', assigned value is 0
     kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false
     kmer-code-2013-trunk/seatac/heavychains-driver.C:58:22: note: Null pointer dereference
2.5 kmer-code-2013-trunk/seatac/heavychains-driver.C:58:22: warning: Possible null pointer dereference: inFileName [nullPointer]
     kmer-code-2013-trunk/seatac/heavychains-driver.C:34:25: note: Assignment 'inFileName=0L', assigned value is 0
     kmer-code-2013-trunk/seatac/heavychains-driver.C:39:40: note: Assuming condition is true
     kmer-code-2013-trunk/seatac/heavychains-driver.C:58:22: note: Null pointer dereference
head kmer-code-2013-trunk/seatac/heavychains-driver.C:59:22: warning: Possible null pointer dereference: outFileName [nullPointer]
     kmer-code-2013-trunk/seatac/heavychains-driver.C:35:25: note: Assignment 'outFileName=0L', assigned value is 0
     kmer-code-2013-trunk/seatac/heavychains-driver.C:38:14: note: Assuming condition is false
     kmer-code-2013-trunk/seatac/heavychains-driver.C:59:22: note: Null pointer dereference
2.5 kmer-code-2013-trunk/seatac/heavychains-driver.C:59:22: warning: Possible null pointer dereference: outFileName [nullPointer]
     kmer-code-2013-trunk/seatac/heavychains-driver.C:35:25: note: Assignment 'outFileName=0L', assigned value is 0
     kmer-code-2013-trunk/seatac/heavychains-driver.C:39:40: note: Assuming condition is true
     kmer-code-2013-trunk/seatac/heavychains-driver.C:59:22: note: Null pointer dereference
2.5 kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:54:20: style: Condition 'c<cnt[i][j]' is always false [knownConditionTrueFalse]
     kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:51:20: note: Assuming that condition 'b<cnt[i][j]' is not redundant
     kmer-code-2013-trunk/sim4dbutils/cleanPolishes-20020626.C:54:20: note: Condition 'c<cnt[i][j]' is always false
head kmer-code-2013-trunk/sim4dbutils/mergePolishes.C:16:81: style: Parameter 'numSeqs' can be declared with const [constParameter]
head kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:471:62: style: Condition 'mr1bgn<mr1END' is always true [knownConditionTrueFalse]
     kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:469:18: note: Assuming that condition 'mr1bgn<mr1END' is not redundant
     kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:471:62: note: Condition 'mr1bgn<mr1END' is always true
head kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:474:62: style: Condition 'mr2bgn<mr2END' is always true [knownConditionTrueFalse]
     kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:469:39: note: Assuming that condition 'mr2bgn<mr2END' is not redundant
     kmer-code-2013-trunk/sim4dbutils/pickBestPair.C:474:62: note: Condition 'mr2bgn<mr2END' is always true
head kmer-code-2013-trunk/snapper/snapper2.H:409:28: style: Parameter 'ps' can be declared with const [constParameter]
head kmer-code-2013-trunk/snapper/thr-polish-dp.C:141:29: style: Parameter 'stringA' can be declared with const [constParameter]
head kmer-code-2013-trunk/snapper/thr-polish-dp.C:142:29: style: Parameter 'stringB' can be declared with const [constParameter]
head kmer-code-2013-trunk/tapper/tagger.C:301:13: style: Variable 'acgt' can be declared with const [constVariable]
head kmer-code-2013-trunk/tapper/tapper.C:129:37: style: Parameter 'tag_in' can be declared with const [constParameter]
head kmer-code-2013-trunk/tapper/tapper.C:484:33: style: Parameter 'posn' can be declared with const [constParameter]
head kmer-code-2013-trunk/tapper/tapper.C:89:21: style: Parameter 'colors' can be declared with const [constParameter]
head kmer-code-2013-trunk/tapper/tapperGlobalData.H:177:57: style: Parameter 'acgt' can be declared with const [constParameter]
head kmer-code-2013-trunk/tapper/tapperResult.H:355:12: style: Variable 'bmmin' can be declared with const [constVariable]
head kmer-code-2013-trunk/tapper/tapperTag.H:33:20: style: Parameter 'id' can be declared with const [constParameter]


DONE