2024-04-14 16:28
ftp://ftp.de.debian.org/debian/pool/main/b/biobambam2/biobambam2_2.0.185+ds.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j1
platform: Linux-5.15.0-102-generic-x86_64-with-glibc2.35
python: 3.10.12
client-version: 1.3.56
compiler: g++ (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0
cppcheck: head 2.13.0
head-info: 01c049d (2024-04-13 21:28:19 +0200)
count: 748 511
elapsed-time: 79.4 92.0
head-timing-info:

old-timing-info:

head results:
biobambam2-2.0.185-release-20221211202123/src/biobambam2/ClipAdapters.cpp:125:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/ClipReinsert.cpp:33:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/DepthInterval.cpp:29:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable refid [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/Licensing.cpp:27:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_NAME [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/Licensing.cpp:35:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/Licensing.cpp:49:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/ResetAlignment.cpp:47:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIBMAUS2_BAMBAM_FUNMAP [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/RunEOFFilter.cpp:37:102: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/Strip12.cpp:38:18: style: Variable 'ranka' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/Strip12.cpp:42:10: style: Variable 'ranka' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/Strip12.cpp:43:10: style: Variable 'ranka' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/biobambam2/UpdateNumericalIndex.cpp:61:101: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bam12auxmerge.cpp:79:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bam12auxmerge.cpp:475:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bam12auxmerge.cpp:45:35: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bam12split.cpp:57:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bam12split.cpp:194:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bam12strip.cpp:57:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bam12strip.cpp:188:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamadapterclip.cpp:54:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamadapterclip.cpp:200:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamadapterclip.cpp:42:35: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bamadapterfind.cpp:869:0: error: #error "Neither PTHREAD_MUTEX_RECURSIVE_NP nor PTHREAD_MUTEX_RECURSIVE are supported for setting up recursive POSIX mutexes" [preprocessorErrorDirective]
biobambam2-2.0.185-release-20221211202123/src/programs/bamadapterhistogram.cpp:49:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamadapterhistogram.cpp:149:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamaddne.cpp:55:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamaddne.cpp:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamaddne.cpp:208:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamalignfrac.cpp:55:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamalignfrac.cpp:234:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge.cpp:74:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable line [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge.cpp:222:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:535:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_NULL [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:557:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_OK [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1112:106: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1196:105: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pa [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1224:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pa [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1241:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pa [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1266:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pa [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1284:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIBMAUS2_BAMBAM_FREAD1 [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1537:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1718:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable streamid [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2250:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2521:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2881:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerrlock [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2960:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerrlock [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3044:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bamMergeQueueFSHLock [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3356:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerrlock [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3436:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3575:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:96:2: warning:inconclusive: Member variable 'ChecksumsAllocator::bamheader' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:128:2: warning:inconclusive: Member variable 'AlignmentTraceContainerAllocator::bamheader' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:146:2: warning:inconclusive: Member variable 'UPointerPair::pa' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:146:2: warning:inconclusive: Member variable 'UPointerPair::pe' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:163:2: warning: Member variable 'UPointerPairList::Ao' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:163:2: warning: Member variable 'UPointerPairList::Ap' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:274:2: warning: Member variable 'DataBlock::bamMergeNext' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:274:2: warning: Member variable 'DataBlock::bamMergeNumPackages' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:274:2: warning: Member variable 'DataBlock::bamMergeNumPackagesProcessed' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:274:2: warning: Member variable 'DataBlock::bamMergeNumPackagesAll' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:365:2: warning: Member variable 'DataBlockAllocator::putbackspace' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:576:2: warning: Member variable 'BlockReadStreamInfo::crc32digest' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:624:2: warning: Member variable 'BlockReadStreamInfo::crc32digest' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1143:2: warning:inconclusive: Member variable 'BamMergeEntry::from' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1143:2: warning:inconclusive: Member variable 'BamMergeEntry::to' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1252:2: warning:inconclusive: Member variable 'HeapEntry::from' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1252:2: warning:inconclusive: Member variable 'HeapEntry::to' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:901:2: style: Struct 'BlockProcessPackage' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1219:2: style: Struct 'NameGet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1236:2: style: Struct 'FlagGet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1308:2: style: Struct 'HeapEntryComparator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2503:15: style: The function 'blockReadQueueEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:781:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2503:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2827:15: style: The function 'blockReadReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:787:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2827:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2832:15: style: The function 'blockProcessReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:927:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2832:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2837:15: style: The function 'blockBamMergePackageReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1381:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2837:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2842:15: style: The function 'blockBamMergeCompressPackageReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2189:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2842:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2847:15: style: The function 'returnDecompressedBlockEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:793:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2847:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2949:15: style: The function 'blockProcessBamHeaderFinishedEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:951:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2949:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3036:15: style: The function 'blockProcessEnqueParsedBamBlockEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:957:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3036:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3262:15: style: The function 'blockBamMergePackageFinishedEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1387:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3262:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3311:15: style: The function 'blockBamMergeCompressPackageFinishedEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2195:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3311:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3128:27: style: Condition 'ok' is always true [knownConditionTrueFalse]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3122:9: note: Assuming that condition 'ok' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3128:27: note: Condition 'ok' is always true
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2481:25: style: The scope of the variable 'info' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1830:25: style: Local variable 'i' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1756:21: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1830:25: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2892:59: style: Local variable 'slock' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2887:28: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2892:59: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3098:27: style: Local variable 'BBMP' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2337:33: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3098:27: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3251:27: style: Local variable 'BBMP' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2337:33: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3251:27: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3278:35: style: Local variable 'BBMCP' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2338:41: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3278:35: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1039:16: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1089:8: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3047:10: style: Variable 'VL[i]' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxsort.cpp:56:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxsort.cpp:186:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bambisect.cpp:80:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bambisect.cpp:175:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bambisect.cpp:50:3: warning:inconclusive: Member variable 'StackNode::parent' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bambisect.cpp:50:3: warning:inconclusive: Member variable 'StackNode::visit' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bambisect.cpp:50:3: warning:inconclusive: Member variable 'StackNode::subvisit' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bambisect.cpp:50:3: warning:inconclusive: Member variable 'StackNode::from' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bambisect.cpp:50:3: warning:inconclusive: Member variable 'StackNode::to' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcat.cpp:56:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcat.cpp:69:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcat.cpp:201:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamchecksort.cpp:76:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamchecksort.cpp:147:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamclipXT.cpp:49:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamclipXT.cpp:189:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamclipreinsert.cpp:48:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamclipreinsert.cpp:192:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:99:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:146:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:224:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:307:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:458:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:845:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1069:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1361:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1421:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:120:2: style: Struct 'BamToFastQInputFileStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:126:2: style: Struct 'BamToFastQInputFileStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:202:2: style: Struct 'RGReplaceInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:178:30: style: The scope of the variable 'vreadgroups' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:44:47: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1006:32: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1007:34: style: Variable 'inputfilename' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1333:32: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1334:34: style: Variable 'inputfilename' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:527:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:592:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:671:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1059:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1304:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3023:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3219:161: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3293:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3311:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3341:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4177:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4266:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:136:2: warning:inconclusive: Member variable 'BamAlignmentHeapElement::start' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:136:2: warning:inconclusive: Member variable 'BamAlignmentHeapElement::end' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:136:2: warning:inconclusive: Member variable 'BamAlignmentHeapElement::readid' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:254:2: warning:inconclusive: Member variable 'KmerPos::readpos' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:254:2: warning:inconclusive: Member variable 'KmerPos::readid' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:354:2: warning:inconclusive: Member variable 'KmerFreq::k' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:354:2: warning:inconclusive: Member variable 'KmerFreq::kcode' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:354:2: warning:inconclusive: Member variable 'KmerFreq::freq' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:740:2: warning:inconclusive: Member variable 'BranchPoint::k' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:740:2: warning:inconclusive: Member variable 'BranchPoint::kmer' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:832:2: warning:inconclusive: Member variable 'KmerLink::k' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:832:2: warning:inconclusive: Member variable 'KmerLink::kfrom' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:832:2: warning:inconclusive: Member variable 'KmerLink::kto' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:832:2: warning:inconclusive: Member variable 'KmerLink::fromfreq' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:832:2: warning:inconclusive: Member variable 'KmerLink::tofreq' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:832:2: warning:inconclusive: Member variable 'KmerLink::rid_start' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:832:2: warning:inconclusive: Member variable 'KmerLink::rid_end' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:918:2: warning:inconclusive: Member variable 'BranchLink::weight' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:918:2: warning:inconclusive: Member variable 'BranchLink::fromweight' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:918:2: warning:inconclusive: Member variable 'BranchLink::toweight' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:918:2: warning:inconclusive: Member variable 'BranchLink::length' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:918:2: warning:inconclusive: Member variable 'BranchLink::link_start' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:918:2: warning:inconclusive: Member variable 'BranchLink::link_end' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1029:2: warning:inconclusive: Member variable 'ConsensusPart::from' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1029:2: warning:inconclusive: Member variable 'ConsensusPart::to' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1130:2: warning:inconclusive: Member variable 'Range::from' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1130:2: warning:inconclusive: Member variable 'Range::to' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3165:2: warning:inconclusive: Member variable 'RefEntry::id' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:859:7: style:inconclusive: Technically the member function 'KmerLinkFromComparator::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:867:7: style:inconclusive: Technically the member function 'KmerLinkToComparator::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:875:7: style:inconclusive: Technically the member function 'KmerLinkToPosComparator::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:886:7: style:inconclusive: Technically the member function 'KmerLinkFromPosComparator::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:984:7: style:inconclusive: Technically the member function 'BranchLinkFromComparator::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:992:7: style:inconclusive: Technically the member function 'BranchLinkToComparator::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1000:7: style:inconclusive: Technically the member function 'BranchLinkFromToComparator::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:399:2: style: Struct 'KmerInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:645:2: style: Struct 'KmerInfoAllocator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:923:2: style: Struct 'BranchLink' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:2436:11: style: Condition 'fromid' is always true [knownConditionTrueFalse]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:2432:17: note: Assuming that condition 'fromid>0' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:2436:11: note: Condition 'fromid' is always true
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4044:39: style: Condition 'ok' is always false [knownConditionTrueFalse]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4041:10: note: Assuming that condition '!ok' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4044:39: note: Condition 'ok' is always false
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:969:8: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:971:3: note: Found duplicate branches for 'if' and 'else'.
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:969:8: note: Found duplicate branches for 'if' and 'else'.
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1008:8: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1010:3: note: Found duplicate branches for 'if' and 'else'.
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1008:8: note: Found duplicate branches for 'if' and 'else'.
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1318:12: style: The scope of the variable 'o' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1939:31: style: The scope of the variable 'Vcompmap' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1422:30: style: Local variable 'ref' shadows outer argument [shadowArgument]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1292:22: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1422:30: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1569:13: style: Local variable 'o' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1318:12: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1569:13: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1578:13: style: Local variable 'o' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1318:12: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1578:13: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1587:13: style: Local variable 'o' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1318:12: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1587:13: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1596:13: style: Local variable 'o' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1318:12: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1596:13: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1644:64: style: Local variable 'BPP' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1617:62: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1644:64: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3900:54: performance: Function parameter 'prefix' should be passed by const reference. [passedByValue]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1978:24: performance: Searching before insertion is not necessary. [stlFindInsert]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1318:14: style: Variable 'o' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1600:10: style: Variable 'ABPNo' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:2004:21: style: Variable 'Vcompmap[V[i]]' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4137:19: style: Variable 'L[dend-dstart]' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4138:11: style: Variable 'numint' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcountflags.cpp:186:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIBMAUS2_BAMBAM_FSECONDARY [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamcountflags.cpp:373:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:62:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:144:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:260:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:57:7: style:inconclusive: Technically the member function 'IntervalHandler::handleRaw' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:72:36: style: Local variable 'D' shadows outer argument [shadowArgument]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:68:48: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:72:36: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:237:13: style: Variable 'prevstart' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepthintersect.cpp:45:139: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DepthInterval [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepthintersect.cpp:159:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepthmerge.cpp:46:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepthmerge.cpp:73:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:36:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:45:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:189:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:102:22: style: Local variable 'name0' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:95:16: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:102:22: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:138:22: style: Local variable 'name1' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:96:16: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:138:22: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamdisthist.cpp:78:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdisthist.cpp:147:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdisthist.cpp:204:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdisthist.cpp:221:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:65:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:151:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:209:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:246:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:359:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:463:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:504:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:306:173: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:856:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1288:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:681:7: style: The function 'operator()' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:627:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:681:7: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:197:13: style: Local variable 'l' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:105:11: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:197:13: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:199:64: style: Local variable 'SP' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:107:62: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:199:64: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:200:31: style: Local variable 'DI' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:108:29: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:200:31: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:207:64: style: Local variable 'SP' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:107:62: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:207:64: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:208:31: style: Local variable 'DI' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:108:29: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:208:31: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:585:13: style: Local variable 'p' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:532:12: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:585:13: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1238:13: style: Local variable 'print_o' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1201:11: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1238:13: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1239:13: style: Local variable 'ld' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1202:11: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1239:13: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1170:9: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1185:10: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:398:14: style: Variable 'KM[key]' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:437:23: style: Variable 'KGCMEAN[it->first]' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1235:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexplode.cpp:65:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexplode.cpp:95:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexplode.cpp:28:34: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderef.cpp:47:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderef.cpp:135:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderef.cpp:28:34: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderef.cpp:38:17: style: Variable 'threads' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderg.cpp:55:143: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderg.cpp:180:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderg.cpp:67:29: style: Local variable 'replaceIn' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderg.cpp:39:27: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderg.cpp:67:29: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderg.cpp:39:27: style: Unused variable: replaceIn [unusedVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:50:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:82:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:144:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:194:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:490:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:428:9: style: Variable 'coutp' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastexploderef.cpp:112:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastexploderef.cpp:226:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastexploderef.cpp:31:34: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastexploderef.cpp:37:17: style: Variable 'threads' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastnumextract.cpp:35:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastnumextract.cpp:53:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastsplit.cpp:53:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastsplit.cpp:74:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfastsplit.cpp:25:33: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:92:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:151:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:831:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:1109:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:1026:5: style: Struct 'UncoveredComp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:1071:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:1068:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:1071:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bamfillquery.cpp:57:105: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfillquery.cpp:271:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilter.cpp:71:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilter.cpp:148:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilteraux.cpp:56:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilteraux.cpp:230:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilteraux.cpp:174:4: style: Redundant condition: !arginfo.hasArg("remove"). 'A || (!A && B)' is equivalent to 'A || B' [redundantCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterbyname.cpp:43:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterbyname.cpp:148:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfiltereofblocks.cpp:35:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfiltereofblocks.cpp:53:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfiltereofblocks.cpp:82:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterflags.cpp:85:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterflags.cpp:220:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader.cpp:107:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader.cpp:285:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:67:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:94:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:179:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:198:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:86:61: style: The scope of the variable 'cbs' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:50:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:253:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kmer [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:277:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seqid [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:394:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:685:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:157:2: warning:inconclusive: Member variable 'Match::seqid' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:157:2: warning:inconclusive: Member variable 'Match::strand' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:157:2: warning:inconclusive: Member variable 'Match::pos' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:157:2: warning:inconclusive: Member variable 'Match::readpos' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:181:2: warning:inconclusive: Member variable 'KMer::kmer' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:181:2: warning:inconclusive: Member variable 'KMer::seqid' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:181:2: warning:inconclusive: Member variable 'KMer::pos' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:181:2: warning:inconclusive: Member variable 'KMer::strand' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:109:2: style: Struct 'KMerBlockTemplate < kl >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterlength.cpp:50:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterlength.cpp:193:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfiltermc.cpp:149:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfiltermc.cpp:236:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilternames.cpp:53:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilternames.cpp:221:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterrefid.cpp:53:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterrefid.cpp:224:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterrg.cpp:53:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterrg.cpp:199:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmatecoordinates.cpp:91:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmatecoordinates.cpp:269:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmatecoordinates.cpp:49:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmatecoordinatesnamesorted.cpp:55:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable text [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmatecoordinatesnamesorted.cpp:262:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmateinformation.cpp:67:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmateinformation.cpp:221:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmateinformation.cpp:83:32: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmateinformation.cpp:191:17: style: Variable 'prevalgnvalid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:56:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:76:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:222:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:167:25: style: Condition 'name[l-1]=='2'' is always true [knownConditionTrueFalse]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:163:20: note: Assuming that condition 'name[l-1]=='1'' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:158:35: note: Assuming that condition 'name[l-1]<='2'' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:167:25: note: Condition 'name[l-1]=='2'' is always true
biobambam2-2.0.185-release-20221211202123/src/programs/bamflagsplit.cpp:118:118: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamflagsplit.cpp:341:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamflagsplit.cpp:707:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamflagsplit.cpp:60:7: style:inconclusive: Technically the member function 'AlPairCmp::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamflagsplit.cpp:346:32: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfrontback.cpp:52:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamfrontback.cpp:268:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheadercat.cpp:38:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheadercat.cpp:64:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap.cpp:265:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap.cpp:494:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap.cpp:623:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap.cpp:105:2: warning: Member variable 'EntriesContainer::entryptr' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap.cpp:454:67: style: Unused variable: algnpool [unusedVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap.cpp:455:52: style: Unused variable: algnfreelist [unusedVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:216:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:423:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:695:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:57:2: warning:inconclusive: Member variable 'ConsensusAccuracy::depthhistogram' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:64:2: style: Struct 'ConsensusAccuracy' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:614:37: style: Local variable 'M' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:354:34: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:614:37: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:649:37: style: Local variable 'M' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:354:34: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:649:37: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:418:49: performance: Searching before insertion is not necessary. Instead of 'Mconsacc[loadedRefId]=ConsensusAccuracy(refseqbases.size())' consider using 'Mconsacc.try_emplace(loadedRefId, ConsensusAccuracy(refseqbases.size()));'. [stlFindInsert]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:461:49: performance: Searching before insertion is not necessary. Instead of 'Mconsacc[loadedRefId]=ConsensusAccuracy(refseqbases.size())' consider using 'Mconsacc.try_emplace(loadedRefId, ConsensusAccuracy(refseqbases.size()));'. [stlFindInsert]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:588:46: performance: Searching before insertion is not necessary. Instead of 'Mconsacc[loadedRefId]=ConsensusAccuracy(refseqbases.size())' consider using 'Mconsacc.try_emplace(loadedRefId, ConsensusAccuracy(refseqbases.size()));'. [stlFindInsert]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:223:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:465:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:737:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:57:2: warning:inconclusive: Member variable 'ConsensusAccuracy::depthhistogram' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:64:2: style: Struct 'ConsensusAccuracy' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:656:37: style: Local variable 'M' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:396:34: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:656:37: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:691:37: style: Local variable 'M' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:396:34: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:691:37: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:460:49: performance: Searching before insertion is not necessary. Instead of 'Mconsacc[loadedRefId]=ConsensusAccuracy(refseqbases.size())' consider using 'Mconsacc.try_emplace(loadedRefId, ConsensusAccuracy(refseqbases.size()));'. [stlFindInsert]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:503:49: performance: Searching before insertion is not necessary. Instead of 'Mconsacc[loadedRefId]=ConsensusAccuracy(refseqbases.size())' consider using 'Mconsacc.try_emplace(loadedRefId, ConsensusAccuracy(refseqbases.size()));'. [stlFindInsert]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:630:46: performance: Searching before insertion is not necessary. Instead of 'Mconsacc[loadedRefId]=ConsensusAccuracy(refseqbases.size())' consider using 'Mconsacc.try_emplace(loadedRefId, ConsensusAccuracy(refseqbases.size()));'. [stlFindInsert]
biobambam2-2.0.185-release-20221211202123/src/programs/bamindex.cpp:55:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable streameof [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamindex.cpp:81:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:150:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:176:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable extended [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:433:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:574:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:690:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:851:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:371:15: style: The scope of the variable 'unif' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:362:21: performance: Function parameter 'chromregex' should be passed by const reference. [passedByValue]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:226:15: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:236:8: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:703:32: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcommenthist.cpp:202:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcommenthist.cpp:302:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammapdist.cpp:69:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammapdist.cpp:307:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:167:140: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:811:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:91:2: style: Struct 'MarkDuplicatesRewriteRequest' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:662:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:652:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:662:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:706:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:703:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:706:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:728:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:725:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:728:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:63:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:64:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:680:18: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:693:11: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:700:9: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:716:11: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:722:9: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:310:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:921:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:984:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1141:140: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1865:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:124:7: style:inconclusive: Technically the member function 'PairActiveCountTemplate < libmaus2 :: bambam :: ReadEndsFreeList >::operator==' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1124:11: style: The destructor '~PositionTrackCallback' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:257:11: note: Virtual destructor in base class
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1124:11: note: Destructor in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1714:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1702:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1714:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1759:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1756:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1759:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:905:30: style: Local variable 'bkey' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:881:27: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:905:30: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1014:30: style: Local variable 'bkey' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:990:27: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1014:30: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:71:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:72:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:79:47: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1732:18: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1746:11: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1753:9: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1769:11: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1775:9: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:255:140: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:955:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:88:2: warning:inconclusive: Member variable 'OptEntry::rank' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:88:2: warning:inconclusive: Member variable 'OptEntry::refrank' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:93:2: style: Struct 'OptEntry' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:135:2: style: Struct 'OptMark' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:164:2: style: Struct 'NameInput' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:194:2: style: Struct 'NameArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:225:2: style: Struct 'BamInputCallback' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:781:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:771:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:781:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:825:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:822:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:825:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:847:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:844:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:847:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:68:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:69:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:799:18: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:812:11: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:819:9: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:835:11: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:841:9: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:182:183: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:325:140: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:1029:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:88:2: warning:inconclusive: Member variable 'OptEntry::rank' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:88:2: warning:inconclusive: Member variable 'OptEntry::refrank' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:93:2: style: Struct 'OptEntry' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:135:2: style: Struct 'OptMark' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:234:2: style: Struct 'NameInput' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:264:2: style: Struct 'NameArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:295:2: style: Struct 'BamInputCallback' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:852:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:842:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:852:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:896:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:893:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:896:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:918:7: style: The if condition is the same as the previous if condition [duplicateCondition]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:915:7: note: First condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:918:7: note: Second condition
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:68:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:69:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:870:18: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:883:11: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:890:9: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:906:11: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:912:9: style: Variable 'dupcnt' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bammaskflags.cpp:59:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammaskflags.cpp:220:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammdnm.cpp:73:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammdnm.cpp:350:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammdnm.cpp:51:43: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bammerge.cpp:55:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammerge.cpp:85:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammerge.cpp:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bammerge.cpp:67:2: style: Struct 'SimpleThreadPoolTerminate' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamnumericalindex.cpp:60:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable streameof [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamnumericalindex.cpp:89:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamnumericalindexstats.cpp:35:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamnumericalindexstats.cpp:53:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrandomtag.cpp:56:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrandomtag.cpp:155:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrank.cpp:48:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrank.cpp:181:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:94:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:129:149: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:145:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:165:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:229:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:246:122: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:378:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:65:53: performance: Function parameter 'igroup' should be passed by const reference. [passedByValue]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:155:42: style: Parameter 'group' can be declared as reference to const [constParameterReference]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:73:32: style: Parameter 'one' can be declared as pointer to const. However it seems that 'rank_cmp' is a callback function, if 'one' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:211:45: note: You might need to cast the function pointer here
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:73:32: note: Parameter 'one' can be declared as pointer to const
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:73:47: style: Parameter 'two' can be declared as pointer to const. However it seems that 'rank_cmp' is a callback function, if 'two' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:211:45: note: You might need to cast the function pointer here
biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:73:47: note: Parameter 'two' can be declared as pointer to const
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecalculatecigar.cpp:54:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecalculatecigar.cpp:71:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecalculatecigar.cpp:283:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecompress.cpp:61:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecompress.cpp:205:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecompress.cpp:52:14: style: The scope of the variable 'numerical' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecompress.cpp:108:6: style: The scope of the variable 'r' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecompress.cpp:109:11: style: The scope of the variable 't' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecompress.cpp:110:11: style: The scope of the variable 'last' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrecompress.cpp:111:11: style: The scope of the variable 'lcnt' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:94:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:140:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:209:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:435:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:43:2: warning:inconclusive: Member variable 'Element::p' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:43:2: warning:inconclusive: Member variable 'Element::c' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:72:2: warning:inconclusive: Member variable 'Key::p' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:72:2: warning:inconclusive: Member variable 'Key::c' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:126:2: warning:inconclusive: Member variable 'EElement::c' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:126:2: warning:inconclusive: Member variable 'EElement::f' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:52:7: style:inconclusive: Technically the member function 'Element::deserialise' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:263:5: style:inconclusive: Statements following 'throw' will never be executed. [unreachableCode]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:236:25: style: Local variable 'V' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:194:20: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:236:25: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:398:22: style: Local variable 'V' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:194:20: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:398:22: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:413:21: style: Local variable 'V' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:194:20: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:413:21: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:287:8: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:317:8: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:328:8: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:333:8: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:343:8: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefinterval.cpp:83:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefinterval.cpp:184:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefinterval.cpp:62:30: style: Variable 'reference' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamrefinterval.cpp:63:33: style: Variable 'outputprefix' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreheader.cpp:45:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreheader.cpp:70:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreheader.cpp:257:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreheader.cpp:86:20: style: Condition 'numrest>1' is always true [knownConditionTrueFalse]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreheader.cpp:79:15: note: Assuming that condition 'numrest==1' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/bamreheader.cpp:86:20: note: Condition 'numrest>1' is always true
biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:45:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:76:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:97:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:282:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:64:2: style: Struct 'ReplaceChecksumsUpdate' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:111:20: style: Condition 'numrest>1' is always true [knownConditionTrueFalse]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:105:15: note: Assuming that condition 'numrest==1' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:111:20: note: Condition 'numrest>1' is always true
biobambam2-2.0.185-release-20221211202123/src/programs/bamreset.cpp:52:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamreset.cpp:216:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsalvage.cpp:53:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsalvage.cpp:68:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsalvage.cpp:209:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamscrapcount.cpp:78:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamscrapcount.cpp:111:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamseqchksum.cpp:81:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamseqchksum.cpp:182:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamseqchksum.cpp:46:9: style: The scope of the variable 'prevtime' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:42:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:123:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:166:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:37:35: style: Local variable 'D' shadows outer argument [shadowArgument]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:31:69: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:37:35: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:62:35: style: Local variable 'D' shadows outer argument [shadowArgument]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:31:69: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:62:35: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:134:35: style: Local variable 'D' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:93:43: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:134:35: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:39:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_BEST_SPEED [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:439:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:187:142: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable block_sort_control_input_bam [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:85:104: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_format_cram [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:162:6: style: The scope of the variable 'returncode' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:79:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:162:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:367:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:1491:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:620:19: style: Variable 'prevalgnvalid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:736:19: style: Variable 'prevalgnvalid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:842:19: style: Variable 'prevalgnvalid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:948:19: style: Variable 'prevalgnvalid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:1052:19: style: Variable 'prevalgnvalid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:1156:19: style: Variable 'prevalgnvalid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:1261:19: style: Variable 'prevalgnvalid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:324:20: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsplit.cpp:52:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsplit.cpp:65:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsplit.cpp:139:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsplit.cpp:35:33: style: int result is returned as long value. If the return value is long to avoid loss of information, then you have loss of information. [truncLongCastReturn]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsplitdiv.cpp:51:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsplitdiv.cpp:64:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsplitdiv.cpp:147:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamsplitdiv.cpp:94:30: style: Unused variable: filenames [unusedVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamstreamingmarkduplicates.cpp:70:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamstreamingmarkduplicates.cpp:190:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtagconversion.cpp:52:122: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtagconversion.cpp:207:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:206:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:425:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:1068:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:1201:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:1258:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:459:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:249:117: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_DEFAULT_COMPRESSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:129:2: style: Struct 'BamToFastQInputFileStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:138:2: style: Struct 'BamToFastQInputFileStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:197:61: performance: Function parameter 's_auxtags' should be passed by const reference. [passedByValue]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:1011:32: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:1013:34: style: Variable 'inputfilename' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtoname.cpp:57:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtoname.cpp:154:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtoname.cpp:226:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtoname.cpp:69:32: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtoname.cpp:70:34: style: Variable 'inputfilename' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtoname.cpp:175:32: style: Variable 'inputformat' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/bamvalidate.cpp:275:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamvalidate.cpp:87:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamzztoname.cpp:48:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamzztoname.cpp:184:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:65:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fgTransService [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:101:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UnRep_RepChar [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:312:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:718:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1068:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1075:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1084:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1127:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:627:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:819:42: warning: Assert statement modifies 'ih'. [assignmentInAssert]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:126:2: style: Class 'StdInputBinStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:183:2: style: Class 'StdISOInputSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:755:9: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:769:9: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:69:16: style: The scope of the variable 'ucharset' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:692:12: style: Local variable 'hitLen' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:221:14: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:692:12: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:805:19: style: Local variable 'ok' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:659:9: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:805:19: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:716:29: warning: Either the condition 'qita!=queries.end()' is redundant or there is possible dereference of an invalid iterator: qita. [derefInvalidIteratorRedundantCheck]
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:736:15: note: Assuming that condition 'qita!=queries.end()' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:716:29: note: Dereference of an invalid iterator
biobambam2-2.0.185-release-20221211202123/src/programs/fastabgzfextract.cpp:37:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastabgzfextract.cpp:119:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastaexplod.cpp:38:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastaexplod.cpp:89:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastaselectreg.cpp:52:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastaselectreg.cpp:117:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastaselectreg.cpp:75:17: style: The scope of the variable 'spat' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:64:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_DEFAULT_COMPRESSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:177:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:297:141: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:372:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:418:183: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:450:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable namescheme [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:702:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:970:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:1210:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:756:11: style: Condition 'NI_1.isfirst' is always true [knownConditionTrueFalse]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:733:29: note: Assuming that condition '!NI_1.isfirst' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:740:14: note: Assuming condition is false
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:756:11: note: Condition 'NI_1.isfirst' is always true
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:351:5: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:159:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:770:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_NULL [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:792:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_OK [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1657:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1959:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIBMAUS2_BAMBAM_FUNMAP [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2359:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fragmentBufferPointersMerged [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2819:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3154:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3467:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerrlock [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4013:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_DEFAULT_COMPRESSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4040:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4177:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4292:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:192:2: warning:inconclusive: Member variable 'ChecksumsAllocator::bamheader' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:216:2: warning:inconclusive: Member variable 'FastQPtr::namestart' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:216:2: warning:inconclusive: Member variable 'FastQPtr::nameend' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:216:2: warning:inconclusive: Member variable 'FastQPtr::basestart' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:216:2: warning:inconclusive: Member variable 'FastQPtr::baseend' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:216:2: warning:inconclusive: Member variable 'FastQPtr::qstart' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:216:2: warning:inconclusive: Member variable 'FastQPtr::qend' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:296:2: warning: Member variable 'NewlineInfo::uLinePtr' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:358:2: warning: Member variable 'NewlineInfoAllocator::putbackspace' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:575:2: warning: Member variable 'DataBlockAllocator::putbackspace' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:811:2: warning: Member variable 'BlockReadStreamInfo::crc32digest' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:858:2: warning: Member variable 'BlockReadStreamInfo::crc32digest' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1136:2: style: Struct 'BlockProcessPackage' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1225:2: style: Struct 'BlockProcessNewlineStorePackage' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3136:15: style: The function 'blockReadQueueEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1016:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3136:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3405:15: style: The function 'blockReadReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1022:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3405:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3410:15: style: The function 'blockProcessReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1252:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3410:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3415:15: style: The function 'blockProcessNewlineCountPackageReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1332:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3415:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3420:15: style: The function 'blockProcessNewlineStorePackageReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1338:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3420:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3425:15: style: The function 'blockProcessLineParsePackageReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1546:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3425:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3430:15: style: The function 'blockProcessBamEncodePackageReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1826:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3430:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3435:15: style: The function 'bamStreamMergePackageReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2231:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3435:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3440:15: style: The function 'bamBgzfCompressionPackageReturnEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2768:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3440:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3446:15: style: The function 'returnDecompressedBlockEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1028:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3446:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3511:15: style: The function 'blockLineCountEnqueEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1258:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3511:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3522:15: style: The function 'blockProcessNewlineCountCompleteEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1264:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3522:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3543:15: style: The function 'blockProcessLineParseCheckEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1344:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3543:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3571:15: style: The function 'blockProcessNewlineStoreCompleteEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1270:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3571:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3598:15: style: The function 'blockProcessLineParseCompleteEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1552:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3598:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3756:15: style: The function 'blockProcessBamEncodePackageFinishedEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1832:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3756:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3825:15: style: The function 'bamStreamMergePackageFinishedEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2237:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3825:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3949:15: style: The function 'bamBgzfCompressionPackageFinishedEvent' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2774:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3949:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3996:15: style: The function 'bamStreamMergePackageStatsUpdate' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2249:15: note: Virtual function in base class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3996:15: note: Function in derived class
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2532:20: style: Condition 'ap0==ap0e' is always true [knownConditionTrueFalse]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2527:22: note: Assuming that condition 'ap0!=ap0e' is not redundant
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2532:20: note: Condition 'ap0==ap0e' is always true
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1303:25: style: The scope of the variable 'info' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2334:52: style: The scope of the variable 'merge' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2336:12: style: The scope of the variable 'merge_o' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3113:25: style: The scope of the variable 'info' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3525:25: style: The scope of the variable 'info' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3545:25: style: The scope of the variable 'info' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3574:25: style: The scope of the variable 'info' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1740:19: style: Local variable 'P' shadows outer argument [shadowArgument]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1575:70: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1740:19: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3491:59: style: Local variable 'slock' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3486:41: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3491:59: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3613:37: style: Local variable 'ptr' shadows outer argument [shadowArgument]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3598:82: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3613:37: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3741:27: style: Local variable 'BSMP' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2949:34: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3741:27: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3796:42: style: Local variable 'slock' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3789:40: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3796:42: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3803:31: style: Local variable 'BBCP' shadows outer variable [shadowVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2950:38: note: Shadowed declaration
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3803:31: note: Shadow variable
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1305:48: style: Unused variable: Vout [unusedVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3667:9: style: Variable 'L[i]' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3921:11: style: Variable 'L[i]' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4129:20: style: Variable 'rgid' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobampar.cpp:44:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobampar.cpp:59:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobampar.cpp:95:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:42:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:142:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:187:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:206:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:352:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:475:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:74:2: warning:inconclusive: Member variable 'Gene::start' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:193:2: warning:inconclusive: Member variable 'Entry::start' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:193:2: warning:inconclusive: Member variable 'Entry::exon_number' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:193:2: warning:inconclusive: Member variable 'Entry::rank' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:320:2: warning:inconclusive: Member variable 'GeneObjectNameGet::c' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:320:2: warning:inconclusive: Member variable 'GeneObjectNameGet::G' is not initialized in the constructor. [uninitMemberVar]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:301:7: style:inconclusive: Technically the member function 'GeneObjectComparator::operator()' can be const. [functionConst]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:198:2: style: Struct 'Entry' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:289:2: style: Struct 'GeneObject' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:299:2: style: Struct 'GeneObjectComparator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
biobambam2-2.0.185-release-20221211202123/src/programs/normalisefasta.cpp:78:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/normalisefasta.cpp:152:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/normalisefasta.cpp:240:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/normalisefasta.cpp:260:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/normalisefasta.cpp:224:11: style: Variable 'ioffset' is assigned a value that is never used. [unreadVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/populaterefcache.cpp:35:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/populaterefcache.cpp:68:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfconcat.cpp:91:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfconcat.cpp:47:17: style: The scope of the variable 'vout' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfconcat.cpp:51:33: style: Unused variable: E [unusedVariable]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfdiff.cpp:179:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfdiff.cpp:63:107: style: Parameter 'ptr' can be declared as reference to const [constParameterReference]
biobambam2-2.0.185-release-20221211202123/src/programs/vcffilterfilterflags.cpp:62:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcffilterinfo.cpp:62:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcffiltersamples.cpp:62:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfpatchcontigprepend.cpp:61:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfreplacecontigs.cpp:48:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfreplacecontigs.cpp:157:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfreplacecontigs.cpp:54:24: style: The scope of the variable 'S' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfreplacecontigsmap.cpp:49:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfreplacecontigsmap.cpp:160:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfreplacecontigsmap.cpp:56:24: style: The scope of the variable 'S' can be reduced. [variableScope]
biobambam2-2.0.185-release-20221211202123/src/programs/vcfsort.cpp:61:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/test/bamcmp.cpp:74:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/test/bamtosam.cpp:28:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:123:1: error: The one definition rule is violated, different classes/structs have the same name 'AlignmentTraceContainerAllocator' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:88:1: note: The one definition rule is violated, different classes/structs have the same name 'AlignmentTraceContainerAllocator'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:123:1: note: The one definition rule is violated, different classes/structs have the same name 'AlignmentTraceContainerAllocator'
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:34:1: error: The one definition rule is violated, different classes/structs have the same name 'IntervalHandler' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:763:1: note: The one definition rule is violated, different classes/structs have the same name 'IntervalHandler'
biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:34:1: note: The one definition rule is violated, different classes/structs have the same name 'IntervalHandler'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1246:1: error: The one definition rule is violated, different classes/structs have the same name 'HeapEntry' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:128:1: note: The one definition rule is violated, different classes/structs have the same name 'HeapEntry'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1246:1: note: The one definition rule is violated, different classes/structs have the same name 'HeapEntry'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1246:1: error: The one definition rule is violated, different classes/structs have the same name 'HeapEntry' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:129:1: note: The one definition rule is violated, different classes/structs have the same name 'HeapEntry'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1246:1: note: The one definition rule is violated, different classes/structs have the same name 'HeapEntry'
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:108:1: error: The one definition rule is violated, different classes/structs have the same name 'BamToFastQInputFileStream' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:105:1: note: The one definition rule is violated, different classes/structs have the same name 'BamToFastQInputFileStream'
biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:108:1: note: The one definition rule is violated, different classes/structs have the same name 'BamToFastQInputFileStream'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:237:1: error: The one definition rule is violated, different classes/structs have the same name 'DataBlock' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:448:1: note: The one definition rule is violated, different classes/structs have the same name 'DataBlock'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:237:1: note: The one definition rule is violated, different classes/structs have the same name 'DataBlock'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:375:1: error: The one definition rule is violated, different classes/structs have the same name 'BlockReadStreamInfo' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:602:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockReadStreamInfo'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:375:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockReadStreamInfo'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:673:1: error: The one definition rule is violated, different classes/structs have the same name 'BlockReadStreamInfoVector' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:907:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockReadStreamInfoVector'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:673:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockReadStreamInfoVector'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:796:1: error: The one definition rule is violated, different classes/structs have the same name 'BlockReadDispatcher' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1031:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockReadDispatcher'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:796:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockReadDispatcher'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:960:1: error: The one definition rule is violated, different classes/structs have the same name 'BlockProcessDispatcher' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1273:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockProcessDispatcher'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:960:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockProcessDispatcher'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2273:1: error: The one definition rule is violated, different classes/structs have the same name 'BlockReadControl' [ctuOneDefinitionRuleViolation]
biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2868:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockReadControl'
biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2273:1: note: The one definition rule is violated, different classes/structs have the same name 'BlockReadControl'
diff:
head biobambam2-2.0.185-release-20221211202123/src/biobambam2/Licensing.cpp:35:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/biobambam2/Licensing.cpp:49:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bam12auxmerge.cpp:475:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bam12split.cpp:194:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bam12strip.cpp:188:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamadapterclip.cpp:200:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamadapterhistogram.cpp:149:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamaddne.cpp:208:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamaddne.cpp:65:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamalignfrac.cpp:234:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge.cpp:222:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1112:106: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1196:105: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pa [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1224:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pa [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1241:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pa [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1266:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pa [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1284:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIBMAUS2_BAMBAM_FREAD1 [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1537:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:1718:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable streamid [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2250:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2521:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2881:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerrlock [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:2960:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerrlock [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3044:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bamMergeQueueFSHLock [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3356:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerrlock [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3436:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:3575:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:485:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seqid [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:535:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_NULL [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxmerge2.cpp:557:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_OK [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamauxsort.cpp:186:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bambisect.cpp:175:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcat.cpp:201:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcat.cpp:69:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamchecksort.cpp:147:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamclipXT.cpp:189:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamclipreinsert.cpp:192:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1069:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1361:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:1421:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:146:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:224:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:307:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:458:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcollate2.cpp:845:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1059:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:1304:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3023:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3219:161: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3293:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3311:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:3341:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4177:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:4266:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:592:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamconsensus.cpp:671:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamcountflags.cpp:373:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:144:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdepth.cpp:260:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdepthintersect.cpp:159:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdepthmerge.cpp:73:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:189:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdifference.cpp:45:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdisthist.cpp:147:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdisthist.cpp:204:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdisthist.cpp:221:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:151:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:209:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:246:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:359:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:463:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamdownsamplerandom.cpp:504:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:1288:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamexondepth.cpp:856:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamexplode.cpp:95:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderef.cpp:135:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamexploderg.cpp:180:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:144:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:194:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:490:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfastcat.cpp:82:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfastexploderef.cpp:226:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfastnumextract.cpp:53:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfastsplit.cpp:74:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:1109:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:151:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfeaturecount.cpp:831:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfillquery.cpp:271:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilter.cpp:148:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilteraux.cpp:230:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterbyname.cpp:148:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfiltereofblocks.cpp:53:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfiltereofblocks.cpp:82:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterflags.cpp:220:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader.cpp:285:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:179:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:198:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:86:61: style: The scope of the variable 'cbs' can be reduced. [variableScope]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterheader2.cpp:94:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:253:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kmer [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:277:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seqid [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:394:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterk.cpp:685:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterlength.cpp:193:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfiltermc.cpp:236:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilternames.cpp:221:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterrefid.cpp:224:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfilterrg.cpp:199:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmatecoordinates.cpp:269:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmatecoordinatesnamesorted.cpp:262:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfixmateinformation.cpp:221:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:222:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfixpairinfo.cpp:76:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamflagsplit.cpp:341:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamflagsplit.cpp:707:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamfrontback.cpp:268:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamheadercat.cpp:64:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamheap.cpp:494:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamheap.cpp:623:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:423:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamheap2.cpp:695:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:465:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamheap3.cpp:737:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamindex.cpp:81:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:176:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable extended [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:433:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:574:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:690:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcomment.cpp:851:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcommenthist.cpp:202:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcommenthist.cpp:302:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/bamintervalcommenthist.cpp:67:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammapdist.cpp:307:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates.cpp:811:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1124:11: style: The destructor '~PositionTrackCallback' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
     biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:257:11: note: Virtual destructor in base class
     biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1124:11: note: Destructor in derived class
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1141:140: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:1865:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:921:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicates2.cpp:984:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesopt.cpp:955:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:1029:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammarkduplicatesoptdist.cpp:325:140: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammaskflags.cpp:220:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammdnm.cpp:350:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammerge.cpp:254:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bammerge.cpp:85:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamnumericalindex.cpp:89:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamnumericalindexstats.cpp:53:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrandomtag.cpp:155:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrank.cpp:181:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:129:149: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:145:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:165:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:229:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:246:122: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamranksort.cpp:378:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrecalculatecigar.cpp:283:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrecalculatecigar.cpp:71:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrecompress.cpp:205:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:140:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable p [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:209:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrefextract.cpp:435:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamrefinterval.cpp:184:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamreheader.cpp:257:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamreheader.cpp:70:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:282:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:76:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamreplacechecksums.cpp:97:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamreset.cpp:216:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsalvage.cpp:209:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsalvage.cpp:68:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamscrapcount.cpp:111:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamseqchksum.cpp:182:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:123:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsimpledepth.cpp:166:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:162:6: style: The scope of the variable 'returncode' can be reduced. [variableScope]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:187:142: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable block_sort_control_input_bam [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:439:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsormadup.cpp:85:104: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_format_cram [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:1491:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:162:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsort.cpp:367:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsplit.cpp:139:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsplit.cpp:65:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsplitdiv.cpp:147:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamsplitdiv.cpp:64:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamstreamingmarkduplicates.cpp:190:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtagconversion.cpp:207:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:1068:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:1201:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:1258:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:249:117: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_DEFAULT_COMPRESSION [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:425:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtofastq.cpp:459:95: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtoname.cpp:154:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamtoname.cpp:226:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamvalidate.cpp:87:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/bamzztoname.cpp:184:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:101:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UnRep_RepChar [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1068:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1075:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1084:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1119:11: style: The comparison 'ret == EXIT_SUCCESS' is always true because 'ret' and 'EXIT_SUCCESS' represent the same value. [knownConditionTrueFalse]
     biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1116:12: note: 'ret' is assigned value 'EXIT_SUCCESS' here.
     biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1119:11: note: The comparison 'ret == EXIT_SUCCESS' is always true because 'ret' and 'EXIT_SUCCESS' represent the same value.
head biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:1127:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:312:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:627:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/blastnxmltobam.cpp:718:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastabgzfextract.cpp:119:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastaexplod.cpp:89:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastaselectreg.cpp:117:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:1210:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:177:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:297:141: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:372:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:418:183: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:450:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable namescheme [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:702:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam.cpp:970:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PACKAGE_VERSION [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1657:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:1959:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LIBMAUS2_BAMBAM_FUNMAP [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2359:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fragmentBufferPointersMerged [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:2819:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3154:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:3467:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerrlock [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4013:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_DEFAULT_COMPRESSION [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4040:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4177:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:4292:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:770:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_NULL [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobam2.cpp:792:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Z_OK [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobampar.cpp:59:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/fastqtobampar.cpp:95:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:142:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:187:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:206:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:352:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/filtergtf.cpp:475:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/normalisefasta.cpp:152:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/normalisefasta.cpp:240:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/normalisefasta.cpp:260:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/populaterefcache.cpp:68:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/vcfconcat.cpp:75:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcfconcat.cpp:91:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/vcfdiff.cpp:165:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcfdiff.cpp:179:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/vcffilterfilterflags.cpp:46:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcffilterfilterflags.cpp:62:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/vcffilterinfo.cpp:46:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcffilterinfo.cpp:62:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/vcffiltersamples.cpp:46:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcffiltersamples.cpp:62:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/vcfpatchcontigprepend.cpp:45:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcfpatchcontigprepend.cpp:61:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcfreplacecontigs.cpp:157:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcfreplacecontigsmap.cpp:160:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/src/programs/vcfsort.cpp:45:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/src/programs/vcfsort.cpp:61:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
2.13.0 biobambam2-2.0.185-release-20221211202123/test/bamcmp.cpp:70:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EXIT_SUCCESS [valueFlowBailoutIncompleteVar]
head biobambam2-2.0.185-release-20221211202123/test/bamcmp.cpp:74:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]


DONE