2025-06-30 19:05
ftp://ftp.de.debian.org/debian/pool/main/s/snap-aligner/snap-aligner_2.0.3+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j6
platform: Linux-6.1.0-37-amd64-x86_64-with-glibc2.36
python: 3.11.2
client-version: 1.3.67
compiler: g++ (Debian 12.2.0-14+deb12u1) 12.2.0
cppcheck: head 2.17.0
head-info: dfa16af (2025-06-30 19:43:56 +0200)
count: 2391 2302
elapsed-time: 62.4 63.1
head-timing-info:

old-timing-info:

head results:
snap-2.0.3/SNAPLib/AlignerStats.h:53:12: style:inconclusive: Member variable 'AlignerStats::lvCalls' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/AlignerStats.cpp:41:5: note: Member variable 'AlignerStats::lvCalls' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerStats.h:53:12: note: Member variable 'AlignerStats::lvCalls' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Compat.h:477:18: style:inconclusive: Technically the member function 'FileMapper::getFileSize' can be const. [functionConst]
snap-2.0.3/SNAPLib/AlignerStats.h:45:5: style: Struct 'AlignerStats' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/AlignerStats.h:93:14: style: The destructor '~AlignerStats' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerStats.h:34:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/AlignerStats.h:93:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/AlignerStats.h:95:18: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerStats.h:36:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/AlignerStats.h:95:18: note: Function in derived class
snap-2.0.3/SNAPLib/AlignerStats.h:97:18: style: The function 'printHistograms' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerStats.h:38:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/AlignerStats.h:97:18: note: Function in derived class
snap-2.0.3/SNAPLib/AlignerStats.cpp:100:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AlignerStats.cpp:98:26: style:inconclusive: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignerStats.h:95:43: note: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'.
snap-2.0.3/SNAPLib/AlignerStats.cpp:98:26: note: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'.
snap-2.0.3/SNAPLib/VariableSizeMap.h:278:23: debug: Failed to instantiate template "VariableSizeMapBase". The checking continues anyway. [templateInstantiation]
snap-2.0.3/SNAPLib/Genome.h:374:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _MM_HINT_T2 [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:142:47: debug: Function::addArguments found argument 'a' with varid 0. [varid0]
snap-2.0.3/SNAPLib/VariableSizeVector.h:152:39: debug: Function::addArguments found argument 'a' with varid 0. [varid0]
snap-2.0.3/SNAPLib/VariableSizeVector.h:205:60: debug: Function::addArguments found argument 'a' with varid 0. [varid0]
snap-2.0.3/SNAPLib/Seed.h:181:40: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-2.0.3/SNAPLib/Genome.h:385:13: warning: Member variable 'Contig::projEndLocation' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::Table' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::tableSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::keySizeInBytes' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::elementSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::usedElementCount' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::ownsMemoryForTable' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::valueSizeInBytes' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::valueCount' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::invalidValueValue' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/Seed.h:55:12: warning:inconclusive: Member variable 'Seed::bases' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Seed.h:55:12: warning:inconclusive: Member variable 'Seed::reverseComplement' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.h:240:9: warning: Member variable 'PerHashTableBatch::entries' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Genome.h:391:32: style:inconclusive: Member variable 'Contig::originalContigNumber' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Genome.h:385:118: note: Member variable 'Contig::originalContigNumber' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Genome.h:391:32: note: Member variable 'Contig::originalContigNumber' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Genome.h:390:32: style:inconclusive: Member variable 'Contig::internalContigNumber' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Genome.h:385:163: note: Member variable 'Contig::internalContigNumber' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Genome.h:390:32: note: Member variable 'Contig::internalContigNumber' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenomeIndex.h:276:16: style:inconclusive: Member variable 'IndexBuildStats::seedsWithMultipleOccurrences' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/GenomeIndex.h:271:56: note: Member variable 'IndexBuildStats::seedsWithMultipleOccurrences' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenomeIndex.h:276:16: note: Member variable 'IndexBuildStats::seedsWithMultipleOccurrences' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Genome.h:495:17: style:inconclusive: Technically the member function 'GenomeLocationOrderedByOriginalContigs::operator>=' can be const. [functionConst]
snap-2.0.3/SNAPLib/Genome.h:513:17: style:inconclusive: Technically the member function 'GenomeLocationOrderedByOriginalContigs::operator>' can be const. [functionConst]
snap-2.0.3/SNAPLib/Genome.h:535:17: style:inconclusive: Technically the member function 'GenomeLocationOrderedByOriginalContigs::operator<' can be const. [functionConst]
snap-2.0.3/SNAPLib/Genome.h:557:17: style:inconclusive: Technically the member function 'GenomeLocationOrderedByOriginalContigs::operator<=' can be const. [functionConst]
snap-2.0.3/SNAPLib/Genome.h:579:17: style:inconclusive: Technically the member function 'GenomeLocationOrderedByOriginalContigs::operator==' can be const. [functionConst]
snap-2.0.3/SNAPLib/Genome.h:584:17: style:inconclusive: Technically the member function 'GenomeLocationOrderedByOriginalContigs::operator!=' can be const. [functionConst]
snap-2.0.3/SNAPLib/Genome.h:642:30: style:inconclusive: Technically the member function 'ContigAndPos::getContig' can be const. [functionConst]
snap-2.0.3/SNAPLib/Genome.h:643:16: style:inconclusive: Technically the member function 'ContigAndPos::getPos' can be const. [functionConst]
snap-2.0.3/SNAPLib/Seed.h:140:16: style:inconclusive: Technically the member function 'Seed::getBase' can be const. [functionConst]
snap-2.0.3/SNAPLib/Seed.h:150:17: style:inconclusive: Technically the member function 'Seed::toString' can be const. [functionConst]
snap-2.0.3/SNAPLib/Seed.h:158:20: style:inconclusive: Technically the member function 'Seed::hash64' can be const. [functionConst]
snap-2.0.3/SNAPLib/ApproximateCounter.h:22:20: performance:inconclusive: Technically the member function 'ApproximateCounter::hash' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/GenomeIndex.h:35:19: style:inconclusive: Technically the member function 'GenomeIndex::getGenome' can be const. [functionConst]
snap-2.0.3/SNAPLib/Util.h:449:5: style: Struct 'IdPair' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Util.h:480:5: style: Struct 'IdIntPair' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Util.h:484:5: style: Struct 'IdIntPair' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Util.h:531:2: style: Class 'NWaiter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/GenomeIndex.h:132:3: style: Class 'OverflowBackpointerAnchor' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/GenericFile_Blob.h:41:17: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:45:17: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:41:17: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:42:14: style: The function 'getchar' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:50:17: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:42:14: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:43:16: style: The function 'gets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:55:16: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:43:16: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:44:14: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:58:14: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:44:14: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:45:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:61:15: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:45:15: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:46:11: style: The destructor '~GenericFile_Blob' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:66:11: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/GenericFile_Blob.h:46:11: note: Destructor in derived class
snap-2.0.3/SNAPLib/GenericFile_map.h:33:11: style: The destructor '~GenericFile_map' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile_Blob.h:46:11: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/GenericFile_map.h:33:11: note: Destructor in derived class
snap-2.0.3/SNAPLib/GenericFile_map.h:34:17: style: The function 'prefetch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:68:17: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_map.h:34:17: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_map.h:35:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile_Blob.h:45:15: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_map.h:35:15: note: Function in derived class
snap-2.0.3/SNAPLib/HashTable.h:169:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/HashTable.h:181:28: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/HashTable.h:187:28: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/HashTable.h:192:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/HashTable.h:197:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Util.h:292:26: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Util.h:352:26: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Util.h:383:27: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Seed.h:181:32: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:33:42: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:34:43: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:55:42: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:56:43: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:72:42: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:73:43: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:94:42: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:95:43: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/HashTable.h:123:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Util.h:303:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Util.h:321:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Util.h:364:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AlignmentResult.cpp:29:60: style:inconclusive: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentResult.h:75:52: note: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:29:60: note: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:29:80: style:inconclusive: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentResult.h:75:71: note: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:29:80: note: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:53:55: style:inconclusive: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentResult.h:76:43: note: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:53:55: note: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:53:75: style:inconclusive: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentResult.h:76:62: note: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:53:75: note: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:68:60: style:inconclusive: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentResult.h:128:52: note: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:68:60: note: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:68:80: style:inconclusive: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentResult.h:128:71: note: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:68:80: note: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:92:51: style:inconclusive: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentResult.h:129:43: note: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:92:51: note: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:92:71: style:inconclusive: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentResult.h:129:62: note: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-2.0.3/SNAPLib/AlignmentResult.cpp:92:71: note: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-2.0.3/SNAPLib/HashTable.h:95:23: style: Local variable 'entry' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/HashTable.h:90:19: note: Shadowed declaration
snap-2.0.3/SNAPLib/HashTable.h:95:23: note: Shadow variable
snap-2.0.3/SNAPLib/Genome.h:495:68: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Genome.h:513:67: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Genome.h:535:67: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Genome.h:557:68: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Genome.h:579:68: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Genome.h:584:68: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Seed.h:107:33: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Seed.h:111:34: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Seed.h:115:33: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Seed.h:119:34: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Seed.h:123:34: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/Seed.h:127:34: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/HashTable.h:123:19: style: Variable 'entry' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/HashTable.h:172:53: style: Parameter 'entry' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/HashTable.h:177:50: style: Parameter 'entry' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Util.h:513:19: portability: Shifting signed 64-bit value by 63 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
snap-2.0.3/SNAPLib/Util.h:518:19: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
snap-2.0.3/SNAPLib/FixedSizeMap.h:225:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable K [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:50:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:159:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:383:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:21:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable big [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:26:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable big [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:56:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable grow [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:78:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable V [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:116:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable grow [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:136:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable V [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:144:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compare [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:154:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compare [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:183:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable V [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:192:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable V [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:235:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable V [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:408:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable entries [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:461:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:478:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:504:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:543:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable occupied [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:564:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable capacity [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:617:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _tombstone [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:629:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _tombstone [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:324:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:371:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:390:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable entries [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:62:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Entry [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:119:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Entry [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:152:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Entry [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/ApproximateCounter.cpp:29:30: style:inconclusive: Technically the member function 'ApproximateCounter::getCount' can be const. [functionConst]
snap-2.0.3/SNAPLib/ApproximateCounter.h:13:14: note: Technically the member function 'ApproximateCounter::getCount' can be const.
snap-2.0.3/SNAPLib/ApproximateCounter.cpp:29:30: note: Technically the member function 'ApproximateCounter::getCount' can be const.
snap-2.0.3/SNAPLib/ApproximateCounter.cpp:34:45: portability: Shifting signed 64-bit value by 63 bits is implementation-defined behaviour. See condition at line 34. [shiftTooManyBitsSigned]
snap-2.0.3/SNAPLib/ApproximateCounter.cpp:34:18: note: Assuming that condition 'r<64' is not redundant
snap-2.0.3/SNAPLib/ApproximateCounter.cpp:34:45: note: Shift
snap-2.0.3/SNAPLib/VariableSizeVector.h:129:24: debug: Failed to instantiate template "VariableSizeVector". The checking continues anyway. [templateInstantiation]
snap-2.0.3/SNAPLib/AffineGap.h:150:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:264:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:660:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:51:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:638:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin::backtraceMatched' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin::backtraceD' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/ParallelTask.h:271:5: warning: Member variable 'ParallelWorker::manager' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/ParallelTask.h:271:5: warning: Member variable 'ParallelWorker::threadNum' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/ParallelTask.h:271:5: warning: Member variable 'ParallelWorker::numThreads' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::unclippedData' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::unclippedQuality' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::idLength' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::dataLength' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::unclippedLength' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::frontClippedLength' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::FASTQCommentLength' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::localBuffer' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::rcData' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::rcQuality' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::externalData' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:254:9: warning: Member variable 'Read::externalQuality' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Read.h:864:5: warning: Member variable 'ReadWithOwnMemory::ownBuffer' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/FixedSizeMap.h:241:17: style: Unused private function: 'FixedSizeMap::checkBloomFilter' [unusedPrivateFunction]
snap-2.0.3/SNAPLib/FixedSizeMap.h:241:17: note: Unused private function: 'FixedSizeMap::checkBloomFilter'
snap-2.0.3/SNAPLib/FixedSizeMap.h:241:17: note: Unused private function: 'FixedSizeMap::checkBloomFilter'
snap-2.0.3/SNAPLib/FixedSizeMap.h:250:17: style: Unused private function: 'FixedSizeMap::addToBloomFilter' [unusedPrivateFunction]
snap-2.0.3/SNAPLib/FixedSizeMap.h:250:17: note: Unused private function: 'FixedSizeMap::addToBloomFilter'
snap-2.0.3/SNAPLib/FixedSizeMap.h:250:17: note: Unused private function: 'FixedSizeMap::addToBloomFilter'
snap-2.0.3/SNAPLib/BigAlloc.h:139:13: style:inconclusive: Member variable 'CountingBigAllocator::allocationGranularity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/BigAlloc.h:130:108: note: Member variable 'CountingBigAllocator::allocationGranularity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BigAlloc.h:139:13: note: Member variable 'CountingBigAllocator::allocationGranularity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Read.h:750:22: style:inconclusive: Member variable 'Read::clippingState' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Read.h:257:13: note: Member variable 'Read::clippingState' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Read.h:750:22: note: Member variable 'Read::clippingState' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Read.h:779:15: style:inconclusive: Member variable 'Read::upcaseForwardRead' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Read.h:258:13: note: Member variable 'Read::upcaseForwardRead' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Read.h:779:15: note: Member variable 'Read::upcaseForwardRead' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Read.h:743:21: style:inconclusive: Member variable 'Read::readGroup' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Read.h:259:13: note: Member variable 'Read::readGroup' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Read.h:743:21: note: Member variable 'Read::readGroup' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Read.h:751:13: style:inconclusive: Member variable 'Read::additionalFrontClipping' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Read.h:261:76: note: Member variable 'Read::additionalFrontClipping' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Read.h:751:13: note: Member variable 'Read::additionalFrontClipping' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeMap.h:256:9: style:inconclusive: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeMap.h:50:36: note: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeMap.h:256:9: note: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeMap.h:258:9: style:inconclusive: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::occupied' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeMap.h:60:9: note: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::occupied' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeMap.h:258:9: note: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::occupied' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BigAlloc.h:93:6: warning:inconclusive: Class 'BigAllocator' which has virtual members does not have a virtual destructor. [virtualDestructor]
snap-2.0.3/SNAPLib/BigAlloc.h:135:12: style:inconclusive: Technically the member function 'CountingBigAllocator::getMemoryUsed' can be const. [functionConst]
snap-2.0.3/SNAPLib/BigAlloc.h:170:10: style:inconclusive: Technically the member function 'ThreadHeap::free' can be const. [functionConst]
snap-2.0.3/SNAPLib/FixedSizeMap.h:16:20: style:inconclusive: Technically the member function 'NumericHash::operator()' can be const. [functionConst]
snap-2.0.3/SNAPLib/FixedSizeMap.h:81:10: performance:inconclusive: Technically the member function 'FixedSizeMap::resize' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/FixedSizeMap.h:168:16: style:inconclusive: Technically the member function 'FixedSizeMap::getSize' can be const. [functionConst]
snap-2.0.3/SNAPLib/FixedSizeMap.h:171:10: style:inconclusive: Technically the member function 'FixedSizeMap::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/FixedSizeMap.h:197:7: performance:inconclusive: Technically the member function 'FixedSizeMap::key' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/FixedSizeMap.h:202:8: performance:inconclusive: Technically the member function 'FixedSizeMap::value' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/FixedSizeMap.h:241:17: style:inconclusive: Technically the member function 'FixedSizeMap::checkBloomFilter' can be const. [functionConst]
snap-2.0.3/SNAPLib/FixedSizeMap.h:283:10: performance:inconclusive: Technically the member function 'FixedSizeMap::isPowerOf2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/FixedSizeMap.h:271:14: style:inconclusive: Technically the member function 'FixedSizeMap::Entry::operatordelete[]' can be const. [functionConst]
snap-2.0.3/SNAPLib/LandauVishkin.h:366:10: style:inconclusive: Technically the member function 'LandauVishkin::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/LandauVishkin.h:369:10: style:inconclusive: Technically the member function 'LandauVishkin::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/LandauVishkin.h:377:16: performance:inconclusive: Technically the member function 'LandauVishkin::countPerfectMatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/VariableSizeMap.h:460:14: style:inconclusive: Technically the member function 'VariableSizeMultiMap::valueIterator::hasValue' can be const. [functionConst]
snap-2.0.3/SNAPLib/ParallelTask.h:279:9: style:inconclusive: Technically the member function 'ParallelWorker::getThreadNum' can be const. [functionConst]
snap-2.0.3/SNAPLib/ParallelTask.h:280:9: style:inconclusive: Technically the member function 'ParallelWorker::getNumThreads' can be const. [functionConst]
snap-2.0.3/SNAPLib/DataWriter.h:267:10: style:inconclusive: Technically the member function 'StdoutAsyncFile::isQueueEmpty' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:514:26: style:inconclusive: Technically the member function 'Read::getBatch' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:522:31: style:inconclusive: Technically the member function 'Read::getOriginalAlignedLocation' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:523:25: style:inconclusive: Technically the member function 'Read::getOriginalMAPQ' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:524:25: style:inconclusive: Technically the member function 'Read::getOriginalSAMFlags' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:525:25: style:inconclusive: Technically the member function 'Read::getOriginalFrontClipping' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:526:25: style:inconclusive: Technically the member function 'Read::getOriginalBackClipping' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:527:25: style:inconclusive: Technically the member function 'Read::getOriginalFrontHardClipping' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:528:25: style:inconclusive: Technically the member function 'Read::getOriginalBackHardClipping' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:529:28: style:inconclusive: Technically the member function 'Read::getOriginalRNEXT' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:530:25: style:inconclusive: Technically the member function 'Read::getOriginalRNEXTLength' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:531:25: style:inconclusive: Technically the member function 'Read::getOriginalPNEXT' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:640:14: style:inconclusive: Technically the member function 'Read::computeReverseCompliment' can be const. [functionConst]
snap-2.0.3/SNAPLib/Read.h:786:21: performance:inconclusive: Technically the member function 'Read::assureLocalBufferLargeEnough' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/Read.h:871:10: style:inconclusive: Technically the member function 'ReadWithOwnMemory::dispose' can be const. [functionConst]
snap-2.0.3/SNAPLib/VariableSizeMap.h:94:16: style:inconclusive: Technically the member function 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::size' can be const. [functionConst]
snap-2.0.3/SNAPLib/VariableSizeMap.h:97:16: style:inconclusive: Technically the member function 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::getCapacity' can be const. [functionConst]
snap-2.0.3/SNAPLib/DataWriter.h:242:29: warning: The class 'StdoutAsyncFile' defines member function with name 'open' also defined in its parent class 'AsyncFile'. [duplInheritedMember]
snap-2.0.3/SNAPLib/Compat.h:397:23: note: Parent function 'AsyncFile::open'
snap-2.0.3/SNAPLib/DataWriter.h:242:29: note: Derived function 'StdoutAsyncFile::open'
snap-2.0.3/SNAPLib/Read.h:871:10: warning: The class 'ReadWithOwnMemory' defines member function with name 'dispose' also defined in its parent class 'Read'. [duplInheritedMember]
snap-2.0.3/SNAPLib/Read.h:274:14: note: Parent function 'Read::dispose'
snap-2.0.3/SNAPLib/Read.h:871:10: note: Derived function 'ReadWithOwnMemory::dispose'
snap-2.0.3/SNAPLib/BigAlloc.h:92:5: style: Class 'BigAllocator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/BigAlloc.h:130:5: style: Class 'CountingBigAllocator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/BigAlloc.h:156:5: style: Struct 'ThreadHeap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/FixedSizeMap.h:36:5: style: Class 'FixedSizeMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:403:5: style: Class 'VariableSizeMapBig' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:432:5: style: Class 'VariableSizeMultiMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/DataReader.h:51:12: style: Struct 'DataBatch' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/DataReader.h:83:12: style: Struct 'DataBatch' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/DataReader.h:203:5: style: Class 'BatchTracker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Read.h:92:5: style: Struct 'ReadClippingType' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Read.h:866:5: style: Class 'ReadWithOwnMemory' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/AlignmentAdjuster.h:34:5: style: Class 'AlignmentAdjuster' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/ParallelTask.h:50:5: style: Class 'ParallelTask < WorkerContext >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:49:5: style: Class 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/BigAlloc.h:133:19: style: The function 'allocate' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/BigAlloc.h:95:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/BigAlloc.h:133:19: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.h:240:10: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Compat.h:400:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.h:240:10: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.h:244:24: style: The function 'getWriter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Compat.h:419:21: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.h:244:24: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.h:245:24: style: The function 'getReader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Compat.h:436:21: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.h:245:24: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.h:249:12: style: The function 'getSize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Compat.h:402:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.h:249:12: note: Function in derived class
snap-2.0.3/SNAPLib/LandauVishkin.h:171:34: style: Condition 'patternLen>end' is always false [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/LandauVishkin.h:165:13: note: end is assigned '(patternLen)<(textLen)?(patternLen):(textLen)' here.
snap-2.0.3/SNAPLib/LandauVishkin.h:171:34: note: Condition 'patternLen>end' is always false
snap-2.0.3/SNAPLib/BigAlloc.h:158:24: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BigAlloc.h:172:37: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/FixedSizeMap.h:183:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/FixedSizeMap.h:199:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/FixedSizeMap.h:204:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/VariableSizeVector.h:78:19: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/ParallelTask.h:179:6: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/ParallelTask.h:187:25: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/VariableSizeMap.h:119:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/LandauVishkin.h:384:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.h:384:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.h:386:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.h:388:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/VariableSizeVector.h:192:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/VariableSizeMap.h:278:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/VariableSizeMap.h:290:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/VariableSizeMap.h:56:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Read.h:838:35: style: Unsigned expression 'i' can't be negative so it is unnecessary to test it. [unsignedPositive]
snap-2.0.3/SNAPLib/AlignmentAdjuster.cpp:28:52: style:inconclusive: Function 'AlignmentAdjuster' argument 1 names different: declaration 'genome' definition '_genome'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignmentAdjuster.h:34:37: note: Function 'AlignmentAdjuster' argument 1 names different: declaration 'genome' definition '_genome'.
snap-2.0.3/SNAPLib/AlignmentAdjuster.cpp:28:52: note: Function 'AlignmentAdjuster' argument 1 names different: declaration 'genome' definition '_genome'.
snap-2.0.3/SNAPLib/ParallelTask.h:177:11: style:inconclusive: Function 'forkWorker' argument 1 names different: declaration 'threadContext' definition 'forkArg'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ParallelTask.h:68:34: note: Function 'forkWorker' argument 1 names different: declaration 'threadContext' definition 'forkArg'.
snap-2.0.3/SNAPLib/ParallelTask.h:177:11: note: Function 'forkWorker' argument 1 names different: declaration 'threadContext' definition 'forkArg'.
snap-2.0.3/SNAPLib/ParallelTask.h:185:11: style:inconclusive: Function 'threadWorker' argument 1 names different: declaration 'threadContext' definition 'threadArg'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ParallelTask.h:66:36: note: Function 'threadWorker' argument 1 names different: declaration 'threadContext' definition 'threadArg'.
snap-2.0.3/SNAPLib/ParallelTask.h:185:11: note: Function 'threadWorker' argument 1 names different: declaration 'threadContext' definition 'threadArg'.
snap-2.0.3/SNAPLib/LandauVishkin.h:198:25: style: Local variable 'p' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:163:17: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.h:198:25: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.h:199:25: style: Local variable 't' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:164:17: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.h:199:25: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.h:201:21: style: Local variable 'end' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:165:9: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.h:201:21: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.h:202:29: style: Local variable 'pend' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:166:17: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.h:202:29: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.h:212:21: style: Local variable 'end' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:165:9: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.h:212:21: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.h:213:29: style: Local variable 'pend' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:166:17: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.h:213:29: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.h:227:21: style: Local variable 'end' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:165:9: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.h:227:21: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.h:228:29: style: Local variable 'pend' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:166:17: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.h:228:29: note: Shadow variable
snap-2.0.3/SNAPLib/VariableSizeVector.h:111:30: style: Parameter 'value' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/LandauVishkin.h:369:32: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/LandauVishkin.h:369:51: style: Parameter 'allocator' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Read.h:894:15: style: Variable 'aux' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/VariableSizeMap.h:176:16: style: Variable 'final' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/VariableSizeMap.h:299:16: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/VariableSizeMap.h:314:16: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/VariableSizeVector.h:129:47: style: Parameter 'other' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/VariableSizeVector.h:144:12: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/FixedSizeMap.h:182:16: style: Variable 'final' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/LandauVishkin.h:202:34: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:213:34: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:228:34: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:166:17: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:202:29: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:213:29: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/LandauVishkin.h:228:29: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Read.h:911:27: style: Variable 'ownBufferUsed' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Read.h:934:33: style: Variable 'extraBufferUsed' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AlignmentAdjuster.cpp:81:32: style: Variable 'basesClippedBefore' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AlignmentAdjuster.cpp:82:31: style: Variable 'basesClippedAfter' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AlignmentAdjuster.cpp:87:31: style: Variable 'basesClippedAfter' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:506:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeqToCode [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Bam.cpp:3378:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:380:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1080:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _MM_HINT_T2 [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1786:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _MM_HINT_T2 [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1892:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _MM_HINT_T2 [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2060:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UnusedScoreValue [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2080:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UnusedScoreValue [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2307:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UnusedScoreValue [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/AlignerOptions.h:61:2: warning: Member variable 'SNAPFile::isCompressed' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::readerContext' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::alignStart' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::alignTime' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxDist' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxDistForIndels' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::numSeedsFromCommandLine' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::seedCoverage' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::minWeightToCheck' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxHits' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::detailedStats' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::extraSearchDepth' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::useAffineGap' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::ignoreAlignmentAdjustmentForOm' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::altAwareness' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::emitALTAlignments' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxSecondaryAlignmentAdditionalEditDistance' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxSecondaryAlignments' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxSecondaryAlignmentsPerContig' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxScoreGapToPreferNonALTAlignment' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::minReadLength' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::matchReward' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::subPenalty' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::gapOpenPenalty' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::gapExtendPenalty' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::fivePrimeEndBonus' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::threePrimeEndBonus' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::useSoftClipping' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxHits_' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxDist_' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'AlignerContext::maxDistForIndels_' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'TaskContextBase::totalThreads' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'TaskContextBase::bindToProcessors' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'TaskContextBase::time' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'TaskContextBase::threadNum' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'TaskContextBase::doneWaiter' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'TaskContextBase::runningThreads' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-2.0.3/SNAPLib/AlignerContext.cpp:61:17: warning: Member variable 'TaskContextBase::pRunningThreads' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-2.0.3/SNAPLib/AffineGap.h:30:5: warning: Member variable 'AffineGap::qProfile' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGap.h:30:5: warning: Member variable 'AffineGap::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGap.h:35:5: warning: Member variable 'AffineGap::qProfile' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGap.h:35:5: warning: Member variable 'AffineGap::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:38:5: warning: Member variable 'ReadQueueElement::totalReads' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin < 1 >::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin < 1 >::backtraceMatched' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin < 1 >::backtraceD' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin < -1 >::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin < -1 >::backtraceMatched' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.h:48:5: warning: Member variable 'LandauVishkin < -1 >::backtraceD' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/RangeSplitter.h:109:23: style:inconclusive: Member variable 'RangeSplittingPairedReadSupplier::underlyingReader' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/RangeSplitter.h:97:127: note: Member variable 'RangeSplittingPairedReadSupplier::underlyingReader' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/RangeSplitter.h:109:23: note: Member variable 'RangeSplittingPairedReadSupplier::underlyingReader' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerContext.h:111:42: style:inconclusive: Member variable 'AlignerContext::argc' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/AlignerContext.cpp:69:5: note: Member variable 'AlignerContext::argc' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerContext.h:111:42: note: Member variable 'AlignerContext::argc' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AffineGap.h:400:6: style:inconclusive: Technically the member function 'AffineGap::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/AffineGap.h:403:6: style:inconclusive: Technically the member function 'AffineGap::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/BaseAligner.h:122:17: performance:inconclusive: Technically the member function 'BaseAligner::getName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/BaseAligner.h:124:17: style:inconclusive: Technically the member function 'BaseAligner::checkedAllSeeds' can be const. [functionConst]
snap-2.0.3/SNAPLib/BaseAligner.h:127:10: style:inconclusive: Technically the member function 'BaseAligner::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/BaseAligner.h:130:10: style:inconclusive: Technically the member function 'BaseAligner::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/BaseAligner.h:132:17: style:inconclusive: Technically the member function 'BaseAligner::getExplorePopularSeeds' can be const. [functionConst]
snap-2.0.3/SNAPLib/BaseAligner.h:135:17: style:inconclusive: Technically the member function 'BaseAligner::getStopOnFirstHit' can be const. [functionConst]
snap-2.0.3/SNAPLib/BaseAligner.h:215:10: performance:inconclusive: Technically the member function 'BaseAligner::decomposeGenomeLocation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:139:9: style:inconclusive: Technically the member function 'AffineGapVectorized < 1 >::computeGaplessScore' can be const. [functionConst]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1342:10: style:inconclusive: Technically the member function 'AffineGapVectorized < 1 >::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1345:10: style:inconclusive: Technically the member function 'AffineGapVectorized < 1 >::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:139:9: style:inconclusive: Technically the member function 'AffineGapVectorized < -1 >::computeGaplessScore' can be const. [functionConst]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1342:10: style:inconclusive: Technically the member function 'AffineGapVectorized < -1 >::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1345:10: style:inconclusive: Technically the member function 'AffineGapVectorized < -1 >::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/LandauVishkin.h:366:10: style:inconclusive: Technically the member function 'LandauVishkin < 1 >::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/LandauVishkin.h:369:10: style:inconclusive: Technically the member function 'LandauVishkin < 1 >::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/LandauVishkin.h:377:16: performance:inconclusive: Technically the member function 'LandauVishkin < 1 >::countPerfectMatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/LandauVishkin.h:366:10: style:inconclusive: Technically the member function 'LandauVishkin < -1 >::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/LandauVishkin.h:369:10: style:inconclusive: Technically the member function 'LandauVishkin < -1 >::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/LandauVishkin.h:377:16: performance:inconclusive: Technically the member function 'LandauVishkin < -1 >::countPerfectMatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/PairedAligner.h:80:25: warning: The class 'PairedAlignerContext' defines member variable with name 'useSoftClipping' also defined in its parent class 'AlignerContext'. [duplInheritedMember]
snap-2.0.3/SNAPLib/AlignerContext.h:131:42: note: Parent variable 'AlignerContext::useSoftClipping'
snap-2.0.3/SNAPLib/PairedAligner.h:80:25: note: Derived variable 'PairedAlignerContext::useSoftClipping'
snap-2.0.3/SNAPLib/AlignerOptions.h:95:5: style: Struct 'AlignerOptions' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:92:5: style: Class 'ReadSupplierQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:105:5: style: Class 'ReadSupplierQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:184:5: style: Class 'ReadSupplierFromQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/PairedAligner.h:42:5: style: Class 'PairedAlignerContext' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/PairedAligner.h:100:5: style: Struct 'PairedAlignerOptions' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < DataBatch , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/AlignerOptions.h:170:18: style: The function 'usageMessage' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerOptions.h:53:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/AlignerOptions.h:170:18: note: Function in derived class
snap-2.0.3/SNAPLib/AlignerOptions.h:172:18: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerOptions.h:55:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/AlignerOptions.h:172:18: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:62:14: style: The destructor '~RangeSplittingReadSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:177:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:62:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:64:11: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:176:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:64:11: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:66:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:179:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:66:18: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:69:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:180:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:69:18: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:81:6: style: The destructor '~RangeSplittingReadSupplierGenerator' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:197:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:81:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:83:19: style: The function 'generateNewReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:195:27: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:83:19: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:84:20: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:196:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:84:20: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:98:14: style: The destructor '~RangeSplittingPairedReadSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:187:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:98:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:100:18: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:186:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:100:18: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:102:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:189:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:102:18: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:105:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:190:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:105:18: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:118:6: style: The destructor '~RangeSplittingPairedReadSupplierGenerator' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:204:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:118:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:120:25: style: The function 'generateNewPairedReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:202:33: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:120:25: note: Function in derived class
snap-2.0.3/SNAPLib/RangeSplitter.h:121:20: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:203:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/RangeSplitter.h:121:20: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:107:14: style: The destructor '~ReadSupplierQueue' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:197:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:107:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:111:19: style: The function 'generateNewReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:195:27: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:111:19: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:112:25: style: The function 'generateNewPairedReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:202:33: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:112:25: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:113:20: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:196:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:113:20: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:185:6: style: The destructor '~ReadSupplierFromQueue' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:177:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:185:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:187:11: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:176:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:187:11: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:189:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:179:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:189:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:192:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:180:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:192:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:206:6: style: The destructor '~PairedReadSupplierFromQueue' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:187:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:206:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:208:10: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:186:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:208:10: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:210:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:189:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:210:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:213:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:190:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:213:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:48:18: style: The function 'initialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:75:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:48:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:50:27: style: The function 'newStats' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:78:27: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:50:27: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:52:18: style: The function 'runTask' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:81:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:52:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:54:18: style: The function 'runIterationThread' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:84:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:54:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:60:10: style: The function 'isPaired' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:89:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:60:10: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:66:18: style: The function 'typeSpecificBeginIteration' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:86:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:66:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:67:18: style: The function 'typeSpecificNextIteration' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:87:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:67:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:102:18: style: The function 'usageMessage' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerOptions.h:170:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:102:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:104:18: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerOptions.h:172:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:104:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.h:106:18: style: The function 'isPaired' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerOptions.h:185:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.h:106:18: note: Function in derived class
snap-2.0.3/SNAPLib/AlignerContext.cpp:470:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/AlignerContext.cpp:471:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/AlignerContext.cpp:278:59: warning: Either the condition 'index==NULL' is redundant or there is possible null pointer dereference: index. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/AlignerContext.cpp:267:23: note: Assuming that condition 'index==NULL' is not redundant
snap-2.0.3/SNAPLib/AlignerContext.cpp:278:59: note: Null pointer dereference
snap-2.0.3/SNAPLib/AlignerContext.cpp:278:129: warning: Either the condition 'index==NULL' is redundant or there is possible null pointer dereference: index. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/AlignerContext.cpp:267:23: note: Assuming that condition 'index==NULL' is not redundant
snap-2.0.3/SNAPLib/AlignerContext.cpp:278:129: note: Null pointer dereference
snap-2.0.3/SNAPLib/AlignerContext.cpp:280:9: warning: Either the condition 'index==NULL' is redundant or there is possible null pointer dereference: index. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/AlignerContext.cpp:267:23: note: Assuming that condition 'index==NULL' is not redundant
snap-2.0.3/SNAPLib/AlignerContext.cpp:280:9: note: Null pointer dereference
snap-2.0.3/SNAPLib/AffineGap.h:204:26: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:41:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AlignerContext.cpp:266:52: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/VariableSizeVector.h:192:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:348:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:743:50: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:921:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1262:50: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGap.h:327:18: style: The scope of the variable 'action' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:619:39: style: The scope of the variable 'zeroes' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:734:68: style: The scope of the variable 'matrixIdx' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1141:35: style: The scope of the variable 'zeroes' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1255:68: style: The scope of the variable 'matrixIdx' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AlignerContext.cpp:86:95: style:inconclusive: Function 'runAlignment' argument 4 names different: declaration 'nArgsConsumed' definition 'argsConsumed'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignerContext.h:50:83: note: Function 'runAlignment' argument 4 names different: declaration 'nArgsConsumed' definition 'argsConsumed'.
snap-2.0.3/SNAPLib/AlignerContext.cpp:86:95: note: Function 'runAlignment' argument 4 names different: declaration 'nArgsConsumed' definition 'argsConsumed'.
snap-2.0.3/SNAPLib/AlignerContext.cpp:677:9: style:inconclusive: Function 'parseOptions' argument 1 names different: declaration 'argc' definition 'i_argc'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignerContext.h:72:38: note: Function 'parseOptions' argument 1 names different: declaration 'argc' definition 'i_argc'.
snap-2.0.3/SNAPLib/AlignerContext.cpp:677:9: note: Function 'parseOptions' argument 1 names different: declaration 'argc' definition 'i_argc'.
snap-2.0.3/SNAPLib/AlignerContext.cpp:678:18: style:inconclusive: Function 'parseOptions' argument 2 names different: declaration 'argv' definition 'i_argv'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignerContext.h:72:57: note: Function 'parseOptions' argument 2 names different: declaration 'argv' definition 'i_argv'.
snap-2.0.3/SNAPLib/AlignerContext.cpp:678:18: note: Function 'parseOptions' argument 2 names different: declaration 'argv' definition 'i_argv'.
snap-2.0.3/SNAPLib/AlignerContext.cpp:679:17: style:inconclusive: Function 'parseOptions' argument 3 names different: declaration 'version' definition 'i_version'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AlignerContext.h:72:75: note: Function 'parseOptions' argument 3 names different: declaration 'version' definition 'i_version'.
snap-2.0.3/SNAPLib/AlignerContext.cpp:679:17: note: Function 'parseOptions' argument 3 names different: declaration 'version' definition 'i_version'.
snap-2.0.3/SNAPLib/AlignerContext.cpp:690:21: style: Local variable 'options' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AlignerContext.h:99:42: note: Shadowed declaration
snap-2.0.3/SNAPLib/AlignerContext.cpp:690:21: note: Shadow variable
snap-2.0.3/SNAPLib/AlignerContext.cpp:727:13: style: Local variable 'argsConsumed' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/AlignerContext.cpp:680:15: note: Shadowed declaration
snap-2.0.3/SNAPLib/AlignerContext.cpp:727:13: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGapVectorized.h:403:25: style: Local variable 'patternIdx' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:343:13: note: Shadowed declaration
snap-2.0.3/SNAPLib/AffineGapVectorized.h:403:25: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGapVectorized.h:616:33: style: Local variable 'h' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:442:24: note: Shadowed declaration
snap-2.0.3/SNAPLib/AffineGapVectorized.h:616:33: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGapVectorized.h:974:21: style: Local variable 'patternIdx' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:916:13: note: Shadowed declaration
snap-2.0.3/SNAPLib/AffineGapVectorized.h:974:21: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1138:29: style: Local variable 'h' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1011:24: note: Shadowed declaration
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1138:29: note: Shadow variable
snap-2.0.3/SNAPLib/BaseAligner.h:130:32: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/BaseAligner.h:130:51: style: Parameter 'allocator' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/BaseAligner.h:309:53: style: Parameter 'result' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/AffineGap.h:202:20: style: Variable 'qRowProfile' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/AffineGap.h:403:28: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/AffineGap.h:403:47: style: Parameter 'allocator' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:743:27: style: Variable 'backtracePointersVec' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1262:27: style: Variable 'backtracePointersRow' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1345:32: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1345:51: style: Parameter 'allocator' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/AffineGap.h:327:25: style: Variable 'action' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:690:35: style: Variable 'textOffsetAdj' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1211:35: style: Variable 'textOffsetAdj' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/BigAlloc.cpp:446:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAP_PRIVATE [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/BigAlloc.cpp:537:15: style:inconclusive: Technically the member function 'BigAllocator::amountAllocated' can be const. [functionConst]
snap-2.0.3/SNAPLib/BigAlloc.h:97:12: note: Technically the member function 'BigAllocator::amountAllocated' can be const.
snap-2.0.3/SNAPLib/BigAlloc.cpp:537:15: note: Technically the member function 'BigAllocator::amountAllocated' can be const.
snap-2.0.3/SNAPLib/BigAlloc.cpp:576:15: style:inconclusive: Technically the member function 'BigAllocator::checkCanaries' can be const. [functionConst]
snap-2.0.3/SNAPLib/BigAlloc.h:100:10: note: Technically the member function 'BigAllocator::checkCanaries' can be const.
snap-2.0.3/SNAPLib/BigAlloc.cpp:576:15: note: Technically the member function 'BigAllocator::checkCanaries' can be const.
snap-2.0.3/SNAPLib/BigAlloc.cpp:466:7: warning: If memory allocation fails, then there is a possible null pointer dereference: (unsigned long*)mem [nullPointerOutOfMemory]
snap-2.0.3/SNAPLib/BigAlloc.cpp:450:30: note: Assuming allocation function fails
snap-2.0.3/SNAPLib/BigAlloc.cpp:450:17: note: Assignment 'mem=(char*)mmap(NULL,sizeToAllocate,PROT_READ|PROT_WRITE,flags,-1,0)', assigned value is 0
snap-2.0.3/SNAPLib/BigAlloc.cpp:466:7: note: Null pointer dereference
snap-2.0.3/SNAPLib/BigAlloc.cpp:467:26: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
snap-2.0.3/SNAPLib/BigAlloc.cpp:450:30: note: Assuming allocation function fails
snap-2.0.3/SNAPLib/BigAlloc.cpp:450:17: note: Assignment 'mem=(char*)mmap(NULL,sizeToAllocate,PROT_READ|PROT_WRITE,flags,-1,0)', assigned value is 0
snap-2.0.3/SNAPLib/BigAlloc.cpp:467:26: note: Null pointer addition
snap-2.0.3/SNAPLib/BigAlloc.cpp:450:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:475:27: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:517:19: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:626:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:636:12: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:466:7: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:476:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:524:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:565:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/BigAlloc.cpp:578:10: style: The scope of the variable 'allOK' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/BigAlloc.cpp:591:39: style:inconclusive: Function 'allocate' argument 1 names different: declaration 'amountToAllocate' definition 'sizeToAllocate'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BigAlloc.h:133:35: note: Function 'allocate' argument 1 names different: declaration 'amountToAllocate' definition 'sizeToAllocate'.
snap-2.0.3/SNAPLib/BigAlloc.cpp:591:39: note: Function 'allocate' argument 1 names different: declaration 'amountToAllocate' definition 'sizeToAllocate'.
snap-2.0.3/SNAPLib/BigAlloc.cpp:500:22: style: Parameter 'memoryToCommit' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/BigAlloc.cpp:578:16: style: Variable 'allOK' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/BigAlloc.cpp:582:19: style: Variable 'allOK' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/BufferedAsync.h:25:1: style: The class 'BufferedAsyncReader' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
snap-2.0.3/SNAPLib/BufferedAsync.h:48:1: style: The class 'BufferedAsyncWriter' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:80:22: style:inconclusive: Technically the member function 'BufferedAsyncReader::atEnd' can be const. [functionConst]
snap-2.0.3/SNAPLib/BufferedAsync.h:30:25: note: Technically the member function 'BufferedAsyncReader::atEnd' can be const.
snap-2.0.3/SNAPLib/BufferedAsync.cpp:80:22: note: Technically the member function 'BufferedAsyncReader::atEnd' can be const.
snap-2.0.3/SNAPLib/BufferedAsync.h:33:25: style:inconclusive: Technically the member function 'BufferedAsyncReader::getWaitTimeInMillis' can be const. [functionConst]
snap-2.0.3/SNAPLib/BufferedAsync.h:55:25: style:inconclusive: Technically the member function 'BufferedAsyncWriter::getWaitTimeInMillis' can be const. [functionConst]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:46:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:47:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:113:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:151:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:152:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:178:10: style: The scope of the variable 'ok' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:33:12: style:inconclusive: Function 'open' argument 3 names different: declaration 'length' definition 'bytes'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BufferedAsync.h:28:69: note: Function 'open' argument 3 names different: declaration 'length' definition 'bytes'.
snap-2.0.3/SNAPLib/BufferedAsync.cpp:33:12: note: Function 'open' argument 3 names different: declaration 'length' definition 'bytes'.
snap-2.0.3/SNAPLib/BufferedAsync.cpp:34:12: style:inconclusive: Function 'open' argument 4 names different: declaration 'bufferSize' definition 'i_bufferSize'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BufferedAsync.h:28:84: note: Function 'open' argument 4 names different: declaration 'bufferSize' definition 'i_bufferSize'.
snap-2.0.3/SNAPLib/BufferedAsync.cpp:34:12: note: Function 'open' argument 4 names different: declaration 'bufferSize' definition 'i_bufferSize'.
snap-2.0.3/SNAPLib/BufferedAsync.cpp:144:12: style:inconclusive: Function 'open' argument 2 names different: declaration 'bufferSize' definition 'i_bufferSize'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BufferedAsync.h:51:54: note: Function 'open' argument 2 names different: declaration 'bufferSize' definition 'i_bufferSize'.
snap-2.0.3/SNAPLib/BufferedAsync.cpp:144:12: note: Function 'open' argument 2 names different: declaration 'bufferSize' definition 'i_bufferSize'.
snap-2.0.3/SNAPLib/BufferedAsync.cpp:212:16: style: Local variable 'start' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:207:12: note: Shadowed declaration
snap-2.0.3/SNAPLib/BufferedAsync.cpp:212:16: note: Shadow variable
snap-2.0.3/SNAPLib/BufferedAsync.cpp:162:11: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/BufferedAsync.cpp:178:13: style: Variable 'ok' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.h:382:17: warning: Either the condition 'cigarLen>=cigarBufSize' is redundant or the array 'cigarBuf[2032]' is accessed at index 2032, which is out of bounds. [arrayIndexOutOfBoundsCond]
snap-2.0.3/SNAPLib/SAM.h:377:22: note: Assuming that condition 'cigarLen>=cigarBufSize' is not redundant
snap-2.0.3/SNAPLib/SAM.h:382:17: note: Array index out of bounds
snap-2.0.3/SNAPLib/SAM.h:407:17: warning: Either the condition 'cigarLen>=cigarBufSize' is redundant or the array 'cigarBuf[2032]' is accessed at index 2032, which is out of bounds. [arrayIndexOutOfBoundsCond]
snap-2.0.3/SNAPLib/SAM.h:402:22: note: Assuming that condition 'cigarLen>=cigarBufSize' is not redundant
snap-2.0.3/SNAPLib/SAM.h:407:17: note: Array index out of bounds
snap-2.0.3/SNAPLib/AlignerOptions.cpp:39:17: warning: Member variable 'AlignerOptions::nInputs' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:39:17: warning: Member variable 'AlignerOptions::inputs' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:39:17: warning: Member variable 'AlignerOptions::internalScoreTag' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/SAM.h:356:5: warning: Member variable 'SAMAlignment::qNameLength' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AlignerOptions.h:106:25: style:inconclusive: Member variable 'AlignerOptions::seedCountSpecified' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:66:5: note: Member variable 'AlignerOptions::seedCountSpecified' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:106:25: note: Member variable 'AlignerOptions::seedCountSpecified' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:104:25: style:inconclusive: Member variable 'AlignerOptions::numSeedsFromCommandLine' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:68:5: note: Member variable 'AlignerOptions::numSeedsFromCommandLine' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:104:25: note: Member variable 'AlignerOptions::numSeedsFromCommandLine' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:102:25: style:inconclusive: Member variable 'AlignerOptions::maxDistFraction' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:83:5: note: Member variable 'AlignerOptions::maxDistFraction' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:102:25: note: Member variable 'AlignerOptions::maxDistFraction' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:160:25: style:inconclusive: Member variable 'AlignerOptions::maxScoreGapToPreferNonALTAlignment' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:100:5: note: Member variable 'AlignerOptions::maxScoreGapToPreferNonALTAlignment' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:160:25: note: Member variable 'AlignerOptions::maxScoreGapToPreferNonALTAlignment' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:140:25: style:inconclusive: Member variable 'AlignerOptions::useSoftClipping' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:101:5: note: Member variable 'AlignerOptions::useSoftClipping' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:140:25: note: Member variable 'AlignerOptions::useSoftClipping' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:135:25: style:inconclusive: Member variable 'AlignerOptions::flattenMAPQAtOrBelow' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:102:5: note: Member variable 'AlignerOptions::flattenMAPQAtOrBelow' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.h:135:25: note: Member variable 'AlignerOptions::flattenMAPQAtOrBelow' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/AlignerOptions.cpp:1061:17: style:inconclusive: Technically the member function 'AlignerOptions::passFilter' can be const. [functionConst]
snap-2.0.3/SNAPLib/AlignerOptions.h:183:10: note: Technically the member function 'AlignerOptions::passFilter' can be const.
snap-2.0.3/SNAPLib/AlignerOptions.cpp:1061:17: note: Technically the member function 'AlignerOptions::passFilter' can be const.
snap-2.0.3/SNAPLib/SAM.h:368:20: style:inconclusive: Technically the member function 'SAMAlignment::getUnclippedStart' can be const. [functionConst]
snap-2.0.3/SNAPLib/SAM.h:393:20: style:inconclusive: Technically the member function 'SAMAlignment::getUnclippedEnd' can be const. [functionConst]
snap-2.0.3/SNAPLib/Bam.h:64:12: style:inconclusive: Technically the member function 'BAMHeader::size' can be const. [functionConst]
snap-2.0.3/SNAPLib/Bam.h:129:12: style:inconclusive: Technically the member function 'BAMAlignment::size' can be const. [functionConst]
snap-2.0.3/SNAPLib/Bam.h:194:17: performance:inconclusive: Technically the member function 'BAMAlignment::validate' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/Bam.h:320:10: style:inconclusive: Technically the member function 'BAMAlignAux::isValidValType' can be const. [functionConst]
snap-2.0.3/SNAPLib/FASTQ.h:202:13: warning: Class 'FASTQWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/FASTQ.h:202:13: warning: Class 'FASTQWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/FASTQ.h:200:9: style: Class 'FASTQWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SAM.h:163:5: style: Class 'SAMFormat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Bam.h:401:9: style: Class 'BAMReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/FASTQ.h:42:18: style: The destructor '~FASTQReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:135:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/FASTQ.h:42:18: note: Destructor in derived class
snap-2.0.3/SNAPLib/FASTQ.h:57:22: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:139:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:57:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:59:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:140:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:59:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:61:22: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:144:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:61:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:64:22: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:147:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:64:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:98:18: style: The destructor '~PairedInterleavedFASTQReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:157:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/FASTQ.h:98:18: note: Destructor in derived class
snap-2.0.3/SNAPLib/FASTQ.h:111:22: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:161:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:111:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:113:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:162:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:113:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:115:22: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:164:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:115:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:118:22: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:165:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:118:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:121:32: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:167:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:121:32: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:135:18: style: The destructor '~PairedFASTQReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:157:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/FASTQ.h:135:18: note: Destructor in derived class
snap-2.0.3/SNAPLib/FASTQ.h:141:22: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:161:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:141:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:143:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:162:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:143:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:157:22: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:164:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:157:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:160:22: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:165:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:160:22: note: Function in derived class
snap-2.0.3/SNAPLib/FASTQ.h:163:32: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:167:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/FASTQ.h:163:32: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:58:18: style: The destructor '~SAMReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:135:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/SAM.h:58:18: note: Destructor in derived class
snap-2.0.3/SNAPLib/SAM.h:62:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:140:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:62:22: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:64:22: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:139:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:64:22: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:72:22: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:144:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:72:22: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:75:22: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:147:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:75:22: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:165:18: style: The function 'getSortInfo' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:50:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:165:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:167:18: style: The function 'setupReaderContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:82:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:167:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:170:33: style: The function 'getWriterSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:88:33: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:170:33: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:172:18: style: The function 'writeHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:90:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:172:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:176:18: style: The function 'writePairs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:94:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:176:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:183:18: style: The function 'writeRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:101:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:183:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:194:18: style: The function 'writeRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:111:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.h:194:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.h:403:18: style: The destructor '~BAMReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:157:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/Bam.h:403:18: note: Destructor in derived class
snap-2.0.3/SNAPLib/Bam.h:407:22: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:139:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.h:407:22: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.h:426:14: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:161:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.h:426:14: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.h:431:14: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:164:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.h:431:14: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.h:434:14: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:165:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.h:434:14: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.h:437:32: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:167:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.h:437:32: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.h:444:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:162:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.h:444:22: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.h:412:29: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/SAM.h:424:30: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Bam.h:222:52: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:225:53: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:228:53: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:231:54: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:234:53: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:237:54: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:240:53: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:245:69: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:248:53: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:251:55: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:278:83: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:353:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:375:26: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:438:19: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.h:52:47: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:55:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:58:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:58:49: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:78:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:81:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:84:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:84:49: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:109:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:112:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:115:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:121:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:124:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:124:57: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:127:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:127:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:219:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:245:53: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:318:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:318:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:353:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:368:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:368:46: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:372:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:372:62: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:384:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.h:384:54: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGap.cpp:434:27: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-2.0.3/SNAPLib/AffineGap.cpp:43:21: warning: Member variable 'AffineGapWithCigar::qProfile' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGap.cpp:43:21: warning: Member variable 'AffineGapWithCigar::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGap.cpp:14:21: warning: Member variable 'AffineGapWithCigar::qProfile' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGap.cpp:14:21: warning: Member variable 'AffineGapWithCigar::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGap.cpp:73:21: performance:inconclusive: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/AffineGap.h:462:10: note: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/AffineGap.cpp:73:21: note: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/AlignerOptions.cpp:673:33: style: Checking if unsigned expression 'writeBufferSize' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:709:29: style: Checking if unsigned expression 'matchReward' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:721:28: style: Checking if unsigned expression 'subPenalty' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:733:32: style: Checking if unsigned expression 'gapOpenPenalty' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:745:34: style: Checking if unsigned expression 'gapExtendPenalty' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:757:35: style: Checking if unsigned expression 'fivePrimeEndBonus' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:769:36: style: Checking if unsigned expression 'threePrimeEndBonus' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/AlignerOptions.cpp:1062:11: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.h:368:69: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.h:393:67: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/AffineGap.cpp:434:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AffineGap.cpp:126:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGap.cpp:442:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.h:386:27: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.h:386:13: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.h:412:27: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.h:424:27: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:189:28: style: The scope of the variable 'nEdits' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGap.cpp:273:9: style: The scope of the variable 'n_res' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGap.cpp:348:30: style: Local variable 'j' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:347:25: note: Shadowed declaration
snap-2.0.3/SNAPLib/AffineGap.cpp:348:30: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGap.cpp:370:30: style: Local variable 'j' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:369:25: note: Shadowed declaration
snap-2.0.3/SNAPLib/AffineGap.cpp:370:30: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGap.cpp:200:16: style: Variable 'qRowProfile' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/AffineGap.cpp:189:35: style: Variable 'nEdits' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:347:27: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:347:39: style: Variable 'countM' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:369:27: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:347:25: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:347:32: style: Variable 'countM' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGap.cpp:369:25: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/CommandProcessor.cpp:79:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/CommandProcessor.cpp:100:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/CommandProcessor.cpp:178:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Compat.cpp:1333:0: error: #error "Don't know how to get time in nanos on your platform" [preprocessorErrorDirective]
snap-2.0.3/SNAPLib/Compat.cpp:1333:6: error: #error "Don't know how to get time in nanos on your platform" [preprocessorErrorDirective]
snap-2.0.3/SNAPLib/SeedSequencer.h:35:21: style:inconclusive: Technically the member function 'SeedSequencer::SeedOffset' can be const. [functionConst]
snap-2.0.3/SNAPLib/SeedSequencer.h:40:21: style:inconclusive: Technically the member function 'SeedSequencer::GetWrappedNextSeedToTest' can be const. [functionConst]
snap-2.0.3/SNAPLib/SingleAligner.h:36:5: style: Class 'SingleAlignerContext' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SeedSequencer.h:33:5: style: Class 'SeedSequencer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SingleAligner.h:43:27: style: The function 'newStats' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:78:27: note: Virtual function in base class
snap-2.0.3/SNAPLib/SingleAligner.h:43:27: note: Function in derived class
snap-2.0.3/SNAPLib/SingleAligner.h:45:18: style: The function 'runTask' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:81:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SingleAligner.h:45:18: note: Function in derived class
snap-2.0.3/SNAPLib/SingleAligner.h:47:18: style: The function 'runIterationThread' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:84:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SingleAligner.h:47:18: note: Function in derived class
snap-2.0.3/SNAPLib/SingleAligner.h:49:18: style: The function 'typeSpecificBeginIteration' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:86:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SingleAligner.h:49:18: note: Function in derived class
snap-2.0.3/SNAPLib/SingleAligner.h:50:18: style: The function 'typeSpecificNextIteration' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:87:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SingleAligner.h:50:18: note: Function in derived class
snap-2.0.3/SNAPLib/SingleAligner.h:62:10: style: The function 'isPaired' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerContext.h:89:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SingleAligner.h:62:10: note: Function in derived class
snap-2.0.3/SNAPLib/CommandProcessor.cpp:161:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/CommandProcessor.cpp:134:7: style: Local variable 'argc' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/CommandProcessor.cpp:104:24: note: Shadowed declaration
snap-2.0.3/SNAPLib/CommandProcessor.cpp:134:7: note: Shadow variable
snap-2.0.3/SNAPLib/CommandProcessor.cpp:138:11: style: Local variable 'argv' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/CommandProcessor.cpp:104:43: note: Shadowed declaration
snap-2.0.3/SNAPLib/CommandProcessor.cpp:138:11: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:1064:27: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:42:31: warning: Member variable 'AffineGapVectorizedWithCigar::minScoreParam' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:42:31: warning: Member variable 'AffineGapVectorizedWithCigar::maxScoreParam' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:42:31: warning: Member variable 'AffineGapVectorizedWithCigar::res' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:15:31: warning: Member variable 'AffineGapVectorizedWithCigar::res' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:95:31: performance:inconclusive: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1404:10: note: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:95:31: note: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:1064:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:148:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:193:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:384:46: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:572:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:812:46: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:1086:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:374:9: style: The scope of the variable 'n_res' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:378:38: style: The scope of the variable 'matrixIdx' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:800:9: style: The scope of the variable 'n_res' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:804:38: style: The scope of the variable 'matrixIdx' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:953:12: style:inconclusive: Function 'computeFinalCigarString' argument 8 names different: declaration 'cigarBuf' definition 'cigarBufPtr'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1464:16: note: Function 'computeFinalCigarString' argument 8 names different: declaration 'cigarBuf' definition 'cigarBufPtr'.
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:953:12: note: Function 'computeFinalCigarString' argument 8 names different: declaration 'cigarBuf' definition 'cigarBufPtr'.
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:227:17: style: Local variable 'patternIdx' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:188:9: note: Shadowed declaration
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:227:17: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:610:21: style: Local variable 'patternIdx' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:567:9: note: Shadowed declaration
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:610:21: note: Shadow variable
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:638:0: warning: Redundant code: Found unused function. [constStatement]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:384:23: style: Variable 'backtracePointersRow' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:448:15: style: Variable 'cigarBufStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:812:23: style: Variable 'backtracePointersVec' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:875:15: style: Variable 'cigarBufStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:378:48: style: Variable 'matrixIdx' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:403:27: style: Variable 'matrixIdx' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:406:27: style: Variable 'matrixIdx' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:410:27: style: Variable 'matrixIdx' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:449:41: style: Variable 'nEdits' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:804:48: style: Variable 'matrixIdx' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:830:27: style: Variable 'matrixIdx' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:833:27: style: Variable 'matrixIdx' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:837:27: style: Variable 'matrixIdx' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:876:41: style: Variable 'nEdits' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:892:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Full [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataReader.cpp:971:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable InUse [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataReader.cpp:1456:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Reading [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataReader.cpp:1528:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Full [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataReader.cpp:1569:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable InUse [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2020:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_NULL [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2261:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Error.cpp:34:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Error.cpp:62:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Error.cpp:80:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Error.cpp:96:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Error.cpp:96:5: portability: %lld in format string (no. 2) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/Error.cpp:66:1: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
snap-2.0.3/SNAPLib/Error.cpp:84:1: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
snap-2.0.3/SNAPLib/DataWriter.cpp:461:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CopyFilter [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataWriter.cpp:975:104: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/FASTA.cpp:200:22: style:inconclusive: Function 'ReadFASTAGenome' argument 10 names different: declaration 'autoAlt' definition 'autoALT'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/FASTA.h:45:19: note: Function 'ReadFASTAGenome' argument 10 names different: declaration 'autoAlt' definition 'autoALT'.
snap-2.0.3/SNAPLib/FASTA.cpp:200:22: note: Function 'ReadFASTAGenome' argument 10 names different: declaration 'autoAlt' definition 'autoALT'.
snap-2.0.3/SNAPLib/FASTA.cpp:155:22: style: Parameter 'paddingBuffer' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Bam.cpp:2552:42: warning:inconclusive: The buffer 'bestReadId' may not be null-terminated after the call to strncpy(). [terminateStrncpy]
snap-2.0.3/SNAPLib/Bam.cpp:63:12: warning: Member variable 'BAMReader::extraOffset' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Bam.cpp:2218:5: warning: Member variable 'BAMFilter::currentWriter' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Bam.cpp:2218:5: warning: Member variable 'BAMFilter::currentBuffer' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Bam.cpp:2218:5: warning: Member variable 'BAMFilter::currentBufferBytes' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Bam.cpp:2218:5: warning: Member variable 'BAMFilter::currentOffset' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Bam.cpp:2451:5: warning: Member variable 'DuplicateReadKey::libraryHash' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Bam.cpp:2508:5: warning: Member variable 'DuplicateFragmentKey::libraryHash' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Bam.h:478:29: style:inconclusive: Member variable 'BAMReader::n_ref' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Bam.cpp:63:95: note: Member variable 'BAMReader::n_ref' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Bam.h:478:29: note: Member variable 'BAMReader::n_ref' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Bam.h:477:29: style:inconclusive: Member variable 'BAMReader::data' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Bam.cpp:63:105: note: Member variable 'BAMReader::data' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Bam.h:477:29: note: Member variable 'BAMReader::data' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GzipDataWriter.h:57:16: style:inconclusive: Member variable 'GzipWriterFilterSupplier::multiThreaded' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/GzipDataWriter.h:46:9: note: Member variable 'GzipWriterFilterSupplier::multiThreaded' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GzipDataWriter.h:57:16: note: Member variable 'GzipWriterFilterSupplier::multiThreaded' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Bam.cpp:3280:9: style:inconclusive: Member variable 'BAMIndexSupplier::lastRefId' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Bam.cpp:3237:9: note: Member variable 'BAMIndexSupplier::lastRefId' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Bam.cpp:3280:9: note: Member variable 'BAMIndexSupplier::lastRefId' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < BamDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < BamDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < BamDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < BamDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < BamDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < BamDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Bam.cpp:2457:5: style:inconclusive: Technically the member function 'DuplicateReadKey::operator_uint64' can be const. [functionConst]
snap-2.0.3/SNAPLib/Bam.cpp:2520:5: style:inconclusive: Technically the member function 'DuplicateFragmentKey::operator_uint64' can be const. [functionConst]
snap-2.0.3/SNAPLib/Bam.cpp:2553:17: style:inconclusive: Technically the member function 'DuplicateMateInfo::getBestReadId' can be const. [functionConst]
snap-2.0.3/SNAPLib/Bam.cpp:2555:10: style:inconclusive: Technically the member function 'DuplicateMateInfo::getBestTileXY' can be const. [functionConst]
snap-2.0.3/SNAPLib/Bam.cpp:816:5: style: Class 'BAMFormat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Bam.cpp:2451:5: style: Struct 'DuplicateReadKey' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Bam.cpp:2508:5: style: Struct 'DuplicateFragmentKey' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Bam.cpp:2622:5: style: Class 'BAMDupMarkFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Bam.cpp:3193:5: style: Class 'BAMDupMarkSupplier' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Bam.cpp:3219:5: style: Class 'BAMIndexFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < DuplicateReadKey , DuplicateMateInfo , 150 , MapNumericHash < DuplicateReadKey > , 70 , 0 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < DuplicateReadKey , DuplicateMateInfo , 150 , MapNumericHash < DuplicateReadKey > , 70 , 0 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < DuplicateFragmentKey , DuplicateMateInfo , 150 , MapNumericHash < DuplicateFragmentKey > , 70 , 0 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < DuplicateFragmentKey , DuplicateMateInfo , 150 , MapNumericHash < DuplicateFragmentKey > , 70 , 0 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint32_t , VariableSizeVector < BAMChunk , 150 , false > , 150 , MapNumericHash < uint32_t > , 80 , -1 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < uint32_t , VariableSizeVector < BAMChunk , 150 , false > , 150 , MapNumericHash < uint32_t > , 80 , -1 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < unsigned long , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < BamDupMarkEntry , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < uint64_t , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < BAMChunk , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/GzipDataWriter.h:52:14: style: The destructor '~GzipWriterFilterSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:81:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/GzipDataWriter.h:52:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.h:59:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:85:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.h:59:33: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.h:61:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:88:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.h:61:18: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.h:62:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:89:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.h:62:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:818:18: style: The function 'getSortInfo' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:50:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:818:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:820:18: style: The function 'setupReaderContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:82:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:820:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:823:33: style: The function 'getWriterSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:88:33: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:823:33: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:825:18: style: The function 'writeHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:90:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:825:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:829:18: style: The function 'writePairs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:94:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:829:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:836:18: style: The function 'writeRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:101:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:836:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:846:18: style: The function 'writeRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/FileFormat.h:111:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:846:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:2220:14: style: The destructor '~BAMFilter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:58:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/Bam.cpp:2220:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/Bam.cpp:2224:15: style: The function 'inHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:61:16: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:2224:15: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:2227:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:64:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:2227:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:2229:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:70:24: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:2229:20: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:2628:6: style: The destructor '~BAMDupMarkFilter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Bam.cpp:2220:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/Bam.cpp:2628:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/Bam.cpp:2652:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Bam.cpp:2229:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:2652:20: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:2657:18: style: The function 'onRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Bam.cpp:2232:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:2657:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3196:14: style: The destructor '~BAMDupMarkSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:81:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/Bam.cpp:3196:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3198:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:85:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:3198:33: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3201:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:88:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:3201:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3202:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:89:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:3202:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3223:18: style: The function 'onRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Bam.cpp:2232:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:3223:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3244:14: style: The destructor '~BAMIndexSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:81:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/Bam.cpp:3244:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3246:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:85:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:3246:33: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3249:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:88:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:3249:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3250:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:89:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/Bam.cpp:3250:18: note: Function in derived class
snap-2.0.3/SNAPLib/Bam.cpp:3452:19: style: Condition 'bsize==0' is always false [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/Bam.cpp:3450:37: note: Assignment 'bsize=h->BSIZE()+1', assigned value is greater than 0
snap-2.0.3/SNAPLib/Bam.cpp:3452:19: note: Condition 'bsize==0' is always false
snap-2.0.3/SNAPLib/Bam.cpp:3351:37: warning: If resource allocation fails, then there is a possible null pointer dereference: index [nullPointerOutOfResources]
snap-2.0.3/SNAPLib/Bam.cpp:3349:24: note: Assuming allocation function fails
snap-2.0.3/SNAPLib/Bam.cpp:3349:24: note: Assignment 'index=fopen(indexFileName,"wb")', assigned value is 0
snap-2.0.3/SNAPLib/Bam.cpp:3351:37: note: Null pointer dereference
snap-2.0.3/SNAPLib/Bam.cpp:3353:38: warning: If resource allocation fails, then there is a possible null pointer dereference: index [nullPointerOutOfResources]
snap-2.0.3/SNAPLib/Bam.cpp:3349:24: note: Assuming allocation function fails
snap-2.0.3/SNAPLib/Bam.cpp:3349:24: note: Assignment 'index=fopen(indexFileName,"wb")', assigned value is 0
snap-2.0.3/SNAPLib/Bam.cpp:3353:38: note: Null pointer dereference
snap-2.0.3/SNAPLib/Bam.cpp:3366:42: warning: If resource allocation fails, then there is a possible null pointer dereference: index [nullPointerOutOfResources]
snap-2.0.3/SNAPLib/Bam.cpp:3349:24: note: Assuming allocation function fails
snap-2.0.3/SNAPLib/Bam.cpp:3349:24: note: Assignment 'index=fopen(indexFileName,"wb")', assigned value is 0
snap-2.0.3/SNAPLib/Bam.cpp:3358:18: note: Assuming condition is false
snap-2.0.3/SNAPLib/Bam.cpp:3366:42: note: Null pointer dereference
snap-2.0.3/SNAPLib/Bam.cpp:242:54: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:334:40: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:345:48: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:661:33: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:938:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1546:14: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1559:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1577:12: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1588:6: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1598:10: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1610:14: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1612:14: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1625:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1626:10: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1638:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:1647:10: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:2281:16: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:2713:19: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:2728:24: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:2857:60: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:2863:95: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:3137:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Bam.cpp:158:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:173:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:207:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:292:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:317:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:644:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:656:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:709:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:891:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:988:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1109:79: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1141:79: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1249:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1388:56: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1452:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1533:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1554:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1557:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1557:55: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1562:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1565:20: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1571:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1575:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1575:47: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1582:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1586:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1586:47: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1593:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1596:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1596:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1604:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1607:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1607:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1620:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1623:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1623:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1633:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1645:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1645:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1691:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1695:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1695:55: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1708:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1720:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1727:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1752:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1760:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1773:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1786:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1790:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1791:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1895:56: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:1971:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2080:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2085:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2089:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2094:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2103:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2105:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2109:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2177:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2182:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2186:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2191:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2200:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2202:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2206:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2326:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2335:20: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2346:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2357:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:2368:45: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Bam.cpp:3449:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/FASTQ.cpp:318:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable isValidStartingCharacterForNextLine [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/FASTQ.cpp:673:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:112:17: style:inconclusive: Member variable 'ChimericPairedEndAligner::forceSpacing' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:74:62: note: Member variable 'ChimericPairedEndAligner::forceSpacing' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:112:17: note: Member variable 'ChimericPairedEndAligner::forceSpacing' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:131:10: style:inconclusive: Member variable 'ChimericPairedEndAligner::useSoftClipping' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:76:157: note: Member variable 'ChimericPairedEndAligner::useSoftClipping' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:131:10: note: Member variable 'ChimericPairedEndAligner::useSoftClipping' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:73:10: style:inconclusive: Technically the member function 'ChimericPairedEndAligner::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:100:10: style:inconclusive: Technically the member function 'ChimericPairedEndAligner::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:80:5: warning: Class 'ChimericPairedEndAligner' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:80:5: warning: Class 'ChimericPairedEndAligner' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < util :: IdPair , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:66:14: style: The destructor '~ChimericPairedEndAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:40:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:66:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:75:18: style: The function 'align' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:42:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:75:18: note: Function in derived class
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:102:20: style: The function 'getLocationsScoredWithLandauVishkin' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:80:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:102:20: note: Function in derived class
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:106:20: style: The function 'getLocationsScoredWithAffineGap' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:81:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:106:20: note: Function in derived class
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:351:25: style: Condition '!fitInSecondaryBuffer' is always false [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:322:17: note: Assuming that condition '!fitInSecondaryBuffer' is not redundant
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:345:59: note: Assuming condition is false
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:351:25: note: Condition '!fitInSecondaryBuffer' is always false
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:184:44: style: The scope of the variable 'sumPairScoreAlt' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:52:34: style:inconclusive: Function 'ChimericPairedEndAligner' argument 10 names different: declaration 'disabledOptimizations_' definition 'disabledOptimizations'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:43:34: note: Function 'ChimericPairedEndAligner' argument 10 names different: declaration 'disabledOptimizations_' definition 'disabledOptimizations'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:52:34: note: Function 'ChimericPairedEndAligner' argument 10 names different: declaration 'disabledOptimizations_' definition 'disabledOptimizations'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:53:34: style:inconclusive: Function 'ChimericPairedEndAligner' argument 11 names different: declaration 'useAffineGap' definition 'useAffineGap_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:44:34: note: Function 'ChimericPairedEndAligner' argument 11 names different: declaration 'useAffineGap' definition 'useAffineGap_'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:53:34: note: Function 'ChimericPairedEndAligner' argument 11 names different: declaration 'useAffineGap' definition 'useAffineGap_'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:56:34: style:inconclusive: Function 'ChimericPairedEndAligner' argument 14 names different: declaration 'emitALTAlignments' definition 'emitALTAlignments_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:47:34: note: Function 'ChimericPairedEndAligner' argument 14 names different: declaration 'emitALTAlignments' definition 'emitALTAlignments_'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:56:34: note: Function 'ChimericPairedEndAligner' argument 14 names different: declaration 'emitALTAlignments' definition 'emitALTAlignments_'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:72:34: style:inconclusive: Function 'ChimericPairedEndAligner' argument 30 names different: declaration 'enableHammingScoringBaseAligner' definition 'enableHammingScoringBaseAligner_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:63:34: note: Function 'ChimericPairedEndAligner' argument 30 names different: declaration 'enableHammingScoringBaseAligner' definition 'enableHammingScoringBaseAligner_'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:72:34: note: Function 'ChimericPairedEndAligner' argument 30 names different: declaration 'enableHammingScoringBaseAligner' definition 'enableHammingScoringBaseAligner_'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:130:32: style:inconclusive: Function 'align' argument 4 names different: declaration 'firatALTResult' definition 'firstALTResult'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:79:32: note: Function 'align' argument 4 names different: declaration 'firatALTResult' definition 'firstALTResult'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:130:32: note: Function 'align' argument 4 names different: declaration 'firatALTResult' definition 'firstALTResult'.
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:73:32: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.h:73:51: style: Parameter 'allocator' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/ChimericPairedEndAligner.cpp:184:60: style: Variable 'sumPairScoreAlt' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:2569:17: style: Variable 'bestReadQuality' is assigned an expression that holds the same value. [redundantAssignment]
snap-2.0.3/SNAPLib/Bam.cpp:2567:34: note: Assuming that condition 'totalQuality_==bestReadQuality' is not redundant
snap-2.0.3/SNAPLib/Bam.cpp:2569:17: note: Variable 'bestReadQuality' is assigned an expression that holds the same value.
snap-2.0.3/SNAPLib/Bam.cpp:2574:21: style: Variable 'bestReadQuality' is assigned an expression that holds the same value. [redundantAssignment]
snap-2.0.3/SNAPLib/Bam.cpp:2567:34: note: Assuming that condition 'totalQuality_==bestReadQuality' is not redundant
snap-2.0.3/SNAPLib/Bam.cpp:2574:21: note: Variable 'bestReadQuality' is assigned an expression that holds the same value.
snap-2.0.3/SNAPLib/Bam.cpp:2743:24: style: Variable 'next_i' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/Bam.cpp:2736:24: note: next_i is assigned
snap-2.0.3/SNAPLib/Bam.cpp:2743:24: note: next_i is overwritten
snap-2.0.3/SNAPLib/Bam.cpp:1196:21: style: The scope of the variable 'warningPrinted' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/Bam.cpp:1401:17: style: The scope of the variable 'warningPrinted' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/Bam.cpp:1922:17: style: The scope of the variable 'warningPrinted' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/GenericFile.cpp:59:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/GenericFile.cpp:85:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/GenericFile.cpp:37:14: warning: Member variable 'GenericFile::_mode' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenericFile_stdio.h:31:28: warning: The class 'GenericFile_stdio' defines member function with name 'open' also defined in its parent class 'GenericFile'. [duplInheritedMember]
snap-2.0.3/SNAPLib/GenericFile.cpp:47:27: note: Parent function 'GenericFile::open'
snap-2.0.3/SNAPLib/GenericFile_stdio.h:31:28: note: Derived function 'GenericFile_stdio::open'
snap-2.0.3/SNAPLib/GenericFile_stdio.h:33:17: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:45:17: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:33:17: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:34:14: style: The function 'getchar' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:50:17: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:34:14: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:35:16: style: The function 'gets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:55:16: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:35:16: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:36:14: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:58:14: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:36:14: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:37:11: style: The destructor '~GenericFile_stdio' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:66:11: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:37:11: note: Destructor in derived class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:38:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/GenericFile.h:61:15: note: Virtual function in base class
snap-2.0.3/SNAPLib/GenericFile_stdio.h:38:15: note: Function in derived class
snap-2.0.3/SNAPLib/GenericFile.cpp:47:44: style:inconclusive: Function 'open' argument 1 names different: declaration 'fileName' definition 'filename'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/GenericFile.h:41:42: note: Function 'open' argument 1 names different: declaration 'fileName' definition 'filename'.
snap-2.0.3/SNAPLib/GenericFile.cpp:47:44: note: Function 'open' argument 1 names different: declaration 'fileName' definition 'filename'.
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:62:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:86:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Bam.cpp:528:12: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
snap-2.0.3/SNAPLib/Bam.cpp:528:23: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
snap-2.0.3/SNAPLib/Bam.cpp:528:56: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
snap-2.0.3/SNAPLib/Bam.cpp:529:12: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
snap-2.0.3/SNAPLib/Bam.cpp:529:23: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
snap-2.0.3/SNAPLib/GenericFile_Blob.h:63:14: style:inconclusive: Member variable 'GenericFile_Blob::blobEnd' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:27:144: note: Member variable 'GenericFile_Blob::blobEnd' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenericFile_Blob.h:63:14: note: Member variable 'GenericFile_Blob::blobEnd' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenericFile_Blob.h:45:15: style: Virtual function 'close' is called from destructor '~GenericFile_Blob()' at line 79. Dynamic binding is not used. [virtualCallInConstructor]
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:79:5: note: Calling close
snap-2.0.3/SNAPLib/GenericFile_Blob.h:45:15: note: close is a virtual function
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:27:76: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:27:105: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:27:152: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:89:24: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:43:11: style: Variable 'base' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:428:13: style:inconclusive: Function 'encodeSeq' argument 1 names different: declaration 'nibbles' definition 'encoded'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Bam.h:155:35: note: Function 'encodeSeq' argument 1 names different: declaration 'nibbles' definition 'encoded'.
snap-2.0.3/SNAPLib/Bam.cpp:428:13: note: Function 'encodeSeq' argument 1 names different: declaration 'nibbles' definition 'encoded'.
snap-2.0.3/SNAPLib/Bam.cpp:700:21: style:inconclusive: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Bam.h:468:41: note: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'.
snap-2.0.3/SNAPLib/Bam.cpp:700:21: note: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'.
snap-2.0.3/SNAPLib/Bam.cpp:888:24: style:inconclusive: Function 'getSortInfo' argument 6 names different: declaration 'originalContigNum' definition 'o_refID'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Bam.cpp:818:156: note: Function 'getSortInfo' argument 6 names different: declaration 'originalContigNum' definition 'o_refID'.
snap-2.0.3/SNAPLib/Bam.cpp:888:24: note: Function 'getSortInfo' argument 6 names different: declaration 'originalContigNum' definition 'o_refID'.
snap-2.0.3/SNAPLib/Bam.cpp:2323:12: style:inconclusive: Function 'getRead' argument 1 names different: declaration 'fileOffset' definition 'offset'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Bam.cpp:2234:34: note: Function 'getRead' argument 1 names different: declaration 'fileOffset' definition 'offset'.
snap-2.0.3/SNAPLib/Bam.cpp:2323:12: note: Function 'getRead' argument 1 names different: declaration 'fileOffset' definition 'offset'.
snap-2.0.3/SNAPLib/Bam.cpp:2343:19: style:inconclusive: Function 'getNextRead' argument 1 names different: declaration 'read' definition 'bam'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Bam.cpp:2236:45: note: Function 'getNextRead' argument 1 names different: declaration 'read' definition 'bam'.
snap-2.0.3/SNAPLib/Bam.cpp:2343:19: note: Function 'getNextRead' argument 1 names different: declaration 'read' definition 'bam'.
snap-2.0.3/SNAPLib/Bam.cpp:2344:13: style:inconclusive: Function 'getNextRead' argument 2 names different: declaration 'o_fileOffset' definition 'io_offset'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Bam.cpp:2236:59: note: Function 'getNextRead' argument 2 names different: declaration 'o_fileOffset' definition 'io_offset'.
snap-2.0.3/SNAPLib/Bam.cpp:2344:13: note: Function 'getNextRead' argument 2 names different: declaration 'o_fileOffset' definition 'io_offset'.
snap-2.0.3/SNAPLib/Bam.cpp:3125:40: style:inconclusive: Function 'onRead' argument 1 names different: declaration 'bam' definition 'lastBam'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Bam.cpp:2657:39: note: Function 'onRead' argument 1 names different: declaration 'bam' definition 'lastBam'.
snap-2.0.3/SNAPLib/Bam.cpp:3125:40: note: Function 'onRead' argument 1 names different: declaration 'bam' definition 'lastBam'.
snap-2.0.3/SNAPLib/Bam.cpp:3125:56: style:inconclusive: Function 'onRead' argument 2 names different: declaration 'fileOffset' definition 'lastOffset'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Bam.cpp:2657:51: note: Function 'onRead' argument 2 names different: declaration 'fileOffset' definition 'lastOffset'.
snap-2.0.3/SNAPLib/Bam.cpp:3125:56: note: Function 'onRead' argument 2 names different: declaration 'fileOffset' definition 'lastOffset'.
snap-2.0.3/SNAPLib/Bam.cpp:497:17: style: Local variable 'op' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/Bam.cpp:489:13: note: Shadowed declaration
snap-2.0.3/SNAPLib/Bam.cpp:497:17: note: Shadow variable
snap-2.0.3/SNAPLib/Bam.cpp:1747:26: style: Local variable 'buffer' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/Bam.cpp:1516:20: note: Shadowed declaration
snap-2.0.3/SNAPLib/Bam.cpp:1747:26: note: Shadow variable
snap-2.0.3/SNAPLib/Bam.cpp:1768:27: style: Local variable 'buffer' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/Bam.cpp:1516:20: note: Shadowed declaration
snap-2.0.3/SNAPLib/Bam.cpp:1768:27: note: Shadow variable
snap-2.0.3/SNAPLib/Bam.cpp:2109:25: style: Local variable 'op' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/Bam.cpp:2103:21: note: Shadowed declaration
snap-2.0.3/SNAPLib/Bam.cpp:2109:25: note: Shadow variable
snap-2.0.3/SNAPLib/Bam.cpp:2206:25: style: Local variable 'op' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/Bam.cpp:2200:21: note: Shadowed declaration
snap-2.0.3/SNAPLib/Bam.cpp:2206:25: note: Shadow variable
snap-2.0.3/SNAPLib/Bam.cpp:779:53: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
snap-2.0.3/SNAPLib/VariableSizeMap.h:336:23: performance: Function parameter 'key' should be passed by const reference. [passedByValue]
snap-2.0.3/SNAPLib/VariableSizeMap.h:336:30: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
snap-2.0.3/SNAPLib/VariableSizeMap.h:344:26: performance: Function parameter 'key' should be passed by const reference. [passedByValue]
snap-2.0.3/SNAPLib/VariableSizeMap.h:353:33: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
snap-2.0.3/SNAPLib/VariableSizeMap.h:23:33: performance: Function parameter 'v' should be passed by const reference. [passedByValue]
snap-2.0.3/SNAPLib/VariableSizeMap.h:14:34: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
snap-2.0.3/SNAPLib/GenericFile_map.h:35:15: style: Virtual function 'close' is called from destructor '~GenericFile_map()' at line 58. Dynamic binding is not used. [virtualCallInConstructor]
snap-2.0.3/SNAPLib/GenericFile_map.cpp:58:2: note: Calling close
snap-2.0.3/SNAPLib/GenericFile_map.h:35:15: note: close is a virtual function
snap-2.0.3/SNAPLib/GenericFile_map.cpp:41:140: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenericFile_map.cpp:74:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenericFile_map.cpp:69:15: style: Variable 'pageSize' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/GenericFile_map.cpp:69:6: style: Variable 'pageSize' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:353:14: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Bam.cpp:380:14: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Bam.cpp:429:11: style: Parameter 'ascii' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Bam.cpp:451:14: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:470:14: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:488:14: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:657:19: style: Variable 'rgFromAux' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:672:27: style: Variable 'rgStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:677:31: style: Variable 'lbStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:678:31: style: Variable 'lbEnd' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:697:11: style: Parameter 'endOfBuffer' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Bam.cpp:933:15: style: Variable 'tempFileName' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:1192:15: style: Variable 'read' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:1513:19: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Bam.cpp:1514:20: style: Parameter 'aux' can be declared as pointer to const [constParameterReference]
snap-2.0.3/SNAPLib/Bam.cpp:1522:19: style: Parameter 'internalScoreTag' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Bam.cpp:1638:17: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:2602:15: style: Variable 'libraryName' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:2710:19: style: Variable 'firstBam' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Bam.cpp:3137:13: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenericFile_stdio.cpp:66:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ReadOnly [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/GenericFile_stdio.cpp:38:39: warning: The class 'GenericFile_stdio' defines member function with name 'open' also defined in its parent class 'GenericFile'. [duplInheritedMember]
snap-2.0.3/SNAPLib/GenericFile.h:41:25: note: Parent function 'GenericFile::open'
snap-2.0.3/SNAPLib/GenericFile_stdio.cpp:38:39: note: Derived function 'GenericFile_stdio::open'
snap-2.0.3/SNAPLib/Genome.cpp:35:9: warning: Member variable 'Genome::genomeLocationOfFirstALTContig' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/Genome.h:462:22: style:inconclusive: Member variable 'Genome::maxContigs' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/Genome.cpp:36:106: note: Member variable 'Genome::maxContigs' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Genome.h:462:22: note: Member variable 'Genome::maxContigs' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/Genome.cpp:267:58: style: Condition 'OriginalContigNumToInt(originalContigNumber)<0' is always false [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/Genome.cpp:267:35: note: Calling function 'OriginalContigNumToInt' returns !<=-1
snap-2.0.3/SNAPLib/Genome.cpp:267:58: note: Condition 'OriginalContigNumToInt(originalContigNumber)<0' is always false
snap-2.0.3/SNAPLib/Genome.cpp:216:5: warning: %lld in format string (no. 1) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/Genome.cpp:226:9: portability: %lld in format string (no. 1) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/Genome.cpp:226:9: portability: %lld in format string (no. 4) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/Genome.cpp:356:18: portability: %lld in format string (no. 1) requires 'long long *' but the argument type is '_int64 * {aka signed long *}'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Genome.cpp:356:18: warning: %x in format string (no. 2) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Genome.cpp:356:18: portability: %lld in format string (no. 4) requires 'long long *' but the argument type is '_int64 * {aka signed long *}'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Genome.cpp:356:18: warning: %x in format string (no. 5) requires 'unsigned int *' but the argument type is 'signed int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Genome.cpp:394:37: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Genome.cpp:497:32: warning: %lld in format string (no. 1) requires 'long long *' but the argument type is 'signed long *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Genome.cpp:497:32: warning: %d in format string (no. 2) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Genome.cpp:497:32: warning: %d in format string (no. 3) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/Genome.cpp:45:18: warning: Either the condition 'NULL==bases' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/Genome.cpp:39:14: note: Assuming that condition 'NULL==bases' is not redundant
snap-2.0.3/SNAPLib/Genome.cpp:45:18: note: Null pointer subtraction
snap-2.0.3/SNAPLib/Genome.cpp:46:18: warning: Either the condition 'NULL==bases' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/Genome.cpp:39:14: note: Assuming that condition 'NULL==bases' is not redundant
snap-2.0.3/SNAPLib/Genome.cpp:46:18: note: Null pointer addition
snap-2.0.3/SNAPLib/Genome.cpp:38:14: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Genome.cpp:51:15: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Genome.cpp:52:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Genome.cpp:306:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Genome.cpp:307:43: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Genome.cpp:417:25: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Genome.cpp:415:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Genome.cpp:319:12: style: The scope of the variable 'n' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/Genome.cpp:320:11: style: The scope of the variable 'curName' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/Genome.cpp:646:13: style: The scope of the variable 'count' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/Genome.cpp:653:13: style: The scope of the variable 'count' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/Genome.cpp:35:111: style:inconclusive: Function 'Genome' argument 4 names different: declaration 'maxContigs' definition 'i_maxContigs'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Genome.h:287:37: note: Function 'Genome' argument 4 names different: declaration 'maxContigs' definition 'i_maxContigs'.
snap-2.0.3/SNAPLib/Genome.cpp:35:111: note: Function 'Genome' argument 4 names different: declaration 'maxContigs' definition 'i_maxContigs'.
snap-2.0.3/SNAPLib/Genome.cpp:277:87: style:inconclusive: Function 'loadFromFile' argument 3 names different: declaration 'i_minLocation' definition 'minLocation'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Genome.h:325:24: note: Function 'loadFromFile' argument 3 names different: declaration 'i_minLocation' definition 'minLocation'.
snap-2.0.3/SNAPLib/Genome.cpp:277:87: note: Function 'loadFromFile' argument 3 names different: declaration 'i_minLocation' definition 'minLocation'.
snap-2.0.3/SNAPLib/Genome.cpp:661:69: style:inconclusive: Function 'getProjLocation' argument 2 names different: declaration 'span' definition 'alnSpan'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Genome.h:426:69: note: Function 'getProjLocation' argument 2 names different: declaration 'span' definition 'alnSpan'.
snap-2.0.3/SNAPLib/Genome.cpp:661:69: note: Function 'getProjLocation' argument 2 names different: declaration 'span' definition 'alnSpan'.
snap-2.0.3/SNAPLib/Genome.cpp:145:11: style: Parameter 'contigName' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Genome.cpp:147:15: style: Parameter 'altLiftoverContigFlags' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Genome.cpp:149:15: style: Parameter 'altLiftoverProjContigOffsets' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Genome.cpp:390:19: style: Variable 'nextChunkOfCigar' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Genome.cpp:494:11: style: Variable 'retval' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/Genome.cpp:394:35: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Genome.cpp:394:21: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:1006:28: style: Variable 'genomeLen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:1007:63: style: Variable 'contigNumbersByOriginalOrder' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:1006:18: style: Variable 'genomeLen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:1007:34: style: Variable 'contigNumbersByOriginalOrder' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:1369:29: style: Variable 'newAddFrontClipping' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:1720:36: style: Variable '((char*)fc)[3]' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:1870:29: style: Variable 'newAddFrontClipping' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:2171:20: style: Variable 'dataLength' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:2348:22: style: Variable 'oldOffset' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:2348:12: style: Variable 'oldOffset' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:2728:22: style: Variable 'firstBam' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:3179:22: style: Variable 'fieldScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Bam.cpp:3181:22: style: Variable 'fieldScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/FASTQ.cpp:40:14: warning: Member variable 'FASTQReader::fileName' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/FASTQ.cpp:356:31: warning: Member variable 'PairedInterleavedFASTQReader::fileName' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/FASTQ.cpp:258:40: warning: Either the condition 'NULL==newLine' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/FASTQ.cpp:241:18: note: Assuming that condition 'NULL==newLine' is not redundant
snap-2.0.3/SNAPLib/FASTQ.cpp:258:40: note: Null pointer subtraction
snap-2.0.3/SNAPLib/Bam.cpp:2277:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:2286:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:2290:73: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:2893:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:2938:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:3001:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:3035:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:3081:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:3373:84: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/Bam.cpp:3387:91: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/FASTQ.cpp:41:17: style:inconclusive: Function 'FASTQReader' argument 1 names different: declaration 'data' definition 'i_data'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/FASTQ.h:40:33: note: Function 'FASTQReader' argument 1 names different: declaration 'data' definition 'i_data'.
snap-2.0.3/SNAPLib/FASTQ.cpp:41:17: note: Function 'FASTQReader' argument 1 names different: declaration 'data' definition 'i_data'.
snap-2.0.3/SNAPLib/FASTQ.cpp:63:26: style:inconclusive: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/FASTQ.h:49:34: note: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'.
snap-2.0.3/SNAPLib/FASTQ.cpp:63:26: note: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'.
snap-2.0.3/SNAPLib/FASTQ.cpp:229:53: style:inconclusive: Function 'getReadFromBuffer' argument 2 names different: declaration 'bufferSize' definition 'validBytes'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/FASTQ.h:67:62: note: Function 'getReadFromBuffer' argument 2 names different: declaration 'bufferSize' definition 'validBytes'.
snap-2.0.3/SNAPLib/FASTQ.cpp:229:53: note: Function 'getReadFromBuffer' argument 2 names different: declaration 'bufferSize' definition 'validBytes'.
snap-2.0.3/SNAPLib/FASTQ.cpp:357:17: style:inconclusive: Function 'PairedInterleavedFASTQReader' argument 1 names different: declaration 'data' definition 'i_data'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/FASTQ.h:96:50: note: Function 'PairedInterleavedFASTQReader' argument 1 names different: declaration 'data' definition 'i_data'.
snap-2.0.3/SNAPLib/FASTQ.cpp:357:17: note: Function 'PairedInterleavedFASTQReader' argument 1 names different: declaration 'data' definition 'i_data'.
snap-2.0.3/SNAPLib/FASTQ.cpp:365:62: style:inconclusive: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/FASTQ.h:101:57: note: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'.
snap-2.0.3/SNAPLib/FASTQ.cpp:365:62: note: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'.
snap-2.0.3/SNAPLib/FASTQ.cpp:495:30: style:inconclusive: Function 'writeRead' argument 1 names different: declaration 'readToWrite' definition 'read'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/FASTQ.h:184:30: note: Function 'writeRead' argument 1 names different: declaration 'readToWrite' definition 'read'.
snap-2.0.3/SNAPLib/FASTQ.cpp:495:30: note: Function 'writeRead' argument 1 names different: declaration 'readToWrite' definition 'read'.
snap-2.0.3/SNAPLib/FASTQ.cpp:159:15: style: Variable 'thirdLineCandidate' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/FASTQ.cpp:495:30: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/HashTable.cpp:252:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/HashTable.cpp:249:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/HashTable.cpp:252:88: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/HashTable.cpp:335:16: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/HashTable.cpp:52:19: style: Checking if unsigned expression 'tableSize' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/HashTable.cpp:165:26: style: Checking if unsigned expression 'table->tableSize' is less than zero. [unsignedLessThanZero]
snap-2.0.3/SNAPLib/HashTable.h:109:31: style: Local variable 'nProbesInGetEntryForKey' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/HashTable.cpp:263:8: note: Shadowed declaration
snap-2.0.3/SNAPLib/HashTable.h:109:31: note: Shadow variable
snap-2.0.3/SNAPLib/HashTable.cpp:321:47: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Histogram.cpp:36:5: warning: Class 'Histogram' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/Histogram.cpp:36:5: warning: Class 'Histogram' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/Histogram.cpp:95:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/Histogram.cpp:95:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/DataWriter.cpp:158:14: warning: Member variable 'FileEncoder::writer' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataWriter.cpp:158:14: warning: Member variable 'FileEncoder::lock' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataWriter.cpp:158:14: warning: Member variable 'FileEncoder::encoderBatch' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataWriter.h:225:23: style:inconclusive: Member variable 'FileEncoder::coworker' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataWriter.cpp:164:5: note: Member variable 'FileEncoder::coworker' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataWriter.h:225:23: note: Member variable 'FileEncoder::coworker' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataWriter.cpp:150:30: style:inconclusive: Member variable 'AsyncDataWriter::supplier' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataWriter.cpp:341:5: note: Member variable 'AsyncDataWriter::supplier' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataWriter.cpp:150:30: note: Member variable 'AsyncDataWriter::supplier' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataWriter.cpp:149:15: style:inconclusive: Member variable 'AsyncDataWriter::count' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataWriter.cpp:342:5: note: Member variable 'AsyncDataWriter::count' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataWriter.cpp:149:15: note: Member variable 'AsyncDataWriter::count' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataWriter.cpp:306:14: style:inconclusive: Technically the member function 'FileEncoder::getOffsets' can be const. [functionConst]
snap-2.0.3/SNAPLib/DataWriter.h:210:10: note: Technically the member function 'FileEncoder::getOffsets' can be const.
snap-2.0.3/SNAPLib/DataWriter.cpp:306:14: note: Technically the member function 'FileEncoder::getOffsets' can be const.
snap-2.0.3/SNAPLib/DataWriter.cpp:346:5: warning: Class 'AsyncDataWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/DataWriter.cpp:346:5: warning: Class 'AsyncDataWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/DataWriter.cpp:771:18: warning: The class 'StdoutAsyncFile' defines member function with name 'open' also defined in its parent class 'AsyncFile'. [duplInheritedMember]
snap-2.0.3/SNAPLib/Compat.h:397:23: note: Parent function 'AsyncFile::open'
snap-2.0.3/SNAPLib/DataWriter.cpp:771:18: note: Derived function 'StdoutAsyncFile::open'
snap-2.0.3/SNAPLib/DataWriter.cpp:783:5: style: Class 'StdoutAsyncFileWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/DataWriter.cpp:70:6: style: The destructor '~AsyncDataWriterSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:134:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:70:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:75:25: style: The function 'getWriter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:136:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:75:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:77:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:139:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:77:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:103:14: style: The destructor '~AsyncDataWriter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:94:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:103:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:118:18: style: The function 'getBuffer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:100:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:118:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:120:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:104:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:120:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:122:18: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:109:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:122:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:124:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:112:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:124:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:126:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:115:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:126:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:671:14: style: The destructor '~ComposeFilter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:58:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:671:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:674:15: style: The function 'inHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:61:16: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:674:15: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:680:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:64:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:680:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:686:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:70:24: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:686:20: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:704:14: style: The destructor '~ComposeFilterSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:81:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:704:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:707:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:85:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:707:33: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:710:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:88:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:710:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:716:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:89:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:716:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:787:10: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Compat.h:409:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:787:10: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:790:10: style: The function 'beginWrite' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Compat.h:412:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:790:10: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:793:10: style: The function 'waitForCompletion' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Compat.h:415:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataWriter.cpp:793:10: note: Function in derived class
snap-2.0.3/SNAPLib/DataWriter.cpp:492:28: warning: Either the condition 'newBuffer==NULL' is redundant or there is possible null pointer dereference: newBuffer. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/DataWriter.cpp:488:35: note: Assuming that condition 'newBuffer==NULL' is not redundant
snap-2.0.3/SNAPLib/DataWriter.cpp:492:28: note: Null pointer dereference
snap-2.0.3/SNAPLib/DataWriter.cpp:513:32: warning: Either the condition 'newBuffer==NULL' is redundant or there is possible null pointer dereference: newBuffer. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/DataWriter.cpp:509:39: note: Assuming that condition 'newBuffer==NULL' is not redundant
snap-2.0.3/SNAPLib/DataWriter.cpp:513:32: note: Null pointer dereference
snap-2.0.3/SNAPLib/DataWriter.cpp:210:6: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataWriter.cpp:244:27: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataWriter.cpp:348:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataWriter.cpp:487:39: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataWriter.cpp:508:43: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataWriter.cpp:880:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataWriter.cpp:975:42: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataWriter.cpp:527:25: style: Variable 'write->used' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/DataWriter.cpp:523:33: note: write->used is assigned
snap-2.0.3/SNAPLib/DataWriter.cpp:527:25: note: write->used is overwritten
snap-2.0.3/SNAPLib/DataWriter.cpp:161:28: style:inconclusive: Function 'FileEncoder' argument 3 names different: declaration 'i_supplier' definition 'i_manager'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataWriter.h:180:79: note: Function 'FileEncoder' argument 3 names different: declaration 'i_supplier' definition 'i_manager'.
snap-2.0.3/SNAPLib/DataWriter.cpp:161:28: note: Function 'FileEncoder' argument 3 names different: declaration 'i_supplier' definition 'i_manager'.
snap-2.0.3/SNAPLib/DataWriter.cpp:487:27: style: Local variable 'newBuffer' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/DataWriter.cpp:461:10: note: Shadowed declaration
snap-2.0.3/SNAPLib/DataWriter.cpp:487:27: note: Shadow variable
snap-2.0.3/SNAPLib/DataWriter.cpp:508:31: style: Local variable 'newBuffer' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/DataWriter.cpp:461:10: note: Shadowed declaration
snap-2.0.3/SNAPLib/DataWriter.cpp:508:31: note: Shadow variable
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:297:103: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_DEFAULT_STRATEGY [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataWriter.cpp:275:33: style: Variable 'encode' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/DataWriter.cpp:275:40: style: Variable 'encode' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataWriter.cpp:275:33: style: Variable 'encode' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::highestUsedWeightList' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::wrapCount' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::nAddedToHashTable' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::lowestPossibleScoreOfAnyUnseenLocation' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::currRoundLowestPossibleScoreOfAnyUnseenLocation' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::mostSeedsContainingAnyParticularBase' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::nSeedsApplied' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::minScoreThreshold' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::lvScoresAfterBestFound' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::affineGapScores' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::affineGapScoresAfterBestFound' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::firstPassSeedsNotSkipped' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::highestWeightListChecked' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::totalProbabilityByDepth' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:50:14: warning: Member variable 'BaseAligner::popularSeedsSkipped' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.h:204:9: warning: Member variable 'Candidate::seedOffset' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.h:204:9: warning: Member variable 'Candidate::matchProbability' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.h:204:9: warning: Member variable 'Candidate::origGenomeLocation' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2046:32: warning: Member variable 'HashTableElement::candidatesScored' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2046:32: warning: Member variable 'HashTableElement::bestScoreGenomeLocation' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2046:32: warning: Member variable 'HashTableElement::bestScoreOrigGenomeLocation' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/BaseAligner.h:441:30: style:inconclusive: Member variable 'BaseAligner::extraSearchDepth' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/BaseAligner.cpp:78:57: note: Member variable 'BaseAligner::extraSearchDepth' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:441:30: note: Member variable 'BaseAligner::extraSearchDepth' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:443:30: style:inconclusive: Member variable 'BaseAligner::disabledOptimizations' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/BaseAligner.cpp:80:9: note: Member variable 'BaseAligner::disabledOptimizations' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:443:30: note: Member variable 'BaseAligner::disabledOptimizations' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:164:9: style:inconclusive: Member variable 'BaseAligner::matchReward' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/BaseAligner.cpp:81:33: note: Member variable 'BaseAligner::matchReward' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:164:9: note: Member variable 'BaseAligner::matchReward' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:171:23: style:inconclusive: Member variable 'BaseAligner::alignmentAdjuster' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/BaseAligner.cpp:84:9: note: Member variable 'BaseAligner::alignmentAdjuster' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:171:23: note: Member variable 'BaseAligner::alignmentAdjuster' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:153:7: style:inconclusive: Member variable 'BaseAligner::altAwareness' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/BaseAligner.cpp:85:3: note: Member variable 'BaseAligner::altAwareness' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.h:153:7: note: Member variable 'BaseAligner::altAwareness' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/BaseAligner.cpp:2535:14: style:inconclusive: Technically the member function 'BaseAligner::scoreLimit' can be const. [functionConst]
snap-2.0.3/SNAPLib/BaseAligner.h:146:16: note: Technically the member function 'BaseAligner::scoreLimit' can be const.
snap-2.0.3/SNAPLib/BaseAligner.cpp:2535:14: note: Technically the member function 'BaseAligner::scoreLimit' can be const.
snap-2.0.3/SNAPLib/BaseAligner.cpp:2280:29: style:inconclusive: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const. [functionConst]
snap-2.0.3/SNAPLib/BaseAligner.h:328:14: note: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const.
snap-2.0.3/SNAPLib/BaseAligner.cpp:2280:29: note: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const.
snap-2.0.3/SNAPLib/BaseAligner.cpp:151:13: warning: Class 'BaseAligner' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/BaseAligner.cpp:151:13: warning: Class 'BaseAligner' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2181:61: style: Condition 'bestScore>=score' is always true [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2151:23: note: Assuming that condition 'bestScore>=score' is not redundant
snap-2.0.3/SNAPLib/BaseAligner.cpp:2181:61: note: Condition 'bestScore>=score' is always true
snap-2.0.3/SNAPLib/BaseAligner.cpp:186:22: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:188:22: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:194:33: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:196:33: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:217:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:219:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:228:39: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:229:34: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:230:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:231:32: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:232:38: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:234:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:240:39: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:241:34: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:242:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:243:32: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:244:38: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:246:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1080:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1786:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1892:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1913:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/BaseAligner.cpp:904:16: style: Variable '*score' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/BaseAligner.cpp:892:24: note: *score is assigned
snap-2.0.3/SNAPLib/BaseAligner.cpp:904:16: note: *score is overwritten
snap-2.0.3/SNAPLib/BaseAligner.cpp:904:16: style: Variable '*score' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/BaseAligner.cpp:898:16: note: *score is assigned
snap-2.0.3/SNAPLib/BaseAligner.cpp:904:16: note: *score is overwritten
snap-2.0.3/SNAPLib/BaseAligner.cpp:1296:31: style: Variable 'score' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1193:43: note: score is assigned
snap-2.0.3/SNAPLib/BaseAligner.cpp:1296:31: note: score is overwritten
snap-2.0.3/SNAPLib/BaseAligner.cpp:1307:33: style: Variable 'agScore' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1195:45: note: agScore is assigned
snap-2.0.3/SNAPLib/BaseAligner.cpp:1307:33: note: agScore is overwritten
snap-2.0.3/SNAPLib/BaseAligner.cpp:1296:31: style: Variable 'score' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1282:47: note: score is assigned
snap-2.0.3/SNAPLib/BaseAligner.cpp:1296:31: note: score is overwritten
snap-2.0.3/SNAPLib/BaseAligner.cpp:1307:33: style: Variable 'agScore' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1283:49: note: agScore is assigned
snap-2.0.3/SNAPLib/BaseAligner.cpp:1307:33: note: agScore is overwritten
snap-2.0.3/SNAPLib/BaseAligner.cpp:1296:31: style: Variable 'score' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1287:39: note: score is assigned
snap-2.0.3/SNAPLib/BaseAligner.cpp:1296:31: note: score is overwritten
snap-2.0.3/SNAPLib/BaseAligner.cpp:1307:33: style: Variable 'agScore' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1288:41: note: agScore is assigned
snap-2.0.3/SNAPLib/BaseAligner.cpp:1307:33: note: agScore is overwritten
snap-2.0.3/SNAPLib/BaseAligner.cpp:1126:21: style: The scope of the variable 'scoreGapless' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1185:33: style: The scope of the variable 'limitLeft' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1383:32: style: The scope of the variable 'nearbyGenomeLocation' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/BaseAligner.cpp:55:30: style:inconclusive: Function 'BaseAligner' argument 5 names different: declaration 'i_maxSeedsToUse' definition 'i_maxSeedsToUseFromCommandLine'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BaseAligner.h:52:34: note: Function 'BaseAligner' argument 5 names different: declaration 'i_maxSeedsToUse' definition 'i_maxSeedsToUseFromCommandLine'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:55:30: note: Function 'BaseAligner' argument 5 names different: declaration 'i_maxSeedsToUse' definition 'i_maxSeedsToUseFromCommandLine'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:274:34: style:inconclusive: Function 'AlignRead' argument 1 names different: declaration 'read' definition 'inputRead'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BaseAligner.h:78:34: note: Function 'AlignRead' argument 1 names different: declaration 'read' definition 'inputRead'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:274:34: note: Function 'AlignRead' argument 1 names different: declaration 'read' definition 'inputRead'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:767:11: style:inconclusive: Function 'scoreLocationWithAffineGap' argument 1 names different: declaration 'read' definition 'reads'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BaseAligner.h:411:30: note: Function 'scoreLocationWithAffineGap' argument 1 names different: declaration 'read' definition 'reads'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:767:11: note: Function 'scoreLocationWithAffineGap' argument 1 names different: declaration 'read' definition 'reads'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:927:34: style:inconclusive: Function 'score' argument 9 names different: declaration 'overflowedSecondaryResultsBuffer' definition 'overflowedSecondaryBuffer'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BaseAligner.h:404:34: note: Function 'score' argument 9 names different: declaration 'overflowedSecondaryResultsBuffer' definition 'overflowedSecondaryBuffer'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:927:34: note: Function 'score' argument 9 names different: declaration 'overflowedSecondaryResultsBuffer' definition 'overflowedSecondaryBuffer'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:1517:15: style:inconclusive: Function 'alignAffineGap' argument 1 names different: declaration 'read' definition 'inputRead'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BaseAligner.h:95:15: note: Function 'alignAffineGap' argument 1 names different: declaration 'read' definition 'inputRead'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:1517:15: note: Function 'alignAffineGap' argument 1 names different: declaration 'read' definition 'inputRead'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:1865:25: style:inconclusive: Function 'allocateNewCandidate' argument 1 names different: declaration 'genomeLoation' definition 'genomeLocation'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/BaseAligner.h:428:46: note: Function 'allocateNewCandidate' argument 1 names different: declaration 'genomeLoation' definition 'genomeLocation'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:1865:25: note: Function 'allocateNewCandidate' argument 1 names different: declaration 'genomeLoation' definition 'genomeLocation'.
snap-2.0.3/SNAPLib/BaseAligner.cpp:1117:26: style: Local variable 'score' shadows outer function [shadowFunction]
snap-2.0.3/SNAPLib/BaseAligner.h:395:5: note: Shadowed declaration
snap-2.0.3/SNAPLib/BaseAligner.cpp:1117:26: note: Shadow variable
snap-2.0.3/SNAPLib/BaseAligner.cpp:1141:25: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/BaseAligner.h:434:30: note: Shadowed declaration
snap-2.0.3/SNAPLib/BaseAligner.cpp:1141:25: note: Shadow variable
snap-2.0.3/SNAPLib/BaseAligner.cpp:1649:14: style: Local variable 'scoresForAllAlignments' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/BaseAligner.h:381:14: note: Shadowed declaration
snap-2.0.3/SNAPLib/BaseAligner.cpp:1649:14: note: Shadow variable
snap-2.0.3/SNAPLib/BaseAligner.cpp:1650:14: style: Local variable 'scoresForNonAltAlignments' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/BaseAligner.h:382:14: note: Shadowed declaration
snap-2.0.3/SNAPLib/BaseAligner.cpp:1650:14: note: Shadow variable
snap-2.0.3/SNAPLib/BaseAligner.cpp:1703:18: style: Local variable 'nonALTAlignment' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1656:10: note: Shadowed declaration
snap-2.0.3/SNAPLib/BaseAligner.cpp:1703:18: note: Shadow variable
snap-2.0.3/SNAPLib/BaseAligner.cpp:780:11: style: Variable 'readToScore' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/BaseAligner.cpp:1129:27: style: Variable 'readToScore' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2095:57: style: Parameter 'result' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/BaseAligner.cpp:2130:64: style: Parameter 'elementToScore' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/DataReader.cpp:1390:22: warning: Member variable 'AsyncFileDataReader::fileSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2137:5: warning: Member variable 'DecompressManager::entry' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::batchSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::fileName' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::fileSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::currentMapStartSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::currentMappedBase' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::offset' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::startBytes' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::validBytes' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2599:19: warning: Member variable 'MemMapDataReader::lock' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/DataReader.cpp:134:25: style:inconclusive: Member variable 'ReadBasedDataReader::maxBuffers' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:186:5: note: Member variable 'ReadBasedDataReader::maxBuffers' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:134:25: note: Member variable 'ReadBasedDataReader::maxBuffers' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:159:11: style:inconclusive: Member variable 'ReadBasedDataReader::headerBuffer' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:188:2: note: Member variable 'ReadBasedDataReader::headerBuffer' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:159:11: note: Member variable 'ReadBasedDataReader::headerBuffer' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:161:11: style:inconclusive: Member variable 'ReadBasedDataReader::headerExtra' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:189:2: note: Member variable 'ReadBasedDataReader::headerExtra' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:161:11: note: Member variable 'ReadBasedDataReader::headerExtra' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:136:10: style:inconclusive: Member variable 'ReadBasedDataReader::startedReadingHeader' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:189:41: note: Member variable 'ReadBasedDataReader::startedReadingHeader' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:136:10: note: Member variable 'ReadBasedDataReader::startedReadingHeader' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:135:10: style:inconclusive: Member variable 'ReadBasedDataReader::headerBuffersOutstanding' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:189:70: note: Member variable 'ReadBasedDataReader::headerBuffersOutstanding' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:135:10: note: Member variable 'ReadBasedDataReader::headerBuffersOutstanding' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:817:14: style:inconclusive: Member variable 'StdioDataReader::overflowBufferFilled' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:826:99: note: Member variable 'StdioDataReader::overflowBufferFilled' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:817:14: note: Member variable 'StdioDataReader::overflowBufferFilled' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:816:14: style:inconclusive: Member variable 'StdioDataReader::overflowBuffer' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:827:20: note: Member variable 'StdioDataReader::overflowBuffer' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:816:14: note: Member variable 'StdioDataReader::overflowBuffer' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:1743:12: style:inconclusive: Member variable 'DecompressDataReader::offset' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:1784:53: note: Member variable 'DecompressDataReader::offset' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:1743:12: note: Member variable 'DecompressDataReader::offset' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:1741:18: style:inconclusive: Member variable 'DecompressDataReader::totalExtra' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:1785:5: note: Member variable 'DecompressDataReader::totalExtra' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:1741:18: note: Member variable 'DecompressDataReader::totalExtra' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:1739:18: style:inconclusive: Member variable 'DecompressDataReader::extraBytes' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:1785:31: note: Member variable 'DecompressDataReader::extraBytes' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:1739:18: note: Member variable 'DecompressDataReader::extraBytes' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:2584:21: style:inconclusive: Member variable 'MemMapDataReader::extraUsed' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:2606:9: note: Member variable 'MemMapDataReader::extraUsed' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:2584:21: note: Member variable 'MemMapDataReader::extraUsed' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:2578:21: style:inconclusive: Member variable 'MemMapDataReader::currentMap' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/DataReader.cpp:2607:9: note: Member variable 'MemMapDataReader::currentMap' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:2578:21: note: Member variable 'MemMapDataReader::currentMap' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/DataReader.cpp:199:5: warning: Class 'ReadBasedDataReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/DataReader.cpp:199:5: warning: Class 'ReadBasedDataReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/DataReader.cpp:1788:5: warning: Class 'DecompressDataReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/DataReader.cpp:1788:5: warning: Class 'DecompressDataReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/DataReader.cpp:2617:9: warning: Class 'MemMapDataReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/DataReader.cpp:2617:9: warning: Class 'MemMapDataReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/DataReader.cpp:2446:5: style: Class 'DecompressDataReaderSupplier' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < int64_t , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/DataReader.cpp:53:14: style: The destructor '~ReadBasedDataReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:93:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataReader.cpp:53:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:55:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:96:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:55:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:57:11: style: The function 'readHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:99:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:57:11: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:59:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:102:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:59:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:61:18: style: The function 'getData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:109:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:61:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:63:18: style: The function 'dumpState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:152:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:63:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:65:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:112:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:65:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:67:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:116:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:67:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:69:18: style: The function 'isEOF' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:119:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:69:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:71:23: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:122:23: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:71:23: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:73:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:127:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:73:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:75:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:133:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:75:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:77:20: style: The function 'getFileOffset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:136:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:77:20: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:79:18: style: The function 'getExtra' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:140:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:79:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:81:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:143:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:81:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:787:6: style: The destructor '~StdioDataReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:53:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataReader.cpp:787:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:789:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:55:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:789:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:791:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:81:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:791:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:797:18: style: The function 'startIo' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:86:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:797:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:800:18: style: The function 'waitForBuffer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:89:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:800:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1025:25: style: The function 'getDataReader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:162:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1025:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1342:14: style: The destructor '~AsyncFileDataReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:53:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1342:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1344:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:55:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1344:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1346:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:59:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1346:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1350:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:81:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1350:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1355:18: style: The function 'dumpState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:63:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1355:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1360:18: style: The function 'startIo' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:86:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1360:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1363:18: style: The function 'waitForBuffer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:89:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1363:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1366:18: style: The function 'addBuffer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.cpp:92:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1366:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1634:25: style: The function 'getDataReader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:162:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1634:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1659:14: style: The destructor '~DecompressDataReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:93:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1659:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1661:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:96:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1661:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1663:19: style: The function 'readHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:99:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1663:19: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1665:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:102:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1665:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1667:18: style: The function 'getData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:109:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1667:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1669:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:112:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1669:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1671:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:116:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1671:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1673:18: style: The function 'isEOF' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:119:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1673:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1675:23: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:122:23: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1675:23: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1677:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:127:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1677:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1679:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:133:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1679:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1681:20: style: The function 'getFileOffset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:136:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1681:20: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1683:18: style: The function 'getExtra' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:140:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1683:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:1685:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:143:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:1685:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2127:18: style: The function 'step' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:275:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2127:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2141:29: style: The function 'createWorker' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:256:29: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2141:29: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2450:25: style: The function 'getDataReader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:162:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2450:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2507:14: style: The destructor '~MemMapDataSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:160:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2507:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2509:25: style: The function 'getDataReader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:162:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2509:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2526:14: style: The destructor '~MemMapDataReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:93:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2526:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2528:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:96:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2528:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2530:19: style: The function 'readHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:99:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2530:19: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2532:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:102:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2532:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2534:18: style: The function 'getData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:109:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2534:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2536:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:112:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2536:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2538:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:116:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2538:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2540:18: style: The function 'isEOF' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:119:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2540:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2542:23: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:122:23: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2542:23: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2544:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:127:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2544:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2546:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:133:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2546:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2548:20: style: The function 'getFileOffset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:136:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2548:20: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2550:18: style: The function 'getExtra' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:140:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2550:18: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2552:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:143:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/DataReader.cpp:2552:25: note: Function in derived class
snap-2.0.3/SNAPLib/DataReader.cpp:2193:56: style: Comparing expression of type 'unsigned short' against value 65536. Condition is always false. [compareValueOutOfTypeRangeError]
snap-2.0.3/SNAPLib/DataReader.cpp:2264:71: style: Comparing expression of type 'unsigned short' against value 65536. Condition is always false. [compareValueOutOfTypeRangeError]
snap-2.0.3/SNAPLib/DataReader.cpp:1537:73: style: Condition 'finalStartOffset==fileSize' is always false [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/DataReader.cpp:1534:33: note: finalStartOffset is assigned '(fileSize)<(endingOffset)?(fileSize):(endingOffset)' here.
snap-2.0.3/SNAPLib/DataReader.cpp:1537:73: note: Condition 'finalStartOffset==fileSize' is always false
snap-2.0.3/SNAPLib/DataReader.cpp:2052:29: portability: %llx in format string (no. 1) requires 'unsigned long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/DataReader.cpp:2105:13: portability: %lld in format string (no. 2) requires 'long long' but the argument type is 'ptrdiff_t {aka signed int}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/DataReader.cpp:2109:13: portability: %lld in format string (no. 2) requires 'long long' but the argument type is 'ptrdiff_t {aka signed int}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/DataReader.cpp:2113:13: portability: %lld in format string (no. 2) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/DataReader.cpp:2261:21: portability: %lld in format string (no. 1) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/DataReader.cpp:2261:21: portability: %lld in format string (no. 2) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/DataReader.cpp:2265:21: portability: %lld in format string (no. 1) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/DataReader.cpp:208:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:950:34: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:1394:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:1764:27: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2054:51: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2105:57: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2109:57: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2113:50: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2206:36: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2232:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2295:36: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2320:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2616:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2011:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2013:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2162:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2189:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/DataReader.cpp:2256:35: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:545:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1768:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OverflowBackpointer [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1814:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OverflowBackpointer [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1979:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataReader.cpp:2751:22: style: The scope of the variable 'found' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/DataReader.cpp:2934:9: style: The scope of the variable 'n' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/DataReader.cpp:184:12: style:inconclusive: Function 'ReadBasedDataReader' argument 4 names different: declaration 'bufferSpace' definition 'i_bufferSpace'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:51:97: note: Function 'ReadBasedDataReader' argument 4 names different: declaration 'bufferSpace' definition 'i_bufferSpace'.
snap-2.0.3/SNAPLib/DataReader.cpp:184:12: note: Function 'ReadBasedDataReader' argument 4 names different: declaration 'bufferSpace' definition 'i_bufferSpace'.
snap-2.0.3/SNAPLib/DataReader.cpp:1445:12: style:inconclusive: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:1346:32: note: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'.
snap-2.0.3/SNAPLib/DataReader.cpp:1445:12: note: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'.
snap-2.0.3/SNAPLib/DataReader.cpp:1760:69: style:inconclusive: Function 'ensureSize' argument 2 names different: declaration 'newTotal' definition 'extra'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:1728:48: note: Function 'ensureSize' argument 2 names different: declaration 'newTotal' definition 'extra'.
snap-2.0.3/SNAPLib/DataReader.cpp:1760:69: note: Function 'ensureSize' argument 2 names different: declaration 'newTotal' definition 'extra'.
snap-2.0.3/SNAPLib/DataReader.cpp:1780:12: style:inconclusive: Function 'DecompressDataReader' argument 3 names different: declaration 'totalExtra' definition 'i_totalExtra'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:1657:67: note: Function 'DecompressDataReader' argument 3 names different: declaration 'totalExtra' definition 'i_totalExtra'.
snap-2.0.3/SNAPLib/DataReader.cpp:1780:12: note: Function 'DecompressDataReader' argument 3 names different: declaration 'totalExtra' definition 'i_totalExtra'.
snap-2.0.3/SNAPLib/DataReader.cpp:2000:12: style:inconclusive: Function 'decompress' argument 4 names different: declaration 'inputSize' definition 'inputBytes'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:1690:85: note: Function 'decompress' argument 4 names different: declaration 'inputSize' definition 'inputBytes'.
snap-2.0.3/SNAPLib/DataReader.cpp:2000:12: note: Function 'decompress' argument 4 names different: declaration 'inputSize' definition 'inputBytes'.
snap-2.0.3/SNAPLib/DataReader.cpp:2001:13: style:inconclusive: Function 'decompress' argument 5 names different: declaration 'o_inputUsed' definition 'o_inputRead'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:1690:104: note: Function 'decompress' argument 5 names different: declaration 'o_inputUsed' definition 'o_inputRead'.
snap-2.0.3/SNAPLib/DataReader.cpp:2001:13: note: Function 'decompress' argument 5 names different: declaration 'o_inputUsed' definition 'o_inputRead'.
snap-2.0.3/SNAPLib/DataReader.cpp:2003:12: style:inconclusive: Function 'decompress' argument 7 names different: declaration 'outputSize' definition 'outputBytes'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:1691:30: note: Function 'decompress' argument 7 names different: declaration 'outputSize' definition 'outputBytes'.
snap-2.0.3/SNAPLib/DataReader.cpp:2003:12: note: Function 'decompress' argument 7 names different: declaration 'outputSize' definition 'outputBytes'.
snap-2.0.3/SNAPLib/DataReader.cpp:2004:13: style:inconclusive: Function 'decompress' argument 8 names different: declaration 'o_outputUsed' definition 'o_outputWritten'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:1691:50: note: Function 'decompress' argument 8 names different: declaration 'o_outputUsed' definition 'o_outputWritten'.
snap-2.0.3/SNAPLib/DataReader.cpp:2004:13: note: Function 'decompress' argument 8 names different: declaration 'o_outputUsed' definition 'o_outputWritten'.
snap-2.0.3/SNAPLib/DataReader.cpp:2652:17: style:inconclusive: Function 'init' argument 1 names different: declaration 'fileName' definition 'i_fileName'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:2528:35: note: Function 'init' argument 1 names different: declaration 'fileName' definition 'i_fileName'.
snap-2.0.3/SNAPLib/DataReader.cpp:2652:17: note: Function 'init' argument 1 names different: declaration 'fileName' definition 'i_fileName'.
snap-2.0.3/SNAPLib/DataReader.cpp:2678:12: style:inconclusive: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.cpp:2532:32: note: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'.
snap-2.0.3/SNAPLib/DataReader.cpp:2678:12: note: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'.
snap-2.0.3/SNAPLib/DataReader.cpp:2948:15: style:inconclusive: Function 'releaseBatch' argument 1 names different: declaration 'batch' definition 'removed'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataReader.h:211:33: note: Function 'releaseBatch' argument 1 names different: declaration 'batch' definition 'removed'.
snap-2.0.3/SNAPLib/DataReader.cpp:2948:15: note: Function 'releaseBatch' argument 1 names different: declaration 'batch' definition 'removed'.
snap-2.0.3/SNAPLib/DataReader.cpp:2333:18: style: Local variable 'ok' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2308:14: note: Shadowed declaration
snap-2.0.3/SNAPLib/DataReader.cpp:2333:18: note: Shadow variable
snap-2.0.3/SNAPLib/DataReader.cpp:116:30: style: Parameter 'peer' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/DataReader.cpp:509:17: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/DataReader.cpp:614:17: style: Variable 'info' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/DataReader.cpp:1893:12: style: Variable 'entry' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/DataReader.cpp:1919:12: style: Variable 'old' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/DataReader.cpp:1925:12: style: Variable 'next' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/DataReader.cpp:2103:16: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/DataReader.cpp:2951:15: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:896:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LocationNotYetScored [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1975:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LocationNotYetScored [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3494:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HashTableLookup < int64_t > [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3565:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _MM_HINT_T2 [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3566:1: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _MM_HINT_T2 [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3641:96: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _MM_HINT_T2 [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/DataReader.cpp:566:22: style: Variable 'nextStart' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:575:19: style: Variable 'nextStart' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2026:21: style: Variable 'multiBlock' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2221:19: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2221:13: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2309:19: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2309:13: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2685:22: style: Variable 'oldAmount' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2685:12: style: Variable 'oldAmount' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2751:28: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2756:31: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2934:11: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/DataReader.cpp:2936:11: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::nChunks' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::encoder' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::input' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::inputSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::bufferSizeInit' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::bufferSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::inputUsed' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:344:19: warning: Member variable 'GzipWriterFilter::encoder' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GzipDataWriter.h:85:10: style: Unused private function: 'GzipWriterFilterSupplier::addTranslation' [unusedPrivateFunction]
snap-2.0.3/SNAPLib/GzipDataWriter.h:85:10: note: Unused private function: 'GzipWriterFilterSupplier::addTranslation'
snap-2.0.3/SNAPLib/GzipDataWriter.h:85:10: note: Unused private function: 'GzipWriterFilterSupplier::addTranslation'
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:57:18: style:inconclusive: Member variable 'GzipCompressWorkerManager::chunkSize' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:41:9: note: Member variable 'GzipCompressWorkerManager::chunkSize' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:57:18: note: Member variable 'GzipCompressWorkerManager::chunkSize' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/MultiInputReadSupplier.cpp:35:5: warning: Class 'MultiInputReadSupplier' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/MultiInputReadSupplier.cpp:35:5: warning: Class 'MultiInputReadSupplier' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/MultiInputReadSupplier.cpp:121:5: warning: Class 'MultiInputPairedReadSupplier' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/MultiInputReadSupplier.cpp:121:5: warning: Class 'MultiInputPairedReadSupplier' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:31:14: style: The destructor '~MultiInputReadSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:177:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:31:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:33:19: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:176:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:33:19: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:35:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:179:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:35:18: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:36:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:180:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:36:18: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:58:14: style: The destructor '~MultiInputPairedReadSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:187:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:58:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:60:18: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:186:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:60:18: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:62:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:189:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:62:18: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:64:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:190:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:64:18: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:87:14: style: The destructor '~MultiInputReadSupplierGenerator' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:197:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:87:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:89:27: style: The function 'generateNewReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:195:27: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:89:27: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:90:28: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:196:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:90:28: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:102:14: style: The destructor '~MultiInputPairedReadSupplierGenerator' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:204:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:102:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:104:33: style: The function 'generateNewPairedReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:202:33: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:104:33: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:105:28: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:203:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:105:28: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:39:5: style: Class 'GzipCompressWorkerManager' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:93:5: style: Class 'GzipWriterFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:44:14: style: The destructor '~GzipCompressWorkerManager' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:258:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:44:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:46:18: style: The function 'initialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:254:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:46:18: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:48:29: style: The function 'createWorker' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:256:29: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:48:29: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:50:18: style: The function 'beginStep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:260:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:50:18: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:52:18: style: The function 'finishStep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:262:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:52:18: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:77:14: style: The destructor '~GzipCompressWorker' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:272:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:77:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:79:18: style: The function 'step' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/ParallelTask.h:275:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:79:18: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:95:6: style: The destructor '~GzipWriterFilter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:58:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:95:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:97:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:64:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:97:18: note: Function in derived class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:99:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:70:24: note: Virtual function in base class
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:99:20: note: Function in derived class
snap-2.0.3/SNAPLib/MultiInputReadSupplier.cpp:30:52: style:inconclusive: Function 'MultiInputReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:30:32: note: Function 'MultiInputReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'.
snap-2.0.3/SNAPLib/MultiInputReadSupplier.cpp:30:52: note: Function 'MultiInputReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'.
snap-2.0.3/SNAPLib/MultiInputReadSupplier.cpp:116:64: style:inconclusive: Function 'MultiInputPairedReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/MultiInputReadSupplier.h:57:38: note: Function 'MultiInputPairedReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'.
snap-2.0.3/SNAPLib/MultiInputReadSupplier.cpp:116:64: note: Function 'MultiInputPairedReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'.
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:122:15: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:144:18: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:158:18: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:203:27: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:255:10: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:464:52: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:464:82: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:182:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:220:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:290:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:292:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:338:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:404:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:120:11: style:inconclusive: Function 'initialize' argument 1 names different: declaration 'i_writer' definition 'i_encoder'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:46:35: note: Function 'initialize' argument 1 names different: declaration 'i_writer' definition 'i_encoder'.
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:120:11: note: Function 'initialize' argument 1 names different: declaration 'i_writer' definition 'i_encoder'.
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:478:50: style:inconclusive: Function 'addTranslations' argument 1 names different: declaration 'translation' definition 'moreTranslations'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/GzipDataWriter.h:64:71: note: Function 'addTranslations' argument 1 names different: declaration 'translation' definition 'moreTranslations'.
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:478:50: note: Function 'addTranslations' argument 1 names different: declaration 'translation' definition 'moreTranslations'.
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:490:14: style:inconclusive: Function 'translate' argument 3 names different: declaration 'delta' definition 'o_logicalDelta'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/GzipDataWriter.h:66:67: note: Function 'translate' argument 3 names different: declaration 'delta' definition 'o_logicalDelta'.
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:490:14: note: Function 'translate' argument 3 names different: declaration 'delta' definition 'o_logicalDelta'.
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:495:28: style: Variable 'upper' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:228:18: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:228:12: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/GzipDataWriter.cpp:279:25: style: Variable 'bamExtraData[5]' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ParallelTask.h:124:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doneWaiter [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/ParallelTask.h:231:28: style:inconclusive: Member variable 'ParallelCoworker::manager' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/ParallelTask.cpp:24:87: note: Member variable 'ParallelCoworker::manager' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ParallelTask.h:231:28: note: Member variable 'ParallelCoworker::manager' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ParallelTask.cpp:26:5: warning: Class 'ParallelCoworker' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/ParallelTask.cpp:26:5: warning: Class 'ParallelCoworker' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/ParallelTask.h:50:5: style: Class 'ParallelTask' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/ParallelTask.cpp:23:102: style:inconclusive: Function 'ParallelCoworker' argument 3 names different: declaration 'supplier' definition 'i_manager'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ParallelTask.h:212:88: note: Function 'ParallelCoworker' argument 3 names different: declaration 'supplier' definition 'i_manager'.
snap-2.0.3/SNAPLib/ParallelTask.cpp:23:102: note: Function 'ParallelCoworker' argument 3 names different: declaration 'supplier' definition 'i_manager'.
snap-2.0.3/SNAPLib/ParallelTask.cpp:23:140: style:inconclusive: Function 'ParallelCoworker' argument 5 names different: declaration 'parameter' definition 'i_parameter'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ParallelTask.h:212:130: note: Function 'ParallelCoworker' argument 5 names different: declaration 'parameter' definition 'i_parameter'.
snap-2.0.3/SNAPLib/ParallelTask.cpp:23:140: note: Function 'ParallelCoworker' argument 5 names different: declaration 'parameter' definition 'i_parameter'.
snap-2.0.3/SNAPLib/ParallelTask.cpp:113:22: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ParallelTask.cpp:113:16: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/VariableSizeMap.h:323:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _tombstone [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/VariableSizeMap.h:367:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _empty [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:322:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FilterBothMatesMatch [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:673:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/ProbabilityDistance.cpp:24:22: warning: Member variable 'ProbabilityDistance::d' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/ProbabilityDistance.cpp:24:22: warning: Member variable 'ProbabilityDistance::prev' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/ProbabilityDistance.cpp:44:19: style: Condition 'q>=33' is always true [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/ProbabilityDistance.cpp:32:15: note: Assuming that condition 'q<33' is not redundant
snap-2.0.3/SNAPLib/ProbabilityDistance.cpp:44:19: note: Condition 'q>=33' is always true
snap-2.0.3/SNAPLib/ProbabilityDistance.cpp:59:13: style:inconclusive: Function 'compute' argument 6 names different: declaration 'maxTotalShift' definition 'maxShift'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ProbabilityDistance.h:26:17: note: Function 'compute' argument 6 names different: declaration 'maxTotalShift' definition 'maxShift'.
snap-2.0.3/SNAPLib/ProbabilityDistance.cpp:59:13: note: Function 'compute' argument 6 names different: declaration 'maxTotalShift' definition 'maxShift'.
snap-2.0.3/SNAPLib/LandauVishkin.cpp:521:27: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:14:25: warning: Member variable 'LandauVishkinWithCigar::A' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:14:25: warning: Member variable 'LandauVishkinWithCigar::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:14:25: warning: Member variable 'LandauVishkinWithCigar::backtraceMatched' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:14:25: warning: Member variable 'LandauVishkinWithCigar::backtraceD' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:77:25: performance:inconclusive: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/LandauVishkin.h:510:10: note: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/LandauVishkin.cpp:77:25: note: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/LandauVishkin.cpp:521:20: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:728:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:732:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:130:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:173:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:173:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:244:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:244:57: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:529:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:217:6: style:inconclusive: Same expression used in consecutive assignments of 'lastBestIndels' and 'lastBestD'. [duplicateAssignExpression]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:218:9: note: Same expression used in consecutive assignments of 'lastBestIndels' and 'lastBestD'.
snap-2.0.3/SNAPLib/LandauVishkin.cpp:217:6: note: Same expression used in consecutive assignments of 'lastBestIndels' and 'lastBestD'.
snap-2.0.3/SNAPLib/LandauVishkin.cpp:513:10: style:inconclusive: Function 'computeEditDistanceNormalized' argument 11 names different: declaration 'o_textUsed' definition 'o_addFrontClipping'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/LandauVishkin.h:498:34: note: Function 'computeEditDistanceNormalized' argument 11 names different: declaration 'o_textUsed' definition 'o_addFrontClipping'.
snap-2.0.3/SNAPLib/LandauVishkin.cpp:513:10: note: Function 'computeEditDistanceNormalized' argument 11 names different: declaration 'o_textUsed' definition 'o_addFrontClipping'.
snap-2.0.3/SNAPLib/LandauVishkin.cpp:237:29: style: Local variable 'p' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:163:17: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.cpp:237:29: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.cpp:238:29: style: Local variable 't' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:164:17: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.cpp:238:29: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.cpp:240:25: style: Local variable 'end' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:170:9: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.cpp:240:25: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.cpp:241:33: style: Local variable 'pend' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:171:17: note: Shadowed declaration
snap-2.0.3/SNAPLib/LandauVishkin.cpp:241:33: note: Shadow variable
snap-2.0.3/SNAPLib/LandauVishkin.cpp:31:34: style: Parameter 'last' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:655:11: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:657:11: style: Parameter 'sample' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/LandauVishkin.cpp:701:58: style: Parameter 'i_phredToProbability' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:84:24: style:inconclusive: Member variable 'PairedReadMatcher::freeList' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:122:30: note: Member variable 'PairedReadMatcher::freeList' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:84:24: note: Member variable 'PairedReadMatcher::freeList' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:74:15: style:inconclusive: Member variable 'PairedReadMatcher::currentBatch' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:123:5: note: Member variable 'PairedReadMatcher::currentBatch' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:74:15: note: Member variable 'PairedReadMatcher::currentBatch' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , Read , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < uint64_t , Read , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , ReadWithOwnMemory * , 150 , MapNumericHash < uint64_t > , 80 , 0 , true , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < uint64_t , ReadWithOwnMemory * , 150 , MapNumericHash < uint64_t > , 80 , 0 , true , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , VariableSizeVector < ReadWithOwnMemory * , 150 , false > * , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < uint64_t , VariableSizeVector < ReadWithOwnMemory * , 150 , false > * , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:51:14: style: The destructor '~PairedReadMatcher' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:157:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:51:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:53:18: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:161:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:53:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:55:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:162:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:55:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:58:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:164:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:58:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:61:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:165:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:61:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:63:28: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:167:28: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:63:28: note: Function in derived class
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:150:40: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:155:18: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:159:18: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:165:44: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:179:10: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:266:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:266:38: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:270:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:270:38: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:366:61: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/RangeSplitter.h:90:15: style:inconclusive: Member variable 'RangeSplittingReadSupplierGenerator::numThreads' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:108:43: note: Member variable 'RangeSplittingReadSupplierGenerator::numThreads' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/RangeSplitter.h:90:15: note: Member variable 'RangeSplittingReadSupplierGenerator::numThreads' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/RangeSplitter.h:127:15: style:inconclusive: Member variable 'RangeSplittingPairedReadSupplierGenerator::numThreads' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:208:31: note: Member variable 'RangeSplittingPairedReadSupplierGenerator::numThreads' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/RangeSplitter.h:127:15: note: Member variable 'RangeSplittingPairedReadSupplierGenerator::numThreads' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:133:2: warning: Class 'RangeSplittingReadSupplierGenerator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:133:2: warning: Class 'RangeSplittingReadSupplierGenerator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:221:5: warning: Class 'RangeSplittingPairedReadSupplierGenerator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:221:5: warning: Class 'RangeSplittingPairedReadSupplierGenerator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:125:16: warning: Either the condition '!reader' is redundant or there is possible null pointer dereference: reader. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:121:7: note: Assuming that condition '!reader' is not redundant
snap-2.0.3/SNAPLib/RangeSplitter.cpp:125:16: note: Null pointer dereference
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:266:15: style: Variable 'slash' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:270:15: style: Variable 'space' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:136:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:413:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:36:74: style:inconclusive: Function 'RangeSplitter' argument 3 names different: declaration 'divisonSize_' definition 'divisionSize_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/RangeSplitter.h:41:63: note: Function 'RangeSplitter' argument 3 names different: declaration 'divisonSize_' definition 'divisionSize_'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:36:74: note: Function 'RangeSplitter' argument 3 names different: declaration 'divisonSize_' definition 'divisionSize_'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:106:14: style:inconclusive: Function 'RangeSplittingReadSupplierGenerator' argument 3 names different: declaration 'numThreads' definition 'i_numThreads'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/RangeSplitter.h:80:88: note: Function 'RangeSplittingReadSupplierGenerator' argument 3 names different: declaration 'numThreads' definition 'i_numThreads'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:106:14: note: Function 'RangeSplittingReadSupplierGenerator' argument 3 names different: declaration 'numThreads' definition 'i_numThreads'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:107:26: style:inconclusive: Function 'RangeSplittingReadSupplierGenerator' argument 4 names different: declaration 'context' definition 'i_context'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/RangeSplitter.h:80:121: note: Function 'RangeSplittingReadSupplierGenerator' argument 4 names different: declaration 'context' definition 'i_context'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:107:26: note: Function 'RangeSplittingReadSupplierGenerator' argument 4 names different: declaration 'context' definition 'i_context'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:206:85: style:inconclusive: Function 'RangeSplittingPairedReadSupplierGenerator' argument 4 names different: declaration 'numThreads' definition 'i_numThreads'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/RangeSplitter.h:117:132: note: Function 'RangeSplittingPairedReadSupplierGenerator' argument 4 names different: declaration 'numThreads' definition 'i_numThreads'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:206:85: note: Function 'RangeSplittingPairedReadSupplierGenerator' argument 4 names different: declaration 'numThreads' definition 'i_numThreads'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:207:59: style:inconclusive: Function 'RangeSplittingPairedReadSupplierGenerator' argument 6 names different: declaration 'context' definition 'i_context'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/RangeSplitter.h:117:198: note: Function 'RangeSplittingPairedReadSupplierGenerator' argument 6 names different: declaration 'context' definition 'i_context'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:207:59: note: Function 'RangeSplittingPairedReadSupplierGenerator' argument 6 names different: declaration 'context' definition 'i_context'.
snap-2.0.3/SNAPLib/RangeSplitter.cpp:85:21: style: Variable 'oldPosition' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/RangeSplitter.cpp:85:9: style: Variable 'oldPosition' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:207:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:335:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:900:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/Read.cpp:43:31: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-2.0.3/SNAPLib/Read.cpp:43:65: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-2.0.3/SNAPLib/Read.cpp:43:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Read.cpp:43:57: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Read.cpp:42:18: style: Variable 'n' can be declared as const array [constVariable]
snap-2.0.3/SNAPLib/PairedAligner.cpp:118:34: error: Array 'nSmallHitsByTimeHistogram[32][32]' accessed at index nSmallHitsByTimeHistogram[32][*], which is out of bounds. [arrayIndexOutOfBounds]
snap-2.0.3/SNAPLib/PairedAligner.cpp:113:43: note: Assuming that condition 'nHitsBucket<nHitsBuckets' is not redundant
snap-2.0.3/SNAPLib/PairedAligner.cpp:118:34: note: Array index out of bounds
snap-2.0.3/SNAPLib/PairedAligner.cpp:127:32: error: Array 'nLVCallsByTimeHistogram[32][32]' accessed at index nLVCallsByTimeHistogram[32][*], which is out of bounds. [arrayIndexOutOfBounds]
snap-2.0.3/SNAPLib/PairedAligner.cpp:122:49: note: Assuming that condition 'nLVCallsBucket<nLVCallsBuckets' is not redundant
snap-2.0.3/SNAPLib/PairedAligner.cpp:127:32: note: Array index out of bounds
snap-2.0.3/SNAPLib/PairedAligner.cpp:130:32: error: Array 'mapqByNLVCallsHistogram[71][32]' accessed at index mapqByNLVCallsHistogram[*][32], which is out of bounds. [arrayIndexOutOfBounds]
snap-2.0.3/SNAPLib/PairedAligner.cpp:122:49: note: Assuming that condition 'nLVCallsBucket<nLVCallsBuckets' is not redundant
snap-2.0.3/SNAPLib/PairedAligner.cpp:130:32: note: Array index out of bounds
snap-2.0.3/SNAPLib/PairedAligner.cpp:133:34: error: Array 'mapqByNSmallHitsHistogram[71][32]' accessed at index mapqByNSmallHitsHistogram[*][32], which is out of bounds. [arrayIndexOutOfBounds]
snap-2.0.3/SNAPLib/PairedAligner.cpp:113:9: note: After for loop, nHitsBucket has value 32
snap-2.0.3/SNAPLib/PairedAligner.cpp:123:32: note: Assuming condition is false
snap-2.0.3/SNAPLib/PairedAligner.cpp:133:34: note: Array index out of bounds
snap-2.0.3/SNAPLib/PairedAligner.cpp:520:39: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-2.0.3/SNAPLib/PairedAligner.cpp:520:73: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-2.0.3/SNAPLib/PairedAligner.cpp:513:9: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::pairedReadSupplierGenerator' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::minSpacing' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::maxSpacing' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::forceSpacing' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::intersectingAlignerMaxHits' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::maxCandidatePoolSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::fastqFile1' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::ignoreMismatchedIDs' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::quicklyDropUnpairedReads' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::inferSpacing' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::useSoftClipping' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::maxSeedsSingleEnd' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::minScoreRealignment' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::minScoreGapRealignmentALT' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::minAGScoreImprovement' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::flattenMAPQAtOrBelow' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::enableHammingScoringBaseAligner' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/PairedAligner.cpp:366:23: warning: Member variable 'PairedAlignerContext::pairedEndSpacing' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::index' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::genome' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::genomeSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::maxReadSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::maxHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::maxBigHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::extraSearchDepth' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::maxK' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::maxKForIndels' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::numSeedsFromCommandLine' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::seedCoverage' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::minSpacing' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::maxSpacing' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::seedLen' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::doesGenomeIndexHave64BitLocations' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::nLocationsScoredLandauVishkin' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::nLocationsScoredAffineGap' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::useAffineGap' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::ignoreAlignmentAdjustmentsForOm' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::altAwareness' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::useSoftClip' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::maxScoreGapToPreferNonAltAlignment' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::minBigIndelSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::stopOnFirstHit' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::matchReward' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::subPenalty' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::gapOpenPenalty' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::gapExtendPenalty' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::hashTableHitSets' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::countOfHashTableLookups' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::totalHashTableHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::largestHashTableHit' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::readWithMoreHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::readWithFewerHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::rcReadData' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::rcReadQuality' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::readLen' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::reads' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::reversedRead' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::landauVishkin' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::reverseLandauVishkin' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::affineGap' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::reverseAffineGap' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::rcTranslationTable' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::nTable' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::seedUsed' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::localBestPairProbability' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::scoringCandidatePool' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::scoringCandidatePoolSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::lowestFreeScoringCandidatePoolEntry' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::scoringCandidates' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::scoringMateCandidates' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::lowestFreeScoringMateCandidate' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::mergeAnchorPool' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::firstFreeMergeAnchor' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::mergeAnchorPoolSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::hitsPerContigCounts' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::maxSecondaryAlignmentsPerContig' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:197:5: warning: Member variable 'IntersectingPairedEndAligner::contigCountEpoch' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::currentDisjointHitSet' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::disjointHitSets' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::lookups32' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::lookups64' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::lookupListHead32' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::lookupListHead64' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::maxSeeds' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::nLookupsUsed' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::mostRecentLocationReturned' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::maxMergeDistance' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:296:9: warning: Member variable 'HashTableHitSet::doesGenomeIndexHave64BitLocations' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:173:10: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:176:10: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:535:14: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::MergeAnchor::doesRangeMatch' can be const. [functionConst]
snap-2.0.3/SNAPLib/PairedAligner.cpp:69:27: warning: The struct 'PairedAlignerStats' defines member variable with name 'maxMapq' also defined in its parent struct 'AlignerStats'. [duplInheritedMember]
snap-2.0.3/SNAPLib/AlignerStats.h:65:27: note: Parent variable 'AlignerStats::maxMapq'
snap-2.0.3/SNAPLib/PairedAligner.cpp:69:27: note: Derived variable 'PairedAlignerStats::maxMapq'
snap-2.0.3/SNAPLib/PairedAligner.cpp:81:5: style: Struct 'PairedAlignerStats' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/ParallelTask.h:50:5: style: Class 'ParallelTask < PairedAlignerContext >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:67:11: style: The function 'setLandauVishkin' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:66:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:67:11: note: Function in derived class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:75:11: style: The function 'setAffineGap' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:72:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:75:11: note: Function in derived class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:85:14: style: The destructor '~IntersectingPairedEndAligner' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:40:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:85:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:87:18: style: The function 'align' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:42:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:87:18: note: Function in derived class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:178:20: style: The function 'getLocationsScoredWithLandauVishkin' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:80:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:178:20: note: Function in derived class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:182:20: style: The function 'getLocationsScoredWithAffineGap' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/PairedEndAligner.h:81:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:182:20: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.cpp:83:14: style: The destructor '~PairedAlignerStats' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerStats.h:93:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/PairedAligner.cpp:83:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/PairedAligner.cpp:138:18: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerStats.h:95:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.cpp:138:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.cpp:140:18: style: The function 'printHistograms' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/AlignerStats.h:97:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.cpp:140:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.cpp:140:18: style: The function 'printHistograms' overrides a function in a base class but just delegates back to the base class. [uselessOverride]
snap-2.0.3/SNAPLib/AlignerStats.h:97:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/PairedAligner.cpp:140:18: note: Function in derived class
snap-2.0.3/SNAPLib/PairedAligner.cpp:673:17: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is '_int64 {aka unsigned long}'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/PairedAligner.cpp:150:22: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:154:19: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:409:39: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:410:40: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:520:31: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:520:65: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:629:38: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:630:53: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:636:40: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:637:40: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:742:31: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:753:46: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:765:52: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:777:52: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:190:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:374:38: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:894:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/PairedAligner.cpp:187:52: style:inconclusive: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/PairedAligner.cpp:138:44: note: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'.
snap-2.0.3/SNAPLib/PairedAligner.cpp:187:52: note: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'.
snap-2.0.3/SNAPLib/PairedAligner.cpp:716:20: style: Local variable 'startTime' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/PairedAligner.cpp:657:12: note: Shadowed declaration
snap-2.0.3/SNAPLib/PairedAligner.cpp:716:20: note: Shadow variable
snap-2.0.3/SNAPLib/PairedAligner.cpp:424:63: style: Parameter 'pairedEndSpacing' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/PairedAligner.cpp:519:26: style: Variable 'n' can be declared as const array [constVariable]
snap-2.0.3/SNAPLib/PairedAligner.cpp:964:7: style: Variable 'useful' can be declared as const array [constVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:173:32: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:173:51: style: Parameter 'allocator' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/ReadReader.cpp:44:5: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:139:9: style:inconclusive: Technically the member function 'AffineGapVectorized::computeGaplessScore' can be const. [functionConst]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1342:10: style:inconclusive: Technically the member function 'AffineGapVectorized::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/AffineGapVectorized.h:1345:10: style:inconclusive: Technically the member function 'AffineGapVectorized::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/ReadReader.cpp:31:14: style: The destructor '~SimpleReadReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:135:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/ReadReader.cpp:31:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/ReadReader.cpp:36:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:140:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadReader.cpp:36:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadReader.cpp:38:18: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:139:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadReader.cpp:38:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadReader.cpp:46:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:144:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadReader.cpp:46:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadReader.cpp:49:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:147:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadReader.cpp:49:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:196:25: style:inconclusive: Member variable 'ReadSupplierFromQueue::done' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:632:5: note: Member variable 'ReadSupplierFromQueue::done' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:196:25: note: Member variable 'ReadSupplierFromQueue::done' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:218:25: style:inconclusive: Member variable 'PairedReadSupplierFromQueue::done' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:666:43: note: Member variable 'PairedReadSupplierFromQueue::done' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:218:25: note: Member variable 'PairedReadSupplierFromQueue::done' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:328:20: style:inconclusive: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const. [functionConst]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:151:10: note: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:328:20: note: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:110:20: performance:inconclusive: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:176:10: note: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:110:20: note: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:427:26: style: Condition 'emptyQueue->next==emptyQueue' is always false [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:406:34: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:33:51: style:inconclusive: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_reader' definition 'reader'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:92:35: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_reader' definition 'reader'.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:33:51: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_reader' definition 'reader'.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:41:50: style:inconclusive: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_firstHalfReader' definition 'firstHalfReader'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:99:35: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_firstHalfReader' definition 'firstHalfReader'.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:41:50: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_firstHalfReader' definition 'firstHalfReader'.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:41:79: style:inconclusive: Function 'ReadSupplierQueue' argument 2 names different: declaration 'i_secondHalfReader' definition 'secondHalfReader'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:99:66: note: Function 'ReadSupplierQueue' argument 2 names different: declaration 'i_secondHalfReader' definition 'secondHalfReader'.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:41:79: note: Function 'ReadSupplierQueue' argument 2 names different: declaration 'i_secondHalfReader' definition 'secondHalfReader'.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:50:56: style:inconclusive: Function 'ReadSupplierQueue' argument 1 names different: declaration 'pairedReader' definition 'i_pairedReader'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/ReadSupplierQueue.h:105:41: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'pairedReader' definition 'i_pairedReader'.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:50:56: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'pairedReader' definition 'i_pairedReader'.
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:545:31: style: Variable 'b' can be declared as const array [constVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:546:26: style: Variable 'newBatch' can be declared as const array [constVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:123:17: style: Variable 'worked' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:123:10: style: Variable 'worked' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:291:22: style: Variable 'sizes' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:450:24: style: Variable 'balanceTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:451:27: style: Variable 'bufferWaitTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:452:27: style: Variable 'processingTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:467:28: style: Variable 'processingTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:473:25: style: Variable 'balanceTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:482:24: style: Variable 'processingTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:486:24: style: Variable 'bufferWaitTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:616:20: style: Variable 'processingTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:302:95: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:355:91: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/SeedSequencer.cpp:38:5: warning: Class 'SeedSequencer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/SeedSequencer.cpp:38:5: warning: Class 'SeedSequencer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/SeedSequencer.cpp:38:5: warning: Class 'SeedSequencer' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
snap-2.0.3/SNAPLib/SeedSequencer.h:48:15: style: Class 'SeedSequencer' is unsafe, 'SeedSequencer::offsets' can leak by wrong usage. [unsafeClassCanLeak]
snap-2.0.3/SNAPLib/PriorityQueue.h:116:5: debug: Failed to instantiate template "VariableSizeVector". The checking continues anyway. [templateInstantiation]
snap-2.0.3/SNAPLib/SAM.cpp:3765:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/SAM.cpp:3835:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/SAM.cpp:4073:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable isDuplicate [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/SingleAligner.cpp:207:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::minBigIndelSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::countOfHashTableLookups' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::totalHashTableHits' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::largestHashTableHit' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::readWithMoreHits' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::readWithFewerHits' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::readLen' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::reads' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::affineGap' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::reverseAffineGap' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::localBestPairProbability' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::lowestFreeScoringCandidatePoolEntry' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::lowestFreeScoringMateCandidate' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::firstFreeMergeAnchor' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:210:29: style:inconclusive: Member variable 'IntersectingPairedEndAligner::maxBigHits' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:62:51: note: Member variable 'IntersectingPairedEndAligner::maxBigHits' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:210:29: note: Member variable 'IntersectingPairedEndAligner::maxBigHits' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:211:29: style:inconclusive: Member variable 'IntersectingPairedEndAligner::extraSearchDepth' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:63:5: note: Member variable 'IntersectingPairedEndAligner::extraSearchDepth' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:211:29: note: Member variable 'IntersectingPairedEndAligner::extraSearchDepth' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:239:25: style:inconclusive: Member variable 'IntersectingPairedEndAligner::alignmentAdjuster' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:64:101: note: Member variable 'IntersectingPairedEndAligner::alignmentAdjuster' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:239:25: note: Member variable 'IntersectingPairedEndAligner::alignmentAdjuster' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:225:29: style:inconclusive: Member variable 'IntersectingPairedEndAligner::ignoreAlignmentAdjustmentsForOm' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:64:140: note: Member variable 'IntersectingPairedEndAligner::ignoreAlignmentAdjustmentsForOm' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:225:29: note: Member variable 'IntersectingPairedEndAligner::ignoreAlignmentAdjustmentsForOm' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:227:29: style:inconclusive: Member variable 'IntersectingPairedEndAligner::useSoftClip' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:65:200: note: Member variable 'IntersectingPairedEndAligner::useSoftClip' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:227:29: note: Member variable 'IntersectingPairedEndAligner::useSoftClip' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3962:35: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const. [functionConst]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:770:16: note: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3962:35: note: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3938:46: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const. [functionConst]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:745:14: note: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3938:46: note: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1005:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable length [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1278:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataReaderIsBuffer [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/PriorityQueue.h:42:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable priority [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/PriorityQueue.h:66:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable priority [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/PriorityQueue.h:86:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable priority [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/PriorityQueue.h:108:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable priority [valueFlowBailoutIncompleteVar]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:245:13: style: Condition '!fitInSecondaryBuffer' is always false [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:241:46: note: Calling function 'alignAffineGap' returns 1
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:241:46: note: Assignment 'fitInSecondaryBuffer=alignAffineGap(read0,read1,result,firstALTResult,maxEditDistanceForSecondaryResults,secondaryResultBufferSize,nSecondaryResults,secondaryResults,singleSecondaryBufferSize,maxSecondaryResultsToReturn,nSingleEndSecondaryResultsForFirstRead,nSingleEndSecondaryResultsForSecondRead,singleEndSecondaryResults,maxLVCandidatesForAffineGapBufferSize,nLVCandidatesForAffineGap,lvCandidatesForAffineGap)', assigned value is 1
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:245:13: note: Condition '!fitInSecondaryBuffer' is always false
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1303:79: style: Condition '!ignoreAlignmentAdjustmentsForOm' is always true [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1298:9: note: Assuming that condition '!ignoreAlignmentAdjustmentsForOm' is not redundant
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1303:79: note: Condition '!ignoreAlignmentAdjustmentsForOm' is always true
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2378:79: style: Condition '!ignoreAlignmentAdjustmentsForOm' is always true [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2373:9: note: Assuming that condition '!ignoreAlignmentAdjustmentsForOm' is not redundant
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2378:79: note: Condition '!ignoreAlignmentAdjustmentsForOm' is always true
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:133:16: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:136:33: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:137:36: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:140:44: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:141:47: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:148:25: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:149:28: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:152:36: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:156:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:160:31: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3494:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3497:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3500:23: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3565:1: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3566:1: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3641:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3642:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3644:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3645:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3269:16: style: Variable '*score' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3257:21: note: *score is assigned
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3269:16: note: *score is overwritten
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3269:16: style: Variable '*score' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3263:16: note: *score is assigned
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3269:16: note: *score is overwritten
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3352:14: style: Redundant initialization for 'agScore1'. The initialized value is overwritten before it is read. [redundantInitialization]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3335:18: note: agScore1 is initialized
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3352:14: note: agScore1 is overwritten
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3472:16: style: Variable '*score' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3464:24: note: *score is assigned
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3472:16: note: *score is overwritten
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3011:23: style: The scope of the variable 'agScore2' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3456:13: style: The scope of the variable 'limitLeft' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3868:9: style: The scope of the variable 'readWithFewerHits' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:42:34: style:inconclusive: Function 'IntersectingPairedEndAligner' argument 6 names different: declaration 'maxSeedsFromCommandLine_' definition 'numSeedsFromCommandLine_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:47:34: note: Function 'IntersectingPairedEndAligner' argument 6 names different: declaration 'maxSeedsFromCommandLine_' definition 'numSeedsFromCommandLine_'.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:42:34: note: Function 'IntersectingPairedEndAligner' argument 6 names different: declaration 'maxSeedsFromCommandLine_' definition 'numSeedsFromCommandLine_'.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:59:34: style:inconclusive: Function 'IntersectingPairedEndAligner' argument 23 names different: declaration 'gapExtendPenalty' definition 'gapExtendPenalty_'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:64:34: note: Function 'IntersectingPairedEndAligner' argument 23 names different: declaration 'gapExtendPenalty' definition 'gapExtendPenalty_'.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:59:34: note: Function 'IntersectingPairedEndAligner' argument 23 names different: declaration 'gapExtendPenalty' definition 'gapExtendPenalty_'.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:105:159: style:inconclusive: Function 'getBigAllocatorReservation' argument 5 names different: declaration 'maxSeedsFromCommandLine' definition 'numSeedsFromCommandLine'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:168:147: note: Function 'getBigAllocatorReservation' argument 5 names different: declaration 'maxSeedsFromCommandLine' definition 'numSeedsFromCommandLine'.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:105:159: note: Function 'getBigAllocatorReservation' argument 5 names different: declaration 'maxSeedsFromCommandLine' definition 'numSeedsFromCommandLine'.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3808:29: style:inconclusive: Function 'checkMerge' argument 5 names different: declaration 'newAPairGScore' definition 'newPairAGScore'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:547:29: note: Function 'checkMerge' argument 5 names different: declaration 'newAPairGScore' definition 'newPairAGScore'.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3808:29: note: Function 'checkMerge' argument 5 names different: declaration 'newAPairGScore' definition 'newPairAGScore'.
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:323:10: style: Local variable 'rcReads' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:411:10: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:323:10: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1092:56: style: Local variable 'result' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:257:34: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1092:56: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1134:56: style: Local variable 'result' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:257:34: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1134:56: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1501:10: style: Local variable 'rcReads' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:411:10: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1501:10: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2167:56: style: Local variable 'result' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1444:29: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2167:56: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2209:56: style: Local variable 'result' shadows outer argument [shadowArgument]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1444:29: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2209:56: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2519:10: style: Local variable 'rcReads' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:411:10: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2519:10: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2759:22: style: Local variable 'nonALTAlignment' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2694:10: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2759:22: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2874:23: style: Local variable 'genome' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:206:29: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2874:23: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3009:9: style: Local variable 'readLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:408:14: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3009:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3010:9: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:219:29: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3010:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3061:13: style: Local variable 'patternLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3021:9: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3061:13: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3157:9: style: Local variable 'readLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:408:14: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3157:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3158:9: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:219:29: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3158:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3332:9: style: Local variable 'readLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:408:14: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3332:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3333:9: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:219:29: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3333:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3432:9: style: Local variable 'readLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:408:14: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3432:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3433:9: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:219:29: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3433:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3868:9: style: Local variable 'readWithFewerHits' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:374:45: note: Shadowed declaration
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3868:9: note: Shadow variable
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:347:15: style: Variable 'read' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:387:19: style: Variable 'read' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1525:15: style: Variable 'read' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1565:19: style: Variable 'read' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2504:32: style: Parameter 'nLVCandidatesForAffineGap' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2538:15: style: Variable 'read' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2560:19: style: Variable 'read' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2987:11: style: Variable 'readToScore' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3135:11: style: Variable 'readToScore' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3304:11: style: Variable 'readToScore' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3410:11: style: Variable 'readToScore' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3600:9: style: Variable 'lookup' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3602:9: style: Variable 'lookup' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3865:228: style: Parameter 'candidate' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3865:261: style: Parameter 'mate' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3938:100: style: Parameter 'popularSeedsSkipped' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:612:53: style: Variable 'previousMoreHitsLocation' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:643:42: style: Variable 'previousMoreHitsLocation' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1780:53: style: Variable 'previousMoreHitsLocation' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:1810:42: style: Variable 'previousMoreHitsLocation' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:2809:47: style: Variable 'updatedBestScore' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3010:17: style: Variable 'seedLen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3011:32: style: Variable 'agScore2' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3026:18: style: Variable 'agScore1' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3041:18: style: Variable 'agScore1' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3057:14: style: Variable 'agScore1' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3010:9: style: Variable 'seedLen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3313:24: style: Variable 'origScoreLimit' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3313:9: style: Variable 'origScoreLimit' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadWriter.cpp:37:5: warning: Member variable 'SimpleReadWriter::writesSinceLastTooSlowCheck' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/ReadWriter.cpp:57:14: style: The destructor '~SimpleReadWriter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:210:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/ReadWriter.cpp:57:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/ReadWriter.cpp:62:15: style: The function 'writeHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:213:15: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadWriter.cpp:62:15: note: Function in derived class
snap-2.0.3/SNAPLib/ReadWriter.cpp:64:18: style: The function 'writeReads' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:218:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadWriter.cpp:64:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadWriter.cpp:66:18: style: The function 'writePairs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:225:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadWriter.cpp:66:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadWriter.cpp:69:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:230:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadWriter.cpp:69:18: note: Function in derived class
snap-2.0.3/SNAPLib/ReadWriter.cpp:688:6: style: The destructor '~SimpleReadWriterSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:247:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/ReadWriter.cpp:688:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/ReadWriter.cpp:693:25: style: The function 'getWriter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:238:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadWriter.cpp:693:25: note: Function in derived class
snap-2.0.3/SNAPLib/ReadWriter.cpp:699:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Read.h:240:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/ReadWriter.cpp:699:18: note: Function in derived class
snap-2.0.3/SNAPLib/Util.cpp:248:5: style: Class 'StdioFGetsObject' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Util.cpp:265:5: style: Class 'GenericFileFGetsObject' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/ReadWriter.cpp:724:10: style:inconclusive: Function 'create' argument 4 names different: declaration 'killIfTooSlowbool' definition 'killIfTooSlow'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Read.h:243:36: note: Function 'create' argument 4 names different: declaration 'killIfTooSlowbool' definition 'killIfTooSlow'.
snap-2.0.3/SNAPLib/ReadWriter.cpp:724:10: note: Function 'create' argument 4 names different: declaration 'killIfTooSlowbool' definition 'killIfTooSlow'.
snap-2.0.3/SNAPLib/Util.cpp:282:5: style: Class 'DataReaderFGetsObject' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/Util.cpp:249:19: style: The function 'fgets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Util.cpp:193:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/Util.cpp:249:19: note: Function in derived class
snap-2.0.3/SNAPLib/Util.cpp:266:19: style: The function 'fgets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Util.cpp:193:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/Util.cpp:266:19: note: Function in derived class
snap-2.0.3/SNAPLib/Util.cpp:284:19: style: The function 'fgets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/Util.cpp:193:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/Util.cpp:284:19: note: Function in derived class
snap-2.0.3/SNAPLib/Util.cpp:167:4: portability: %lld in format string (no. 1) requires 'long long' but the argument type is '_uint64 {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/Util.cpp:170:4: portability: %lld in format string (no. 1) requires 'long long' but the argument type is '_uint64 {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/Util.cpp:63:18: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Util.cpp:64:42: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Util.cpp:71:39: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/Util.cpp:64:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/Util.cpp:70:20: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/ReadWriter.cpp:38:28: style: Parameter 'i_internalScoreTag' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/ReadWriter.cpp:662:62: style: Parameter 'i_internalScoreTag' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/Util.cpp:119:93: style:inconclusive: Function 'FormatUIntWithCommas' argument 4 names different: declaration 'desiredWidth' definition 'desiredLength'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/Util.h:20:93: note: Function 'FormatUIntWithCommas' argument 4 names different: declaration 'desiredWidth' definition 'desiredLength'.
snap-2.0.3/SNAPLib/Util.cpp:119:93: note: Function 'FormatUIntWithCommas' argument 4 names different: declaration 'desiredWidth' definition 'desiredLength'.
snap-2.0.3/SNAPLib/Util.cpp:41:21: portability: Shifting signed 64-bit value by 63 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
snap-2.0.3/SNAPLib/Util.cpp:35:5: note: After for loop, highestBitSet has value 63
snap-2.0.3/SNAPLib/Util.cpp:41:21: note: Shift
snap-2.0.3/SNAPLib/Util.cpp:42:24: error: Shifting 64-bit value by 64 bits is undefined behaviour [shiftTooManyBits]
snap-2.0.3/SNAPLib/Util.cpp:35:5: note: After for loop, highestBitSet has value 63
snap-2.0.3/SNAPLib/Util.cpp:41:38: note: Assuming condition is false
snap-2.0.3/SNAPLib/Util.cpp:42:24: note: Shift
snap-2.0.3/SNAPLib/Util.cpp:289:35: style: Variable 'amountAlreadyAdvanced' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Util.cpp:289:13: style: Variable 'amountAlreadyAdvanced' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Util.cpp:357:24: style: Variable 'filenameLen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/Util.cpp:357:12: style: Variable 'filenameLen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadWriter.cpp:226:75: style: Variable 'cumulativeAddBackClipping' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadWriter.cpp:226:49: style: Variable 'cumulativeAddBackClipping' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/ReadWriter.cpp:493:35: style: Variable 'writeOrder[1]' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:35:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:106:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAM_UNMAPPED [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:324:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BigAllocUseHugePages [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/SNAPCommand/SNAPCommand.cpp:33:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/SNAPCommand/SNAPCommand.cpp:54:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULT_NAMED_PIPE_NAME [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/ToFASTQ/ToFASTQ.cpp:36:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/ToFASTQ/ToFASTQ.cpp:92:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NUM_READS_PER_PAIR [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/ToFASTQ/ToFASTQ.cpp:120:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BigAllocUseHugePages [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/ToFASTQ/ToFASTQ.cpp:57:5: warning: Member variable 'ThreadContext::whichThread' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/apps/ToFASTQ/ToFASTQ.cpp:58:9: performance: Variable 'totalReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
snap-2.0.3/apps/ToFASTQ/ToFASTQ.cpp:69:30: style: C-style pointer casting [cstyleCast]
snap-2.0.3/apps/wc/wc.cpp:26:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/wc/wc.cpp:48:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdin [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/wc/wc.cpp:193:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/wc/wc.cpp:31:5: warning: Member variable 'InputFile::fileName' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/apps/wc/wc.cpp:43:28: style: C-style pointer casting [cstyleCast]
snap-2.0.3/apps/wc/wc.cpp:217:36: style: Variable 'lastInputFile' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/import/pdclibhdfs/src/exception.c:83:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINTERNAL [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/exception.c:102:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/exception.c:184:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:119:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:306:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSTANCE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:330:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINTERNAL [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:374:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSTANCE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:395:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINTERNAL [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:428:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:442:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOMEM [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:575:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:638:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINTERNAL [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:827:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:875:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSTANCE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:897:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_ACCMODE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1111:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1162:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1207:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1234:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1312:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1352:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1429:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1501:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1538:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1579:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1609:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1639:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1673:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1715:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1794:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable JNI_FALSE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1852:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1915:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:1995:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2039:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2095:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2143:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2218:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2280:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2327:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2511:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2539:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2582:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2626:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2669:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSTANCE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2811:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSTANCE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2866:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2964:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:457:14: style: Variable 'cur' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:456:9: note: cur is assigned
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:457:14: note: cur is overwritten
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2998:12: warning: Size of pointer 'hdfsFileInfo' used instead of size of its data. [pointerSize]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:65:13: style: struct member 'hdfsJniEnv::env' is never used. [unusedStructMember]
snap-2.0.3/import/pdclibhdfs/src/hdfs.c:2225:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:126:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:143:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:172:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENTER [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:207:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FIND [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:303:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:455:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSTANCE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:542:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STATIC [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:629:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INSTANCE [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:663:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STATIC [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:827:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:1137:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:988:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:1006:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:1150:9: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:998:9: warning: If memory allocation fails, then there is a possible null pointer dereference: options [nullPointerOutOfMemory]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:997:25: note: Assuming allocation function fails
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:997:25: note: Assignment 'options=calloc(noArgs,sizeof(JavaVMOption))', assigned value is 0
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:998:9: note: Null pointer dereference
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:153:15: style: Variable 'ep' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:432:26: style: Parameter 'parms' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:435:13: style: Variable 'env' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:793:11: style: Variable 'error' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:805:11: style: Variable 'JVMPath' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:931:15: style: Variable 'hadoopClassPath' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:932:15: style: Variable 'hadoopClassPathVMArg' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:939:14: style: Variable 'jvmArgDelims' can be declared as const array [constVariable]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:937:30: style: Variable 'cnt' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:791:16: style: Unused variable: jthr [unusedVariable]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:937:26: style: Variable 'cnt' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:940:29: style: Unused variable: savePtr [unusedVariable]
snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:1100:13: style: Variable 'rv' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/import/pdclibhdfs/src/native_mini_dfs.c:54:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/native_mini_dfs.c:143:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/native_mini_dfs.c:157:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/native_mini_dfs.c:175:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/native_mini_dfs.c:195:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/native_mini_dfs.c:221:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:73:5: warning: Member variable 'ThreadContext::whichThread' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:74:9: performance: Variable 'nUnaligned' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:75:9: performance: Variable 'totalReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:121:17: style: Expression is always true because 'else if' condition is opposite to previous condition at line 119. [multiCondition]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:119:20: note: first condition
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:121:17: note: else if condition is opposite to first condition
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:111:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:217:21: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:95:30: style: C-style pointer casting [cstyleCast]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:132:18: style: The scope of the variable 'matched' can be reduced. [variableScope]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:153:18: style: The scope of the variable 'badParse' can be reduced. [variableScope]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:154:20: style: The scope of the variable 'chrNameLen' can be reduced. [variableScope]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:156:25: style: The scope of the variable 'beginningOfFirstNumber' can be reduced. [variableScope]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:156:53: style: The scope of the variable 'stage' can be reduced. [variableScope]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:110:18: style: Checking if unsigned expression 'mapQ' is less than zero. [unsignedLessThanZero]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:285:31: style: Variable 'cigarForCorrect' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:156:59: style: Variable 'stage' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:170:27: style: Variable 'stage' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:184:31: style: Variable 'stage' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:196:39: style: Variable 'stage' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:222:29: style: Variable 'match0' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:223:29: style: Variable 'match1' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:231:32: style: Variable 'match0' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:234:32: style: Variable 'match1' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:238:36: style: Variable 'match0' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:240:36: style: Variable 'match1' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:288:47: style: Variable 'correctGenomeData' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:289:45: style: Variable 'correctLocation' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:290:45: style: Variable 'cigarForCorrect' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:292:47: style: Variable 'correctGenomeData' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:293:45: style: Variable 'correctLocation' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:294:45: style: Variable 'cigarForCorrect' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:261:37: style: Variable 'correctData' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:425:29: style: Variable 'maxEditDistanceSeen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:425:9: style: Variable 'maxEditDistanceSeen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_read.c:38:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:82:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:59:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:89:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:132:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:221:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:251:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:283:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:88:19: style: Checking if unsigned expression 'blockSize' is less than zero. [unsignedLessThanZero]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:99:19: style: Checking if unsigned expression 'blockSize' is less than zero. [unsignedLessThanZero]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:113:55: style: Parameter 'ti' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_threaded.c:240:48: style: Parameter 'ti' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_write.c:38:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:117:13: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:122:9: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:176:13: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:181:9: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:267:14: style: Local variable 'buffer' shadows outer variable [shadowVariable]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:63:10: note: Shadowed declaration
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:267:14: note: Shadow variable
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:452:19: style: Local variable 'writePath' shadows outer variable [shadowVariable]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:65:17: note: Shadowed declaration
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:452:19: note: Shadow variable
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:453:13: style: Local variable 'buffer' shadows outer variable [shadowVariable]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:63:10: note: Shadowed declaration
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:453:13: note: Shadow variable
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:454:11: style: Local variable 'num_written_bytes' shadows outer variable [shadowVariable]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:64:9: note: Shadowed declaration
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:454:11: note: Shadow variable
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:535:15: style: Local variable 'buffer' shadows outer variable [shadowVariable]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:63:10: note: Shadowed declaration
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:535:15: note: Shadow variable
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:536:21: style: Local variable 'writePath' shadows outer variable [shadowVariable]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:65:17: note: Shadowed declaration
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:536:21: note: Shadow variable
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:538:13: style: Local variable 'num_written_bytes' shadows outer variable [shadowVariable]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:64:9: note: Shadowed declaration
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:538:13: note: Shadow variable
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:35:13: style: Variable 'perm' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:455:21: style: Variable 'finfo' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/import/pdclibhdfs/src/test_libhdfs_ops.c:539:23: style: Variable 'finfo' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/tests/AffineGapTest.cpp:9:5: warning: Member variable 'AffineGapTest::editDist' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/tests/AffineGapVectorizedTest.cpp:9:5: warning: Member variable 'AffineGapVectorizedTest::editDist' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/tests/EventTest.cpp:45:26: style: C-style pointer casting [cstyleCast]
snap-2.0.3/tests/EventTest.cpp:89:26: style: C-style pointer casting [cstyleCast]
snap-2.0.3/tests/EventTest.cpp:26:35: style:inconclusive: Function 'init' argument 1 names different: declaration 'parent' definition 'i_parent'. [funcArgNamesDifferent]
snap-2.0.3/tests/EventTest.cpp:12:24: note: Function 'init' argument 1 names different: declaration 'parent' definition 'i_parent'.
snap-2.0.3/tests/EventTest.cpp:26:35: note: Function 'init' argument 1 names different: declaration 'parent' definition 'i_parent'.
snap-2.0.3/tests/EventTest.cpp:56:51: style:inconclusive: Function 'testManyWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'. [funcArgNamesDifferent]
snap-2.0.3/tests/EventTest.cpp:22:42: note: Function 'testManyWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'.
snap-2.0.3/tests/EventTest.cpp:56:51: note: Function 'testManyWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'.
snap-2.0.3/tests/EventTest.cpp:101:53: style:inconclusive: Function 'testSingleWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'. [funcArgNamesDifferent]
snap-2.0.3/tests/EventTest.cpp:23:44: note: Function 'testSingleWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'.
snap-2.0.3/tests/EventTest.cpp:101:53: note: Function 'testSingleWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'.
snap-2.0.3/tests/EventTest.cpp:32:41: style: Parameter 'variable' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/tests/ProbabilityDistanceTest.cpp:11:5: warning: Member variable 'ProbabilityDistanceTest::prob' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/tests/TestLib.cpp:24:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
snap-2.0.3/tests/TestLib.cpp:34:39: style: Variable 'e' can be declared as reference to const [constVariableReference]
snap-2.0.3/tests/TestLib.cpp:9:29: style: Parameter 'filter' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SingleAligner.cpp:43:23: warning: Member variable 'SingleAlignerContext::readSupplierGenerator' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/ParallelTask.h:50:5: style: Class 'ParallelTask < SingleAlignerContext >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SingleAligner.cpp:207:13: portability: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is '_int64 {aka unsigned long}'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:80:12: warning: Member variable 'SortBlock::data' is not assigned a value in 'SortBlock::operator='. [operatorEqVarError]
snap-2.0.3/SNAPLib/SingleAligner.cpp:197:28: warning: Either the condition 'supplier!=NULL' is redundant or there is possible null pointer dereference: supplier. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/SingleAligner.cpp:342:18: note: Assuming that condition 'supplier!=NULL' is not redundant
snap-2.0.3/SNAPLib/SingleAligner.cpp:197:28: note: Null pointer dereference
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:72:17: style:inconclusive: Member variable 'SortBlock::reader' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:60:50: note: Member variable 'SortBlock::reader' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:72:17: note: Member variable 'SortBlock::reader' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:74:17: style:inconclusive: Member variable 'SortBlock::data' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:60:91: note: Member variable 'SortBlock::data' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:74:17: note: Member variable 'SortBlock::data' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:72:17: style:inconclusive: Member variable 'SortBlock::reader' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:61:78: note: Member variable 'SortBlock::reader' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:72:17: note: Member variable 'SortBlock::reader' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:74:17: style:inconclusive: Member variable 'SortBlock::data' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:61:150: note: Member variable 'SortBlock::data' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:74:17: note: Member variable 'SortBlock::data' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:194:37: style:inconclusive: Member variable 'SortedDataFilterSupplier::genome' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:138:9: note: Member variable 'SortedDataFilterSupplier::genome' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:194:37: note: Member variable 'SortedDataFilterSupplier::genome' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:196:37: style:inconclusive: Member variable 'SortedDataFilterSupplier::tempFileName' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:141:9: note: Member variable 'SortedDataFilterSupplier::tempFileName' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:196:37: note: Member variable 'SortedDataFilterSupplier::tempFileName' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:202:37: style:inconclusive: Member variable 'SortedDataFilterSupplier::blocks' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:146:9: note: Member variable 'SortedDataFilterSupplier::blocks' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:202:37: note: Member variable 'SortedDataFilterSupplier::blocks' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SingleAligner.cpp:175:24: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SingleAligner.cpp:261:32: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:177:26: style:inconclusive: Technically the member function 'SortedDataFilterSupplier::getGenome' can be const. [functionConst]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:269:14: style:inconclusive: Technically the member function 'ParallelQueue::QueueElement::isEmpty' can be const. [functionConst]
snap-2.0.3/SNAPLib/PriorityQueue.h:31:17: performance:inconclusive: Technically the member function 'PriorityQueue < ContigAndPos , int64_t >::check' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:299:5: warning: Class 'ParallelQueue' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:299:5: warning: Class 'ParallelQueue' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:486:5: warning: Class 'DataQueue' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:486:5: warning: Class 'DataQueue' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:564:18: style: Virtual function 'nextBatch' is called from constructor 'DataQueueWriter(DataQueue*queue_)' at line 526. Dynamic binding is not used. [virtualCallInConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:526:9: note: Calling nextBatch
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:564:18: note: nextBatch is a virtual function
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:61:5: style: Struct 'SortBlock' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:101:5: style: Class 'SortedDataFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:216:5: style: Class 'ParallelQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:523:5: style: Class 'DataQueueWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:599:5: style: Class 'DataQueueReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:776:5: style: Class 'BufferDataReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < SortEntry , 150 , true >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < SortBlock , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < SortEntry , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:105:14: style: The destructor '~SortedDataFilter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:58:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:105:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:110:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:64:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:110:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:112:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:70:24: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:112:20: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:163:14: style: The destructor '~SortedDataFilterSupplier' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:81:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:163:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:169:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:85:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:169:33: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:171:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:88:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:171:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:172:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:89:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:172:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:530:18: style: The function 'getBuffer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:100:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:530:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:547:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:104:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:547:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:556:18: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:109:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:556:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:564:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:112:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:564:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:579:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:115:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:579:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:603:6: style: The destructor '~DataQueueReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:93:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:603:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:611:10: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:96:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:611:10: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:612:11: style: The function 'readHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:99:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:612:11: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:623:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:102:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:623:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:634:18: style: The function 'getData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:109:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:634:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:637:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:112:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:637:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:645:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:116:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:645:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:648:18: style: The function 'isEOF' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:119:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:648:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:656:23: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:122:23: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:656:23: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:664:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:127:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:664:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:674:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:133:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:674:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:681:20: style: The function 'getFileOffset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:136:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:681:20: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:690:18: style: The function 'getExtra' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:140:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:690:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:697:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:143:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:697:25: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:790:6: style: The destructor '~BufferDataReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:93:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:790:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:798:10: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:96:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:798:10: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:799:11: style: The function 'readHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:99:19: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:799:11: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:810:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:102:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:810:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:821:18: style: The function 'getData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:109:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:821:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:830:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:112:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:830:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:839:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:116:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:839:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:845:18: style: The function 'isEOF' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:119:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:845:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:851:23: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:122:23: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:851:23: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:859:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:127:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:859:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:869:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:133:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:869:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:876:20: style: The function 'getFileOffset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:136:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:876:20: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:885:18: style: The function 'getExtra' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:140:18: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:885:18: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:892:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataReader.h:143:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:892:25: note: Function in derived class
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1371:35: style: Condition 'nBlocksThisThread==0' is always false [knownConditionTrueFalse]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1356:28: note: Assignment 'minPerThread=2', assigned value is 2
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1370:37: note: Assignment 'nBlocksThisThread=(int)((blocks.size()-nBlocksAssigned)<((minPerThread)>((blocks.size()-nBlocksAssigned+(nLeafThreads-i-1))/(nLeafThreads-i))?(minPerThread):((blocks.size()-nBlocksAssigned+(nLeafThreads-i-1))/(nLeafThreads-i)))?(blocks.size()-nBlocksAssigned):((minPerThread)>((blocks.size()-nBlocksAssigned+(nLeafThreads-i-1))/(nLeafThreads-i))?(minPerThread):((blocks.size()-nBlocksAssigned+(nLeafThreads-i-1))/(nLeafThreads-i))))', assigned value is 2
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1371:35: note: Condition 'nBlocksThisThread==0' is always false
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:492:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:572:25: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:762:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:778:18: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1091:35: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SingleAligner.cpp:235:16: style: Local variable 'startTime' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/SingleAligner.cpp:196:12: note: Shadowed declaration
snap-2.0.3/SNAPLib/SingleAligner.cpp:235:16: note: Shadow variable
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1374:17: style: Statements following 'continue' will never be executed. [unreachableCode]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1438:33: style:inconclusive: Function 'sorted' argument 7 names different: declaration 'sortedFilterSupplier' definition 'sortedFilterSuppler'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/DataWriter.h:157:37: note: Function 'sorted' argument 7 names different: declaration 'sortedFilterSupplier' definition 'sortedFilterSuppler'.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1438:33: note: Function 'sorted' argument 7 names different: declaration 'sortedFilterSupplier' definition 'sortedFilterSuppler'.
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:133:15: style: Parameter 'i_internalScoreTag' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:987:26: style: Variable 'previous' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1009:12: style: Variable 'first' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1107:25: style: Variable 'readWaitTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1108:26: style: Variable 'writeWaitTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1126:26: style: Variable 'readWaitTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1137:26: style: Variable 'current' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1139:19: style: Variable 'lastRefID' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1139:33: style: Variable 'lastPos' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1164:31: style: Variable 'writeWaitTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1190:38: style: Variable 'oldBlocks[oldBlockIndex]' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1194:21: style: Variable 'current' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1199:30: style: Variable 'readWaitTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1207:35: style: Variable 'previous' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1226:19: style: Variable 'writeWaitTime' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:988:95: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1115:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1258:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/SAM.cpp:813:18: warning: Either the condition 'fieldLength[posfield]>=posBufferSize' is redundant or the array 'posBuffer[20]' is accessed at index 20, which is out of bounds. [arrayIndexOutOfBoundsCond]
snap-2.0.3/SNAPLib/SAM.cpp:807:35: note: Assuming that condition 'fieldLength[posfield]>=posBufferSize' is not redundant
snap-2.0.3/SNAPLib/SAM.cpp:813:18: note: Array index out of bounds
snap-2.0.3/SNAPLib/SAM.cpp:3294:31: warning: Either the condition 'mateQualValueLen>=mateQualBufferSize' is redundant or the array 'mateQualBuffer[20]' is accessed at index 20, which is out of bounds. [arrayIndexOutOfBoundsCond]
snap-2.0.3/SNAPLib/SAM.cpp:3289:38: note: Assuming that condition 'mateQualValueLen>=mateQualBufferSize' is not redundant
snap-2.0.3/SNAPLib/SAM.cpp:3294:31: note: Array index out of bounds
snap-2.0.3/SNAPLib/SAM.cpp:3312:38: warning: Either the condition 'libraryNameLen>=libraryNameBufferSize' is redundant or the array 'libraryNameBuffer[512]' is accessed at index 512, which is out of bounds. [arrayIndexOutOfBoundsCond]
snap-2.0.3/SNAPLib/SAM.cpp:3307:40: note: Assuming that condition 'libraryNameLen>=libraryNameBufferSize' is not redundant
snap-2.0.3/SNAPLib/SAM.cpp:3312:38: note: Array index out of bounds
snap-2.0.3/SNAPLib/SAM.cpp:3668:42: warning:inconclusive: The buffer 'bestReadId' may not be null-terminated after the call to strncpy(). [terminateStrncpy]
snap-2.0.3/SNAPLib/SAM.cpp:190:12: warning: Member variable 'SAMReader::didInitialSkip' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/SAM.cpp:3111:5: warning: Member variable 'SAMFilter::currentWriter' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/SAM.cpp:3111:5: warning: Member variable 'SAMFilter::currentBuffer' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/SAM.cpp:3111:5: warning: Member variable 'SAMFilter::currentBufferBytes' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/SAM.cpp:3111:5: warning: Member variable 'SAMFilter::currentOffset' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/SAM.cpp:3568:5: warning: Member variable 'DuplicateReadKey::libraryHash' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/SAM.cpp:3624:5: warning: Member variable 'DuplicateFragmentKey::libraryHash' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/SAM.cpp:3710:5: warning: Member variable 'SAMDupMarkFilter::bufferSizeInit' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < OffsetInfo , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < OffsetInfo , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < OffsetInfo , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < OffsetInfo , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < OffsetInfo , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < OffsetInfo , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < SAMDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:31:36: note: Member variable 'VariableSizeVector < SAMDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < SAMDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: style:inconclusive: Member variable 'VariableSizeVector < SAMDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/VariableSizeVector.h:35:55: note: Member variable 'VariableSizeVector < SAMDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/VariableSizeVector.h:242:12: note: Member variable 'VariableSizeVector < SAMDupMarkEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/SAM.cpp:3198:12: performance:inconclusive: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/SAM.cpp:3128:10: note: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/SAM.cpp:3198:12: note: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/SAM.cpp:3343:12: performance:inconclusive: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/SAM.cpp:3130:10: note: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/SAM.cpp:3343:12: note: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace).
snap-2.0.3/SNAPLib/SAM.cpp:3574:5: style:inconclusive: Technically the member function 'DuplicateReadKey::operator_uint64' can be const. [functionConst]
snap-2.0.3/SNAPLib/SAM.cpp:3636:5: style:inconclusive: Technically the member function 'DuplicateFragmentKey::operator_uint64' can be const. [functionConst]
snap-2.0.3/SNAPLib/SAM.cpp:3669:17: style:inconclusive: Technically the member function 'DuplicateMateInfo::getBestReadId' can be const. [functionConst]
snap-2.0.3/SNAPLib/SAM.cpp:3671:10: style:inconclusive: Technically the member function 'DuplicateMateInfo::getBestTileXY' can be const. [functionConst]
snap-2.0.3/SNAPLib/SAM.cpp:3568:5: style: Struct 'DuplicateReadKey' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SAM.cpp:3624:5: style: Struct 'DuplicateFragmentKey' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SAM.cpp:3710:5: style: Class 'SAMDupMarkFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SAM.cpp:4268:5: style: Class 'SAMDupMarkSupplier' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < OffsetInfo , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/VariableSizeVector.h:30:5: style: Class 'VariableSizeVector < SAMDupMarkEntry , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/SAM.cpp:3113:14: style: The destructor '~SAMFilter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:58:18: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/SAM.cpp:3113:14: note: Destructor in derived class
snap-2.0.3/SNAPLib/SAM.cpp:3117:18: style: The function 'inHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:61:16: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.cpp:3117:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.cpp:3122:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:64:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.cpp:3122:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.cpp:3124:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:70:24: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.cpp:3124:20: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.cpp:3716:6: style: The destructor '~SAMDupMarkFilter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/SAM.cpp:3113:14: note: Virtual destructor in base class
snap-2.0.3/SNAPLib/SAM.cpp:3716:6: note: Destructor in derived class
snap-2.0.3/SNAPLib/SAM.cpp:3727:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/SAM.cpp:3124:20: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.cpp:3727:20: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.cpp:4271:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:85:25: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.cpp:4271:33: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.cpp:4276:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:88:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.cpp:4276:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.cpp:4277:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-2.0.3/SNAPLib/DataWriter.h:89:22: note: Virtual function in base class
snap-2.0.3/SNAPLib/SAM.cpp:4277:18: note: Function in derived class
snap-2.0.3/SNAPLib/SAM.cpp:657:14: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/SAM.cpp:814:18: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/SAM.cpp:1292:30: warning: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2076:25: warning: %llu in format string (no. 5) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2076:25: warning: %llu in format string (no. 9) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2076:25: portability: %lld in format string (no. 10) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/SAM.cpp:2312:25: warning: %llu in format string (no. 5) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2312:25: warning: %llu in format string (no. 9) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2312:25: portability: %lld in format string (no. 10) requires 'long long' but the argument type is '_int64 {aka signed long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/SAM.cpp:2650:13: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2654:13: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2745:13: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2749:13: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2775:25: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/SAM.cpp:2788:25: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/SAM.cpp:2820:9: warning: %llu in format string (no. 2) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-2.0.3/SNAPLib/SAM.cpp:2884:23: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/SAM.cpp:2874:24: warning: Either the condition 'NULL==contig' is redundant or there is possible null pointer dereference: contig. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/SAM.cpp:2868:11: note: Assuming that condition 'NULL==contig' is not redundant
snap-2.0.3/SNAPLib/SAM.cpp:2874:24: note: Null pointer dereference
snap-2.0.3/SNAPLib/SAM.cpp:2874:52: warning: Either the condition 'NULL==contig' is redundant or there is possible null pointer dereference: contig. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/SAM.cpp:2868:11: note: Assuming that condition 'NULL==contig' is not redundant
snap-2.0.3/SNAPLib/SAM.cpp:2874:52: note: Null pointer dereference
snap-2.0.3/SNAPLib/SAM.cpp:928:32: warning: Either the condition 'NULL==newLine' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/SAM.cpp:914:18: note: Assuming that condition 'NULL==newLine' is not redundant
snap-2.0.3/SNAPLib/SAM.cpp:928:32: note: Null pointer addition
snap-2.0.3/SNAPLib/SAM.cpp:240:25: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:360:57: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:511:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:1147:22: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:1774:43: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:1828:21: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:2028:39: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:2264:39: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:3462:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:3803:18: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:3813:18: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:4009:27: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/SAM.cpp:45:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:45:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:1142:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:1771:44: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:1771:64: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:2025:40: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:2025:60: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:2261:40: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:2261:59: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/SAM.cpp:3685:17: style: Variable 'bestReadQuality' is assigned an expression that holds the same value. [redundantAssignment]
snap-2.0.3/SNAPLib/SAM.cpp:3683:32: note: Assuming that condition 'totalQuality_==bestReadQuality' is not redundant
snap-2.0.3/SNAPLib/SAM.cpp:3685:17: note: Variable 'bestReadQuality' is assigned an expression that holds the same value.
snap-2.0.3/SNAPLib/SAM.cpp:3691:21: style: Variable 'bestReadQuality' is assigned an expression that holds the same value. [redundantAssignment]
snap-2.0.3/SNAPLib/SAM.cpp:3683:32: note: Assuming that condition 'totalQuality_==bestReadQuality' is not redundant
snap-2.0.3/SNAPLib/SAM.cpp:3691:21: note: Variable 'bestReadQuality' is assigned an expression that holds the same value.
snap-2.0.3/SNAPLib/SAM.cpp:3883:24: style: Variable 'next_i' is reassigned a value before the old one has been used. [redundantAssignment]
snap-2.0.3/SNAPLib/SAM.cpp:3876:24: note: next_i is assigned
snap-2.0.3/SNAPLib/SAM.cpp:3883:24: note: next_i is overwritten
snap-2.0.3/SNAPLib/SAM.cpp:340:34: style: The scope of the variable 'prefixedName' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:1762:21: style: The scope of the variable 'warningPrinted' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:1933:10: style: The scope of the variable 'cigarBuf' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:1936:10: style: The scope of the variable 'cigarBufWithClipping' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:2016:17: style: The scope of the variable 'warningPrinted' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:2151:10: style: The scope of the variable 'cigarBuf' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:2154:10: style: The scope of the variable 'cigarBufWithClipping' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:2252:17: style: The scope of the variable 'warningPrinted' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:4163:16: style: The scope of the variable 'offsetIndex' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:4235:16: style: The scope of the variable 'offsetIndex' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/SAM.cpp:144:26: style:inconclusive: Function 'create' argument 4 names different: declaration 'i_context' definition 'context'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:79:55: note: Function 'create' argument 4 names different: declaration 'i_context' definition 'context'.
snap-2.0.3/SNAPLib/SAM.cpp:144:26: note: Function 'create' argument 4 names different: declaration 'i_context' definition 'context'.
snap-2.0.3/SNAPLib/SAM.cpp:541:77: style:inconclusive: Function 'parseLine' argument 4 names different: declaration 'lineLength' definition 'linelength'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:122:21: note: Function 'parseLine' argument 4 names different: declaration 'lineLength' definition 'linelength'.
snap-2.0.3/SNAPLib/SAM.cpp:541:77: note: Function 'parseLine' argument 4 names different: declaration 'lineLength' definition 'linelength'.
snap-2.0.3/SNAPLib/SAM.cpp:594:26: style:inconclusive: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:134:41: note: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'.
snap-2.0.3/SNAPLib/SAM.cpp:594:26: note: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'.
snap-2.0.3/SNAPLib/SAM.cpp:1328:9: style:inconclusive: Function 'fillMateInfo' argument 20 names different: declaration 'refSpanFromCigar' definition 'myRefSpanFromCigar'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:301:50: note: Function 'fillMateInfo' argument 20 names different: declaration 'refSpanFromCigar' definition 'myRefSpanFromCigar'.
snap-2.0.3/SNAPLib/SAM.cpp:1328:9: note: Function 'fillMateInfo' argument 20 names different: declaration 'refSpanFromCigar' definition 'myRefSpanFromCigar'.
snap-2.0.3/SNAPLib/SAM.cpp:1435:18: style:inconclusive: Function 'createSAMLine' argument 10 names different: declaration 'mateContigName' definition 'matecontigName'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:261:26: note: Function 'createSAMLine' argument 10 names different: declaration 'mateContigName' definition 'matecontigName'.
snap-2.0.3/SNAPLib/SAM.cpp:1435:18: note: Function 'createSAMLine' argument 10 names different: declaration 'mateContigName' definition 'matecontigName'.
snap-2.0.3/SNAPLib/SAM.cpp:2607:33: style:inconclusive: Function 'computeCigarString' argument 12 names different: declaration 'frontHardClipped' definition 'frontHardClipping'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:326:18: note: Function 'computeCigarString' argument 12 names different: declaration 'frontHardClipped' definition 'frontHardClipping'.
snap-2.0.3/SNAPLib/SAM.cpp:2607:33: note: Function 'computeCigarString' argument 12 names different: declaration 'frontHardClipped' definition 'frontHardClipping'.
snap-2.0.3/SNAPLib/SAM.cpp:2608:33: style:inconclusive: Function 'computeCigarString' argument 13 names different: declaration 'backHardClipped' definition 'backHardClipping'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:326:45: note: Function 'computeCigarString' argument 13 names different: declaration 'backHardClipped' definition 'backHardClipping'.
snap-2.0.3/SNAPLib/SAM.cpp:2608:33: note: Function 'computeCigarString' argument 13 names different: declaration 'backHardClipped' definition 'backHardClipping'.
snap-2.0.3/SNAPLib/SAM.cpp:2692:33: style:inconclusive: Function 'computeCigarString' argument 14 names different: declaration 'frontHardClipped' definition 'frontHardClipping'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:332:18: note: Function 'computeCigarString' argument 14 names different: declaration 'frontHardClipped' definition 'frontHardClipping'.
snap-2.0.3/SNAPLib/SAM.cpp:2692:33: note: Function 'computeCigarString' argument 14 names different: declaration 'frontHardClipped' definition 'frontHardClipping'.
snap-2.0.3/SNAPLib/SAM.cpp:2693:33: style:inconclusive: Function 'computeCigarString' argument 15 names different: declaration 'backHardClipped' definition 'backHardClipping'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.h:332:45: note: Function 'computeCigarString' argument 15 names different: declaration 'backHardClipped' definition 'backHardClipping'.
snap-2.0.3/SNAPLib/SAM.cpp:2693:33: note: Function 'computeCigarString' argument 15 names different: declaration 'backHardClipped' definition 'backHardClipping'.
snap-2.0.3/SNAPLib/SAM.cpp:3785:13: style:inconclusive: Function 'onNextBatch' argument 6 names different: declaration 'fromBufferUsed' definition 'fromBytesUsed'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/SAM.cpp:3727:142: note: Function 'onNextBatch' argument 6 names different: declaration 'fromBufferUsed' definition 'fromBytesUsed'.
snap-2.0.3/SNAPLib/SAM.cpp:3785:13: note: Function 'onNextBatch' argument 6 names different: declaration 'fromBufferUsed' definition 'fromBytesUsed'.
snap-2.0.3/SNAPLib/SAM.cpp:158:12: style: Local variable 'headerSize' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/SAM.h:147:29: note: Shadowed declaration
snap-2.0.3/SNAPLib/SAM.cpp:158:12: note: Shadow variable
snap-2.0.3/SNAPLib/SAM.cpp:4054:16: style: Local variable 'offsetIndex' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/SAM.cpp:4035:12: note: Shadowed declaration
snap-2.0.3/SNAPLib/SAM.cpp:4054:16: note: Shadow variable
snap-2.0.3/SNAPLib/SAM.cpp:4096:16: style: Local variable 'offsetIndex' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/SAM.cpp:4035:12: note: Shadowed declaration
snap-2.0.3/SNAPLib/SAM.cpp:4096:16: note: Shadow variable
snap-2.0.3/SNAPLib/SAM.cpp:4163:16: style: Local variable 'offsetIndex' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/SAM.cpp:4035:12: note: Shadowed declaration
snap-2.0.3/SNAPLib/SAM.cpp:4163:16: note: Shadow variable
snap-2.0.3/SNAPLib/SAM.cpp:4194:16: style: Local variable 'offsetIndex' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/SAM.cpp:4035:12: note: Shadowed declaration
snap-2.0.3/SNAPLib/SAM.cpp:4194:16: note: Shadow variable
snap-2.0.3/SNAPLib/SAM.cpp:4235:16: style: Local variable 'offsetIndex' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/SAM.cpp:4035:12: note: Shadowed declaration
snap-2.0.3/SNAPLib/SAM.cpp:4235:16: note: Shadow variable
snap-2.0.3/SNAPLib/SAM.cpp:1437:21: style: Parameter 'matePositionInContig' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/SAM.cpp:1445:15: style: Parameter 'mateBasesClippedBefore' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/SAM.cpp:1446:15: style: Parameter 'mateBasesClippedAfter' can be declared as reference to const [constParameterReference]
snap-2.0.3/SNAPLib/SAM.cpp:76:25: style: Parameter 'read0' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:76:38: style: Parameter 'read1' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:254:15: style: Variable 'endOfLine' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:541:40: style: Parameter 'endOfBuffer' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:547:11: style: Variable 'endOfLine' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:603:26: style: Parameter 'rgLineOffsets' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:692:19: style: Variable 'rgFromAux' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:708:27: style: Variable 'rgStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:713:31: style: Variable 'lbStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:714:31: style: Variable 'lbEnd' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:769:11: style: Parameter 'field' can be declared as const array [constParameter]
snap-2.0.3/SNAPLib/SAM.cpp:770:12: style: Parameter 'fieldLength' can be declared as const array [constParameter]
snap-2.0.3/SNAPLib/SAM.cpp:791:11: style: Parameter 'field' can be declared as const array [constParameter]
snap-2.0.3/SNAPLib/SAM.cpp:792:12: style: Parameter 'fieldLength' can be declared as const array [constParameter]
snap-2.0.3/SNAPLib/SAM.cpp:878:15: style: Variable 'firstNewline' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:963:24: style: Variable 'splitter' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:1311:12: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:1321:12: style: Parameter 'mate' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:1451:12: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:1746:15: style: Variable 'read' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:1828:17: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:2803:50: style: Parameter 'read' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:3174:15: style: Variable 'libraryName' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:3286:23: style: Variable 'mateQualValueStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:3304:27: style: Variable 'libraryNameStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:3462:13: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:3522:39: style: Parameter 'sam' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:3592:43: style: Parameter 'sam' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:3673:43: style: Parameter 'sam' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/SAM.cpp:4201:28: style: Variable 'minfo' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/SAM.cpp:545:16: style: Variable 'prev' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:545:11: style: Variable 'prev' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:963:33: style: Variable 'splitter' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:963:24: style: Variable 'splitter' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:1287:34: style: Variable 'genomeLen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:1296:31: style: Variable 'bytesConsumed' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:1287:24: style: Variable 'genomeLen' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:1474:23: style: Variable 'cigar' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:1548:22: style: Variable 'editDistance' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:1474:17: style: Variable 'cigar' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:1548:9: style: Variable 'editDistance' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:2775:23: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:2788:23: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:2844:7: style: Variable 'sawLeadingS' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:3503:22: style: Variable 'fieldScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:3506:22: style: Variable 'fieldScanned' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:4201:34: style: Variable 'minfo' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/SAM.cpp:4036:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/SAM.cpp:4077:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/SAM.cpp:4144:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/SAM.cpp:4179:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/SAM.cpp:4223:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-2.0.3/SNAPLib/FixedSizeSet.h:20:5: warning: Member variable 'FixedSizeSet::maxSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:14: warning: Member variable 'GenomeIndex::seedLen' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:14: warning: Member variable 'GenomeIndex::hashTableKeySize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:14: warning: Member variable 'GenomeIndex::majorVersion' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:14: warning: Member variable 'GenomeIndex::minorVersion' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:14: warning: Member variable 'GenomeIndex::largeHashTable' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:14: warning: Member variable 'GenomeIndex::locationSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:14: warning: Member variable 'GenomeIndex::overflowTableSize' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1314:5: warning: Member variable 'PerCounterBatch::lowBases' is not initialized in the constructor. [uninitMemberVar]
snap-2.0.3/SNAPLib/GenomeIndex.h:105:15: style:inconclusive: Member variable 'GenomeIndex::overflowTable32' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:64: note: Member variable 'GenomeIndex::overflowTable32' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenomeIndex.h:105:15: note: Member variable 'GenomeIndex::overflowTable32' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenomeIndex.h:90:19: style:inconclusive: Member variable 'GenomeIndex::genome' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:110: note: Member variable 'GenomeIndex::genome' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenomeIndex.h:90:19: note: Member variable 'GenomeIndex::genome' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenomeIndex.h:107:19: style:inconclusive: Member variable 'GenomeIndex::mappedOverflowTable' is in the wrong place in the initializer list. [initializerList]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1112:142: note: Member variable 'GenomeIndex::mappedOverflowTable' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/GenomeIndex.h:107:19: note: Member variable 'GenomeIndex::mappedOverflowTable' is in the wrong place in the initializer list.
snap-2.0.3/SNAPLib/FixedSizeSet.h:100:10: style:inconclusive: Technically the member function 'FixedSizeSet::operatordelete' can be const. [functionConst]
snap-2.0.3/SNAPLib/FixedSizeSet.h:119:10: performance:inconclusive: Technically the member function 'FixedSizeSet::isPowerOf2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-2.0.3/SNAPLib/FixedSizeSet.h:108:14: style:inconclusive: Technically the member function 'FixedSizeSet::Entry::operatordelete[]' can be const. [functionConst]
snap-2.0.3/SNAPLib/FixedSizeVector.h:45:9: style:inconclusive: Technically the member function 'FixedSizeVector::size' can be const. [functionConst]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1827:14: style:inconclusive: Technically the member function 'GenomeIndex::getMajorVersion' can be const. [functionConst]
snap-2.0.3/SNAPLib/GenomeIndex.h:82:6: note: Technically the member function 'GenomeIndex::getMajorVersion' can be const.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1827:14: note: Technically the member function 'GenomeIndex::getMajorVersion' can be const.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1833:14: style:inconclusive: Technically the member function 'GenomeIndex::getMinorVersion' can be const. [functionConst]
snap-2.0.3/SNAPLib/GenomeIndex.h:83:6: note: Technically the member function 'GenomeIndex::getMinorVersion' can be const.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1833:14: note: Technically the member function 'GenomeIndex::getMinorVersion' can be const.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2160:14: style:inconclusive: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const. [functionConst]
snap-2.0.3/SNAPLib/GenomeIndex.h:303:10: note: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2160:14: note: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2287:14: style:inconclusive: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const. [functionConst]
snap-2.0.3/SNAPLib/GenomeIndex.h:304:10: note: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2287:14: note: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1733:2: warning: Class 'OverflowBackpointerAnchor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1733:2: warning: Class 'OverflowBackpointerAnchor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-2.0.3/SNAPLib/GenericFile_stdio.h:31:28: warning: The class 'GenericFile_stdio' defines member function with name 'open' also defined in its parent class 'GenericFile'. [duplInheritedMember]
snap-2.0.3/SNAPLib/GenericFile.h:41:25: note: Parent function 'GenericFile::open'
snap-2.0.3/SNAPLib/GenericFile_stdio.h:31:28: note: Derived function 'GenericFile_stdio::open'
snap-2.0.3/SNAPLib/FixedSizeSet.h:20:5: style: Class 'FixedSizeSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/FixedSizeVector.h:13:5: style: Class 'FixedSizeVector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:737:4: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:815:4: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:949:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:949:17: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:952:9: portability: %lld in format string (no. 1) requires 'long long' but the argument type is '_uint64 {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:952:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:952:9: portability: %lld in format string (no. 3) requires 'long long' but the argument type is '_uint64 {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:952:9: portability: %lld in format string (no. 4) requires 'long long' but the argument type is '_uint64 {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1007:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1007:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1007:5: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1007:5: portability: %lld in format string (no. 4) requires 'long long' but the argument type is '_uint64 {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1007:5: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1007:5: warning: %d in format string (no. 7) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1007:5: portability: %lld in format string (no. 8) requires 'long long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1007:5: warning: %d in format string (no. 10) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: warning: %d in format string (no. 2) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: warning: %d in format string (no. 3) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: portability: %lld in format string (no. 4) requires 'long long *' but the argument type is '_int64 * {aka signed long *}'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: warning: %d in format string (no. 5) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: warning: %d in format string (no. 6) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: warning: %d in format string (no. 7) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: portability: %lld in format string (no. 8) requires 'long long *' but the argument type is 'size_t * {aka unsigned long *}'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: warning: %d in format string (no. 9) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1879:24: warning: %d in format string (no. 10) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:486:91: warning: Either the condition 'NULL==genome' is redundant or there is possible null pointer dereference: genome. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:475:14: note: Assuming that condition 'NULL==genome' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:486:91: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:487:46: warning: Either the condition 'NULL==genome' is redundant or there is possible null pointer dereference: genome. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:475:14: note: Assuming that condition 'NULL==genome' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:487:46: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:489:29: warning: Either the condition 'NULL==genome' is redundant or there is possible null pointer dereference: genome. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:475:14: note: Assuming that condition 'NULL==genome' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:489:29: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:822:4: warning: Either the condition 'NULL==file' is redundant or there is possible null pointer dereference: file. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:817:13: note: Assuming that condition 'NULL==file' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:822:4: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1940:4: warning: Either the condition 'NULL==overflowTableFile' is redundant or there is possible null pointer dereference: overflowTableFile. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1935:13: note: Assuming that condition 'NULL==overflowTableFile' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1940:4: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1941:4: warning: Either the condition 'NULL==overflowTableFile' is redundant or there is possible null pointer dereference: overflowTableFile. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1935:13: note: Assuming that condition 'NULL==overflowTableFile' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1941:4: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2015:4: warning: Either the condition 'NULL==hashTableFile' is redundant or there is possible null pointer dereference: hashTableFile. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2010:13: note: Assuming that condition 'NULL==hashTableFile' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2015:4: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2016:4: warning: Either the condition 'NULL==hashTableFile' is redundant or there is possible null pointer dereference: hashTableFile. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2010:13: note: Assuming that condition 'NULL==hashTableFile' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2016:4: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2039:23: warning: Either the condition 'NULL==tablesFile' is redundant or there is possible null pointer dereference: tablesFile. [nullPointerRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2033:12: note: Assuming that condition 'NULL==tablesFile' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2039:23: note: Null pointer dereference
snap-2.0.3/SNAPLib/GenomeIndex.cpp:358:65: warning: Either the condition 'NULL==contigNameEnd' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:352:30: note: Assuming that condition 'NULL==contigNameEnd' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:358:65: note: Null pointer addition
snap-2.0.3/SNAPLib/GenomeIndex.cpp:359:51: warning: Either the condition 'NULL==contigNameEnd' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:352:30: note: Assuming that condition 'NULL==contigNameEnd' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:359:51: note: Null pointer addition
snap-2.0.3/SNAPLib/GenomeIndex.cpp:365:64: warning: Either the condition 'NULL==contigFlagsEnd' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:359:98: note: Assuming that condition 'NULL==contigFlagsEnd' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:365:64: note: Null pointer addition
snap-2.0.3/SNAPLib/GenomeIndex.cpp:373:74: warning: Either the condition 'NULL==projContigNameEnd' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:367:30: note: Assuming that condition 'NULL==projContigNameEnd' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:373:74: note: Null pointer addition
snap-2.0.3/SNAPLib/GenomeIndex.cpp:374:55: warning: Either the condition 'NULL==projContigNameEnd' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:367:30: note: Assuming that condition 'NULL==projContigNameEnd' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:374:55: note: Null pointer addition
snap-2.0.3/SNAPLib/GenomeIndex.cpp:380:60: warning: Either the condition 'NULL==projContigOffsetEnd' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:374:108: note: Assuming that condition 'NULL==projContigOffsetEnd' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:380:60: note: Null pointer addition
snap-2.0.3/SNAPLib/GenomeIndex.cpp:387:48: warning: Either the condition 'NULL==tmp' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:381:30: note: Assuming that condition 'NULL==tmp' is not redundant
snap-2.0.3/SNAPLib/GenomeIndex.cpp:387:48: note: Null pointer addition
snap-2.0.3/SNAPLib/GenomeIndex.cpp:522:43: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:772:34: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:774:34: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:827:25: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1339:46: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1442:45: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1684:10: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1684:38: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1686:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1686:46: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1696:10: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1696:36: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1698:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1698:44: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1768:41: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1803:15: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1814:15: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1953:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1955:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1967:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1971:29: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2326:17: style: C-style pointer casting [cstyleCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:828:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:833:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:974:53: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:974:86: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1555:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1556:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1968:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1972:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2116:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2142:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2228:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2262:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1554:14: style: The scope of the variable 'locationSize' can be reduced. [variableScope]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:527:97: style:inconclusive: Function 'BuildIndexToDirectory' argument 4 names different: declaration 'directory' definition 'directoryName'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/GenomeIndex.h:158:51: note: Function 'BuildIndexToDirectory' argument 4 names different: declaration 'directory' definition 'directoryName'.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:527:97: note: Function 'BuildIndexToDirectory' argument 4 names different: declaration 'directory' definition 'directoryName'.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1161:57: style:inconclusive: Function 'ComputeBiasTable' argument 2 names different: declaration 'seedSize' definition 'seedLen'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/GenomeIndex.h:178:60: note: Function 'ComputeBiasTable' argument 2 names different: declaration 'seedSize' definition 'seedLen'.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1161:57: note: Function 'ComputeBiasTable' argument 2 names different: declaration 'seedSize' definition 'seedLen'.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1809:60: style:inconclusive: Function 'loadFromFile' argument 1 names different: declaration 'tripFile' definition 'file'. [funcArgNamesDifferent]
snap-2.0.3/SNAPLib/GenomeIndex.h:137:27: note: Function 'loadFromFile' argument 1 names different: declaration 'tripFile' definition 'file'.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1809:60: note: Function 'loadFromFile' argument 1 names different: declaration 'tripFile' definition 'file'.
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1451:19: style: Local variable 'genome' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/GenomeIndex.h:90:19: note: Shadowed declaration
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1451:19: note: Shadow variable
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1452:14: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/GenomeIndex.h:87:9: note: Shadowed declaration
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1452:14: note: Shadow variable
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1610:24: style: Local variable 'entryValue' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1596:20: note: Shadowed declaration
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1610:24: note: Shadow variable
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1618:24: style: Local variable 'entryValue' shadows outer variable [shadowVariable]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1596:20: note: Shadowed declaration
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1618:24: note: Shadow variable
snap-2.0.3/SNAPLib/GenomeIndex.cpp:350:27: style: Variable 'contigNameStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:351:27: style: Variable 'contigNameEnd' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:365:27: style: Variable 'projContigNameStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:366:27: style: Variable 'projContigNameEnd' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:373:27: style: Variable 'projContigOffsetEnd' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:387:27: style: Variable 'projCigarStart' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:388:27: style: Variable 'projCigarEnd' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:848:28: style: Variable 'backpointer' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:974:11: style: Variable 'tableToWriteAsChar' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1034:21: style: Parameter 'biasTable' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1839:38: style: Parameter 'directoryName' can be declared as pointer to const [constParameterPointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:2142:17: style: Variable 'entry' can be declared as pointer to const [constVariablePointer]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1297:26: style: Variable 'distinctSeeds' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1299:23: style: Variable 'distinctSeeds' is assigned a value that is never used. [unreadVariable]
snap-2.0.3/SNAPLib/GenomeIndex.cpp:1450:20: style: Variable 'countOfBases' is assigned a value that is never used. [unreadVariable]
diff:
head snap-2.0.3/SNAPLib/AffineGap.cpp:126:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/AffineGap.cpp:347:25: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/AffineGap.cpp:347:32: style: Variable 'countM' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/AffineGap.cpp:369:25: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/AffineGap.cpp:442:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGap.cpp:442:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/AffineGap.cpp:73:21: performance:inconclusive: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/AffineGap.h:462:10: note: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/AffineGap.cpp:73:21: note: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
head snap-2.0.3/SNAPLib/AffineGap.h:204:26: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGap.h:204:27: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGap.h:44:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
2.17.0 snap-2.0.3/SNAPLib/AffineGap.h:462:10: performance:inconclusive: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/AffineGap.cpp:73:21: note: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/AffineGap.h:462:10: note: Technically the member function 'AffineGapWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:1086:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:1086:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:148:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:193:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:193:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:384:46: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:384:46: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:572:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:572:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:638:0: warning: Redundant code: Found unused function. [constStatement]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:638:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:812:46: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:812:46: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:95:31: performance:inconclusive: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/AffineGapVectorized.h:1404:10: note: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:95:31: note: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.h:1262:50: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.h:1262:50: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.h:1404:10: performance:inconclusive: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/AffineGapVectorized.cpp:95:31: note: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/AffineGapVectorized.h:1404:10: note: Technically the member function 'AffineGapVectorizedWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.h:348:32: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.h:348:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.h:743:50: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.h:743:50: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.h:921:32: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AffineGapVectorized.h:921:32: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/AffineGapVectorized.h:99:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
head snap-2.0.3/SNAPLib/AlignerContext.cpp:278:129: warning: Either the condition 'index==NULL' is redundant or there is possible null pointer dereference: index. [nullPointerRedundantCheck]
     snap-2.0.3/SNAPLib/AlignerContext.cpp:267:23: note: Assuming that condition 'index==NULL' is not redundant
     snap-2.0.3/SNAPLib/AlignerContext.cpp:278:129: note: Null pointer dereference
head snap-2.0.3/SNAPLib/AlignerOptions.cpp:1061:17: style:inconclusive: Technically the member function 'AlignerOptions::passFilter' can be const. [functionConst]
     snap-2.0.3/SNAPLib/AlignerOptions.h:183:10: note: Technically the member function 'AlignerOptions::passFilter' can be const.
     snap-2.0.3/SNAPLib/AlignerOptions.cpp:1061:17: note: Technically the member function 'AlignerOptions::passFilter' can be const.
2.17.0 snap-2.0.3/SNAPLib/AlignerOptions.h:183:10: style:inconclusive: Technically the member function 'AlignerOptions::passFilter' can be const. [functionConst]
     snap-2.0.3/SNAPLib/AlignerOptions.cpp:1061:17: note: Technically the member function 'AlignerOptions::passFilter' can be const.
     snap-2.0.3/SNAPLib/AlignerOptions.h:183:10: note: Technically the member function 'AlignerOptions::passFilter' can be const.
2.17.0 snap-2.0.3/SNAPLib/AlignerStats.cpp:100:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/AlignerStats.cpp:100:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/ApproximateCounter.cpp:29:30: style:inconclusive: Technically the member function 'ApproximateCounter::getCount' can be const. [functionConst]
     snap-2.0.3/SNAPLib/ApproximateCounter.h:13:14: note: Technically the member function 'ApproximateCounter::getCount' can be const.
     snap-2.0.3/SNAPLib/ApproximateCounter.cpp:29:30: note: Technically the member function 'ApproximateCounter::getCount' can be const.
2.17.0 snap-2.0.3/SNAPLib/ApproximateCounter.h:13:14: style:inconclusive: Technically the member function 'ApproximateCounter::getCount' can be const. [functionConst]
     snap-2.0.3/SNAPLib/ApproximateCounter.cpp:29:30: note: Technically the member function 'ApproximateCounter::getCount' can be const.
     snap-2.0.3/SNAPLib/ApproximateCounter.h:13:14: note: Technically the member function 'ApproximateCounter::getCount' can be const.
head snap-2.0.3/SNAPLib/Bam.cpp:1006:18: style: Variable 'genomeLen' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/Bam.cpp:1007:34: style: Variable 'contigNumbersByOriginalOrder' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1109:79: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1109:79: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1141:79: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1141:79: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1249:29: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1249:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1388:56: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1388:56: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1452:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1452:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1533:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1533:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1554:17: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1554:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1557:31: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1557:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1557:55: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1562:17: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1562:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1565:20: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1565:20: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1571:9: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1571:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1575:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1575:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1575:47: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1582:9: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1582:9: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1586:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1586:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1586:47: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:158:11: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:158:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1593:13: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1593:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1596:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1596:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1596:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1604:13: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1604:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1607:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1607:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1607:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1620:13: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1620:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1623:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1623:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1623:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1633:13: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1633:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1645:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1645:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1645:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1691:17: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1691:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1695:31: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1695:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1695:55: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1708:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1708:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1720:22: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1720:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1727:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1727:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:173:12: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:173:12: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1752:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1752:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1760:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1760:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1773:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1773:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1786:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1786:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1790:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1790:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1791:22: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1791:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1895:56: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1895:56: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:1971:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:1971:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:207:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:207:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2080:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2080:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2085:15: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2085:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2089:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2089:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2094:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2094:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2103:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2103:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2105:34: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2105:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2109:31: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2109:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2177:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2177:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2182:15: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2182:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2186:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2186:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2191:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2191:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2200:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2200:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2202:34: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2202:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2206:31: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2206:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2326:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2335:20: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2346:15: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2346:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2348:12: style: Variable 'oldOffset' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/Bam.cpp:2357:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:2368:45: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:2368:45: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:292:33: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:292:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:317:33: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:317:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:3449:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:3449:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.cpp:528:23: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
head snap-2.0.3/SNAPLib/Bam.cpp:528:56: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
head snap-2.0.3/SNAPLib/Bam.cpp:529:23: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:644:29: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:644:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:656:36: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:656:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:709:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:709:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:891:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:891:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.cpp:988:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.cpp:988:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:109:29: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:109:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:112:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:115:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:121:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:124:36: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:124:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:124:57: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:127:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:127:41: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:127:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:219:18: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:219:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:245:53: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:245:53: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:245:69: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:278:83: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:278:84: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:318:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:318:39: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:318:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:353:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:368:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:368:46: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:368:46: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:372:43: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:372:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:372:62: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:384:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:384:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:384:54: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:52:47: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:52:47: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:55:16: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:55:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:58:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:58:49: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:58:49: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:78:18: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:78:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:81:16: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:81:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Bam.h:84:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Bam.h:84:49: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Bam.h:84:49: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/BaseAligner.cpp:1080:26: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/BaseAligner.cpp:1080:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/BaseAligner.cpp:1786:18: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/BaseAligner.cpp:1786:19: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/BaseAligner.cpp:1892:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/BaseAligner.cpp:1892:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/BaseAligner.cpp:1913:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/BaseAligner.cpp:1913:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/BaseAligner.cpp:2280:29: style:inconclusive: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BaseAligner.h:328:14: note: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const.
     snap-2.0.3/SNAPLib/BaseAligner.cpp:2280:29: note: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const.
head snap-2.0.3/SNAPLib/BaseAligner.cpp:2535:14: style:inconclusive: Technically the member function 'BaseAligner::scoreLimit' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BaseAligner.h:146:16: note: Technically the member function 'BaseAligner::scoreLimit' can be const.
     snap-2.0.3/SNAPLib/BaseAligner.cpp:2535:14: note: Technically the member function 'BaseAligner::scoreLimit' can be const.
2.17.0 snap-2.0.3/SNAPLib/BaseAligner.h:146:16: style:inconclusive: Technically the member function 'BaseAligner::scoreLimit' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BaseAligner.cpp:2535:14: note: Technically the member function 'BaseAligner::scoreLimit' can be const.
     snap-2.0.3/SNAPLib/BaseAligner.h:146:16: note: Technically the member function 'BaseAligner::scoreLimit' can be const.
2.17.0 snap-2.0.3/SNAPLib/BaseAligner.h:328:14: style:inconclusive: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BaseAligner.cpp:2280:29: note: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const.
     snap-2.0.3/SNAPLib/BaseAligner.h:328:14: note: Technically the member function 'BaseAligner::ScoreSet::fillInSingleAlignmentResult' can be const.
2.17.0 snap-2.0.3/SNAPLib/BigAlloc.cpp:466:7: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/BigAlloc.cpp:466:7: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/BigAlloc.cpp:467:26: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     snap-2.0.3/SNAPLib/BigAlloc.cpp:450:30: note: Assuming allocation function fails
     snap-2.0.3/SNAPLib/BigAlloc.cpp:450:17: note: Assignment 'mem=(char*)mmap(NULL,sizeToAllocate,PROT_READ|PROT_WRITE,flags,-1,0)', assigned value is 0
     snap-2.0.3/SNAPLib/BigAlloc.cpp:467:26: note: Null pointer addition
head snap-2.0.3/SNAPLib/BigAlloc.cpp:467:26: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     snap-2.0.3/SNAPLib/BigAlloc.cpp:450:30: note: Assuming allocation function fails
     snap-2.0.3/SNAPLib/BigAlloc.cpp:450:17: note: Assignment 'mem=(char*)mmap(NULL,sizeToAllocate,PROT_READ|PROT_WRITE,flags,-1,0)', assigned value is 0
     snap-2.0.3/SNAPLib/BigAlloc.cpp:467:26: note: Null pointer addition
2.17.0 snap-2.0.3/SNAPLib/BigAlloc.cpp:476:30: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/BigAlloc.cpp:476:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/BigAlloc.cpp:524:19: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/BigAlloc.cpp:524:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/BigAlloc.cpp:537:15: style:inconclusive: Technically the member function 'BigAllocator::amountAllocated' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BigAlloc.h:97:12: note: Technically the member function 'BigAllocator::amountAllocated' can be const.
     snap-2.0.3/SNAPLib/BigAlloc.cpp:537:15: note: Technically the member function 'BigAllocator::amountAllocated' can be const.
2.17.0 snap-2.0.3/SNAPLib/BigAlloc.cpp:565:31: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/BigAlloc.cpp:565:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/BigAlloc.cpp:576:15: style:inconclusive: Technically the member function 'BigAllocator::checkCanaries' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BigAlloc.h:100:10: note: Technically the member function 'BigAllocator::checkCanaries' can be const.
     snap-2.0.3/SNAPLib/BigAlloc.cpp:576:15: note: Technically the member function 'BigAllocator::checkCanaries' can be const.
2.17.0 snap-2.0.3/SNAPLib/BigAlloc.h:100:10: style:inconclusive: Technically the member function 'BigAllocator::checkCanaries' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BigAlloc.cpp:576:15: note: Technically the member function 'BigAllocator::checkCanaries' can be const.
     snap-2.0.3/SNAPLib/BigAlloc.h:100:10: note: Technically the member function 'BigAllocator::checkCanaries' can be const.
2.17.0 snap-2.0.3/SNAPLib/BigAlloc.h:97:12: style:inconclusive: Technically the member function 'BigAllocator::amountAllocated' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BigAlloc.cpp:537:15: note: Technically the member function 'BigAllocator::amountAllocated' can be const.
     snap-2.0.3/SNAPLib/BigAlloc.h:97:12: note: Technically the member function 'BigAllocator::amountAllocated' can be const.
head snap-2.0.3/SNAPLib/BufferedAsync.cpp:80:22: style:inconclusive: Technically the member function 'BufferedAsyncReader::atEnd' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BufferedAsync.h:30:25: note: Technically the member function 'BufferedAsyncReader::atEnd' can be const.
     snap-2.0.3/SNAPLib/BufferedAsync.cpp:80:22: note: Technically the member function 'BufferedAsyncReader::atEnd' can be const.
2.17.0 snap-2.0.3/SNAPLib/BufferedAsync.h:30:25: style:inconclusive: Technically the member function 'BufferedAsyncReader::atEnd' can be const. [functionConst]
     snap-2.0.3/SNAPLib/BufferedAsync.cpp:80:22: note: Technically the member function 'BufferedAsyncReader::atEnd' can be const.
     snap-2.0.3/SNAPLib/BufferedAsync.h:30:25: note: Technically the member function 'BufferedAsyncReader::atEnd' can be const.
head snap-2.0.3/SNAPLib/CommandProcessor.cpp:161:35: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/CommandProcessor.cpp:161:36: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Compat.cpp:1333:6: error: #error "Don't know how to get time in nanos on your platform" [preprocessorErrorDirective]
2.17.0 snap-2.0.3/SNAPLib/DataReader.cpp:2011:24: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/DataReader.cpp:2011:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/DataReader.cpp:2013:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/DataReader.cpp:2013:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/DataReader.cpp:2162:34: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/DataReader.cpp:2162:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/DataReader.cpp:2189:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/DataReader.cpp:2189:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/DataReader.cpp:2221:13: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/DataReader.cpp:2256:35: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/DataReader.cpp:2256:35: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/DataReader.cpp:2309:13: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/DataReader.cpp:2685:12: style: Variable 'oldAmount' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/DataWriter.cpp:275:33: style: Variable 'encode' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/DataWriter.cpp:306:14: style:inconclusive: Technically the member function 'FileEncoder::getOffsets' can be const. [functionConst]
     snap-2.0.3/SNAPLib/DataWriter.h:210:10: note: Technically the member function 'FileEncoder::getOffsets' can be const.
     snap-2.0.3/SNAPLib/DataWriter.cpp:306:14: note: Technically the member function 'FileEncoder::getOffsets' can be const.
2.17.0 snap-2.0.3/SNAPLib/DataWriter.h:210:10: style:inconclusive: Technically the member function 'FileEncoder::getOffsets' can be const. [functionConst]
     snap-2.0.3/SNAPLib/DataWriter.cpp:306:14: note: Technically the member function 'FileEncoder::getOffsets' can be const.
     snap-2.0.3/SNAPLib/DataWriter.h:210:10: note: Technically the member function 'FileEncoder::getOffsets' can be const.
2.17.0 snap-2.0.3/SNAPLib/FixedSizeMap.h:241:17: style: Unused private function: 'FixedSizeMap::checkBloomFilter' [unusedPrivateFunction]
head snap-2.0.3/SNAPLib/FixedSizeMap.h:241:17: style: Unused private function: 'FixedSizeMap::checkBloomFilter' [unusedPrivateFunction]
     snap-2.0.3/SNAPLib/FixedSizeMap.h:241:17: note: Unused private function: 'FixedSizeMap::checkBloomFilter'
     snap-2.0.3/SNAPLib/FixedSizeMap.h:241:17: note: Unused private function: 'FixedSizeMap::checkBloomFilter'
2.17.0 snap-2.0.3/SNAPLib/FixedSizeMap.h:250:17: style: Unused private function: 'FixedSizeMap::addToBloomFilter' [unusedPrivateFunction]
head snap-2.0.3/SNAPLib/FixedSizeMap.h:250:17: style: Unused private function: 'FixedSizeMap::addToBloomFilter' [unusedPrivateFunction]
     snap-2.0.3/SNAPLib/FixedSizeMap.h:250:17: note: Unused private function: 'FixedSizeMap::addToBloomFilter'
     snap-2.0.3/SNAPLib/FixedSizeMap.h:250:17: note: Unused private function: 'FixedSizeMap::addToBloomFilter'
head snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:27:105: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenericFile_Blob.cpp:27:152: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenericFile_map.cpp:41:140: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GenericFile_map.cpp:41:141: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenericFile_map.cpp:69:6: style: Variable 'pageSize' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/GenericFile_map.cpp:74:13: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenericFile_map.cpp:74:13: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Genome.cpp:267:58: style: Condition 'OriginalContigNumToInt(originalContigNumber)<0' is always false [knownConditionTrueFalse]
     snap-2.0.3/SNAPLib/Genome.cpp:267:35: note: Calling function 'OriginalContigNumToInt' returns !<=-1
     snap-2.0.3/SNAPLib/Genome.cpp:267:58: note: Condition 'OriginalContigNumToInt(originalContigNumber)<0' is always false
head snap-2.0.3/SNAPLib/Genome.cpp:394:21: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/Genome.cpp:415:39: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Genome.cpp:415:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:1555:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1555:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:1556:21: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1556:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1684:10: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:1684:11: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1684:38: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1686:17: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:1686:18: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1686:46: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1696:10: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:1696:11: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1696:36: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1698:17: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:1698:18: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1698:44: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1827:14: style:inconclusive: Technically the member function 'GenomeIndex::getMajorVersion' can be const. [functionConst]
     snap-2.0.3/SNAPLib/GenomeIndex.h:82:6: note: Technically the member function 'GenomeIndex::getMajorVersion' can be const.
     snap-2.0.3/SNAPLib/GenomeIndex.cpp:1827:14: note: Technically the member function 'GenomeIndex::getMajorVersion' can be const.
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1833:14: style:inconclusive: Technically the member function 'GenomeIndex::getMinorVersion' can be const. [functionConst]
     snap-2.0.3/SNAPLib/GenomeIndex.h:83:6: note: Technically the member function 'GenomeIndex::getMinorVersion' can be const.
     snap-2.0.3/SNAPLib/GenomeIndex.cpp:1833:14: note: Technically the member function 'GenomeIndex::getMinorVersion' can be const.
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:1968:22: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1968:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:1972:22: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:1972:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:2116:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:2116:34: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:2142:25: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:2142:25: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:2160:14: style:inconclusive: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const. [functionConst]
     snap-2.0.3/SNAPLib/GenomeIndex.h:303:10: note: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const.
     snap-2.0.3/SNAPLib/GenomeIndex.cpp:2160:14: note: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const.
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:2228:29: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:2228:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:2262:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:2262:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:2287:14: style:inconclusive: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const. [functionConst]
     snap-2.0.3/SNAPLib/GenomeIndex.h:304:10: note: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const.
     snap-2.0.3/SNAPLib/GenomeIndex.cpp:2287:14: note: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const.
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:2326:17: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:2326:18: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:828:30: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:828:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:833:28: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:833:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.cpp:974:53: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:974:53: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/GenomeIndex.cpp:974:86: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.h:303:10: style:inconclusive: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const. [functionConst]
     snap-2.0.3/SNAPLib/GenomeIndex.cpp:2160:14: note: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const.
     snap-2.0.3/SNAPLib/GenomeIndex.h:303:10: note: Technically the member function 'GenomeIndex::fillInLookedUpResults32' can be const.
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.h:304:10: style:inconclusive: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const. [functionConst]
     snap-2.0.3/SNAPLib/GenomeIndex.cpp:2287:14: note: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const.
     snap-2.0.3/SNAPLib/GenomeIndex.h:304:10: note: Technically the member function 'GenomeIndex::fillInLookedUpResults' can be const.
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.h:82:6: style:inconclusive: Technically the member function 'GenomeIndex::getMajorVersion' can be const. [functionConst]
     snap-2.0.3/SNAPLib/GenomeIndex.cpp:1827:14: note: Technically the member function 'GenomeIndex::getMajorVersion' can be const.
     snap-2.0.3/SNAPLib/GenomeIndex.h:82:6: note: Technically the member function 'GenomeIndex::getMajorVersion' can be const.
2.17.0 snap-2.0.3/SNAPLib/GenomeIndex.h:83:6: style:inconclusive: Technically the member function 'GenomeIndex::getMinorVersion' can be const. [functionConst]
     snap-2.0.3/SNAPLib/GenomeIndex.cpp:1833:14: note: Technically the member function 'GenomeIndex::getMinorVersion' can be const.
     snap-2.0.3/SNAPLib/GenomeIndex.h:83:6: note: Technically the member function 'GenomeIndex::getMinorVersion' can be const.
2.17.0 snap-2.0.3/SNAPLib/GzipDataWriter.cpp:182:15: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GzipDataWriter.cpp:182:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GzipDataWriter.cpp:220:43: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GzipDataWriter.cpp:220:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/GzipDataWriter.cpp:228:12: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/GzipDataWriter.cpp:290:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GzipDataWriter.cpp:290:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GzipDataWriter.cpp:292:24: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GzipDataWriter.cpp:292:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GzipDataWriter.cpp:338:11: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GzipDataWriter.cpp:338:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/GzipDataWriter.cpp:404:29: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/GzipDataWriter.cpp:404:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/GzipDataWriter.cpp:464:82: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/GzipDataWriter.h:85:10: style: Unused private function: 'GzipWriterFilterSupplier::addTranslation' [unusedPrivateFunction]
head snap-2.0.3/SNAPLib/GzipDataWriter.h:85:10: style: Unused private function: 'GzipWriterFilterSupplier::addTranslation' [unusedPrivateFunction]
     snap-2.0.3/SNAPLib/GzipDataWriter.h:85:10: note: Unused private function: 'GzipWriterFilterSupplier::addTranslation'
     snap-2.0.3/SNAPLib/GzipDataWriter.h:85:10: note: Unused private function: 'GzipWriterFilterSupplier::addTranslation'
2.17.0 snap-2.0.3/SNAPLib/HashTable.h:123:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/HashTable.h:123:27: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/HashTable.h:187:28: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/HashTable.h:187:29: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3010:9: style: Variable 'seedLen' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3313:9: style: Variable 'origScoreLimit' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3565:1: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3565:1: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3566:1: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3566:1: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3641:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3641:35: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3642:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3642:35: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3644:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3644:35: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3645:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3645:35: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3938:46: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const. [functionConst]
     snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:745:14: note: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const.
     snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3938:46: note: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const.
head snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3962:35: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const. [functionConst]
     snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:770:16: note: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const.
     snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3962:35: note: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const.
2.17.0 snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:745:14: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const. [functionConst]
     snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3938:46: note: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const.
     snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:745:14: note: Technically the member function 'IntersectingPairedEndAligner::ScoreSet::fillInResult' can be const.
2.17.0 snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:770:16: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const. [functionConst]
     snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.cpp:3962:35: note: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const.
     snap-2.0.3/SNAPLib/IntersectingPairedEndAligner.h:770:16: note: Technically the member function 'IntersectingPairedEndAligner::computeScoreLimit' can be const.
head snap-2.0.3/SNAPLib/LandauVishkin.cpp:130:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/LandauVishkin.cpp:173:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/LandauVishkin.cpp:173:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/LandauVishkin.cpp:173:41: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/LandauVishkin.cpp:244:39: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/LandauVishkin.cpp:244:39: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/LandauVishkin.cpp:244:57: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/LandauVishkin.cpp:529:23: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/LandauVishkin.cpp:529:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/LandauVishkin.cpp:77:25: performance:inconclusive: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/LandauVishkin.h:510:10: note: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/LandauVishkin.cpp:77:25: note: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
head snap-2.0.3/SNAPLib/LandauVishkin.h:202:29: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/LandauVishkin.h:213:29: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/LandauVishkin.h:228:29: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/LandauVishkin.h:384:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/LandauVishkin.h:384:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/LandauVishkin.h:384:31: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/LandauVishkin.h:386:21: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/LandauVishkin.h:386:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/LandauVishkin.h:388:14: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/LandauVishkin.h:388:14: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/LandauVishkin.h:510:10: performance:inconclusive: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/LandauVishkin.cpp:77:25: note: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/LandauVishkin.h:510:10: note: Technically the member function 'LandauVishkinWithCigar::writeCigar' can be static (but you may consider moving to unnamed namespace).
2.17.0 snap-2.0.3/SNAPLib/LandauVishkin.h:76:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TEXT_DIRECTION [valueFlowBailoutIncompleteVar]
2.17.0 snap-2.0.3/SNAPLib/PairedAligner.cpp:190:33: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/PairedAligner.cpp:190:33: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/PairedAligner.cpp:374:38: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/PairedAligner.cpp:374:38: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/PairedAligner.cpp:520:65: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/PairedAligner.cpp:520:73: warning: Obsolete function 'alloca' called. [allocaCalled]
2.17.0 snap-2.0.3/SNAPLib/PairedAligner.cpp:894:29: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/PairedAligner.cpp:894:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:266:38: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/PairedReadMatcher.cpp:270:38: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/ParallelTask.cpp:113:16: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/RangeSplitter.cpp:85:9: style: Variable 'oldPosition' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/Read.cpp:43:57: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Read.cpp:43:65: warning: Obsolete function 'alloca' called. [allocaCalled]
head snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:110:20: performance:inconclusive: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/ReadSupplierQueue.h:176:10: note: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:110:20: note: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace).
head snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:123:10: style: Variable 'worked' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:328:20: style:inconclusive: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const. [functionConst]
     snap-2.0.3/SNAPLib/ReadSupplierQueue.h:151:10: note: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const.
     snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:328:20: note: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const.
2.17.0 snap-2.0.3/SNAPLib/ReadSupplierQueue.h:151:10: style:inconclusive: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const. [functionConst]
     snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:328:20: note: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const.
     snap-2.0.3/SNAPLib/ReadSupplierQueue.h:151:10: note: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const.
2.17.0 snap-2.0.3/SNAPLib/ReadSupplierQueue.h:176:10: performance:inconclusive: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/ReadSupplierQueue.cpp:110:20: note: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/ReadSupplierQueue.h:176:10: note: Technically the member function 'ReadSupplierQueue::deleteElementsOnQueue' can be static (but you may consider moving to unnamed namespace).
head snap-2.0.3/SNAPLib/ReadWriter.cpp:226:49: style: Variable 'cumulativeAddBackClipping' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/SAM.cpp:1142:36: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/SAM.cpp:1142:36: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/SAM.cpp:1287:24: style: Variable 'genomeLen' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/SAM.cpp:1474:17: style: Variable 'cigar' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/SAM.cpp:1548:9: style: Variable 'editDistance' is assigned a value that is never used. [unreadVariable]
2.17.0 snap-2.0.3/SNAPLib/SAM.cpp:1771:44: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/SAM.cpp:1771:44: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/SAM.cpp:1771:64: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/SAM.cpp:2025:40: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/SAM.cpp:2025:40: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/SAM.cpp:2025:60: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/SAM.cpp:2261:40: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/SAM.cpp:2261:40: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/SAM.cpp:2261:59: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/SAM.cpp:2874:52: warning: Either the condition 'NULL==contig' is redundant or there is possible null pointer dereference: contig. [nullPointerRedundantCheck]
     snap-2.0.3/SNAPLib/SAM.cpp:2868:11: note: Assuming that condition 'NULL==contig' is not redundant
     snap-2.0.3/SNAPLib/SAM.cpp:2874:52: note: Null pointer dereference
2.17.0 snap-2.0.3/SNAPLib/SAM.cpp:3128:10: performance:inconclusive: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/SAM.cpp:3198:12: note: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/SAM.cpp:3128:10: note: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace).
2.17.0 snap-2.0.3/SNAPLib/SAM.cpp:3130:10: performance:inconclusive: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/SAM.cpp:3343:12: note: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/SAM.cpp:3130:10: note: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace).
head snap-2.0.3/SNAPLib/SAM.cpp:3198:12: performance:inconclusive: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/SAM.cpp:3128:10: note: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/SAM.cpp:3198:12: note: Technically the member function 'SAMFilter::getAlignmentInfo' can be static (but you may consider moving to unnamed namespace).
head snap-2.0.3/SNAPLib/SAM.cpp:3343:12: performance:inconclusive: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     snap-2.0.3/SNAPLib/SAM.cpp:3130:10: note: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace).
     snap-2.0.3/SNAPLib/SAM.cpp:3343:12: note: Technically the member function 'SAMFilter::updateSAMLine' can be static (but you may consider moving to unnamed namespace).
2.17.0 snap-2.0.3/SNAPLib/SAM.cpp:45:15: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/SAM.cpp:45:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/SAM.cpp:45:34: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/SAM.cpp:545:11: style: Variable 'prev' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/SAM.cpp:963:24: style: Variable 'splitter' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/SAM.h:386:13: style: Variable 'fieldsScanned' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1371:35: style: Condition 'nBlocksThisThread==0' is always false [knownConditionTrueFalse]
     snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1356:28: note: Assignment 'minPerThread=2', assigned value is 2
     snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1370:37: note: Assignment 'nBlocksThisThread=(int)((blocks.size()-nBlocksAssigned)<((minPerThread)>((blocks.size()-nBlocksAssigned+(nLeafThreads-i-1))/(nLeafThreads-i))?(minPerThread):((blocks.size()-nBlocksAssigned+(nLeafThreads-i-1))/(nLeafThreads-i)))?(blocks.size()-nBlocksAssigned):((minPerThread)>((blocks.size()-nBlocksAssigned+(nLeafThreads-i-1))/(nLeafThreads-i))?(minPerThread):((blocks.size()-nBlocksAssigned+(nLeafThreads-i-1))/(nLeafThreads-i))))', assigned value is 2
     snap-2.0.3/SNAPLib/SortedDataWriter.cpp:1371:35: note: Condition 'nBlocksThisThread==0' is always false
head snap-2.0.3/SNAPLib/Util.cpp:289:13: style: Variable 'amountAlreadyAdvanced' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/Util.cpp:357:12: style: Variable 'filenameLen' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/SNAPLib/Util.cpp:64:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Util.cpp:64:42: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/Util.cpp:64:43: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/Util.cpp:70:20: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Util.cpp:70:20: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/Util.cpp:71:39: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/Util.cpp:71:40: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Util.h:292:26: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/Util.h:292:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Util.h:303:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Util.h:303:31: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Util.h:321:28: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Util.h:321:29: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Util.h:352:26: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/Util.h:352:27: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Util.h:364:30: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/Util.h:364:31: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/Util.h:383:27: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/Util.h:383:28: style: C-style pointer casting [cstyleCast]
2.17.0 snap-2.0.3/SNAPLib/VariableSizeMap.h:278:22: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/VariableSizeMap.h:278:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/VariableSizeMap.h:290:22: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/VariableSizeMap.h:290:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
2.17.0 snap-2.0.3/SNAPLib/VariableSizeMap.h:56:19: style: C-style pointer casting [cstyleCast]
head snap-2.0.3/SNAPLib/VariableSizeMap.h:56:19: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/SNAPLib/VariableSizeVector.h:192:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
head snap-2.0.3/apps/ComputeROC/ComputeROC.cpp:425:9: style: Variable 'maxEditDistanceSeen' is assigned a value that is never used. [unreadVariable]
head snap-2.0.3/import/pdclibhdfs/src/jni_helper.c:937:26: style: Variable 'cnt' is assigned a value that is never used. [unreadVariable]


DONE