2022-06-25 07:12
ftp://ftp.de.debian.org/debian/pool/main/s/snap-aligner/snap-aligner_1.0~beta.18+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu  --showtime=top5 --check-library --inconclusive --enable=style,information --template=daca2 -D__GNUC__ --platform=unix64 -rp=temp -j2
platform: Linux-5.4.0-110-generic-x86_64-with-glibc2.29
python: 3.8.10
client-version: 1.3.24
compiler: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
cppcheck: head 2.8
head-info: 63e567e (2022-06-25 08:38:17 +0200)
count: 1340 1313
elapsed-time: 62.8 102.1
head-timing-info:
 Overall time: 0s

old-timing-info:
 Overall time: 0s

head results:
snap-1.0beta.18/SNAPLib/ParallelTask.h:124:11: error: Non-local variable 'common->doneWaiter' will use object that points to local variable 'doneWaiter'. [danglingLifetime]
snap-1.0beta.18/SNAPLib/ParallelTask.h:124:26: note: Address of variable taken here.
snap-1.0beta.18/SNAPLib/ParallelTask.h:110:24: note: Variable created here.
snap-1.0beta.18/SNAPLib/ParallelTask.h:124:11: note: Non-local variable 'common->doneWaiter' will use object that points to local variable 'doneWaiter'.
snap-1.0beta.18/SNAPLib/Seed.h:181:40: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-1.0beta.18/SNAPLib/ParallelTask.h:269:5: warning: Member variable 'ParallelWorker::manager' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/ParallelTask.h:269:5: warning: Member variable 'ParallelWorker::threadNum' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/ParallelTask.h:269:5: warning: Member variable 'ParallelWorker::numThreads' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::unclippedData' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::unclippedQuality' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::idLength' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::dataLength' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::unclippedLength' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::frontClippedLength' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::localBuffer' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::rcData' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::rcQuality' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::externalData' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:225:9: warning: Member variable 'Read::externalQuality' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Read.h:776:5: warning: Member variable 'ReadWithOwnMemory::ownBuffer' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerOptions.h:44:2: warning: Member variable 'SNAPFile::isCompressed' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::Table' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::tableSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::keySizeInBytes' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::elementSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::usedElementCount' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::ownsMemoryForTable' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::valueSizeInBytes' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::valueCount' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/HashTable.h:143:9: warning:inconclusive: Member variable 'SNAPHashTable::invalidValueValue' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/Seed.h:55:12: warning:inconclusive: Member variable 'Seed::bases' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Seed.h:55:12: warning:inconclusive: Member variable 'Seed::reverseComplement' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:234:9: warning: Member variable 'PerHashTableBatch::entries' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::readerContext' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::alignStart' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::alignTime' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::maxDist' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::numSeedsFromCommandLine' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::seedCoverage' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::minWeightToCheck' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::maxHits' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::detailedStats' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::clipping' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::extraSearchDepth' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::noUkkonen' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::noOrderedEvaluation' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::noTruncation' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::maxSecondaryAlignmentAdditionalEditDistance' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::maxSecondaryAlignments' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::maxSecondaryAlignmentsPerContig' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::minReadLength' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::maxHits_' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'AlignerContext::maxDist_' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'TaskContextBase::totalThreads' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'TaskContextBase::bindToProcessors' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'TaskContextBase::time' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'TaskContextBase::threadNum' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'TaskContextBase::doneWaiter' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'TaskContextBase::runningThreads' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:49:17: warning: Member variable 'TaskContextBase::pRunningThreads' is not initialized in the constructor. Maybe it should be initialized directly in the class TaskContextBase? [uninitDerivedMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:24:5: warning: Member variable 'LVResult::matchProbability' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:38:5: warning: Member variable 'ReadQueueElement::totalReads' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin < 1 >::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin < 1 >::backtraceMatched' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin < 1 >::backtraceD' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin < -1 >::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin < -1 >::backtraceMatched' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin < -1 >::backtraceD' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:241:17: style: Unused private function: 'FixedSizeMap::checkBloomFilter' [unusedPrivateFunction]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:250:17: style: Unused private function: 'FixedSizeMap::addToBloomFilter' [unusedPrivateFunction]
snap-1.0beta.18/SNAPLib/BigAlloc.h:130:13: style:inconclusive: Member variable 'CountingBigAllocator::allocationGranularity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/BigAlloc.h:121:108: note: Member variable 'CountingBigAllocator::allocationGranularity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BigAlloc.h:130:13: note: Member variable 'CountingBigAllocator::allocationGranularity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:665:26: style:inconclusive: Member variable 'Read::clippingState' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/Read.h:228:13: note: Member variable 'Read::clippingState' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:665:26: note: Member variable 'Read::clippingState' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:691:15: style:inconclusive: Member variable 'Read::upcaseForwardRead' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/Read.h:229:13: note: Member variable 'Read::upcaseForwardRead' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:691:15: note: Member variable 'Read::upcaseForwardRead' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:660:21: style:inconclusive: Member variable 'Read::readGroup' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/Read.h:230:13: note: Member variable 'Read::readGroup' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:660:21: note: Member variable 'Read::readGroup' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:666:13: style:inconclusive: Member variable 'Read::additionalFrontClipping' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/Read.h:232:76: note: Member variable 'Read::additionalFrontClipping' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:666:13: note: Member variable 'Read::additionalFrontClipping' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:854:11: style:inconclusive: Member variable 'ReadWithOwnMemory::idBuffer' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/Read.h:776:72: note: Member variable 'ReadWithOwnMemory::idBuffer' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Read.h:854:11: note: Member variable 'ReadWithOwnMemory::idBuffer' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/RangeSplitter.h:109:23: style:inconclusive: Member variable 'RangeSplittingPairedReadSupplier::underlyingReader' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/RangeSplitter.h:97:127: note: Member variable 'RangeSplittingPairedReadSupplier::underlyingReader' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/RangeSplitter.h:109:23: note: Member variable 'RangeSplittingPairedReadSupplier::underlyingReader' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenomeIndex.h:270:16: style:inconclusive: Member variable 'IndexBuildStats::seedsWithMultipleOccurrences' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:265:56: note: Member variable 'IndexBuildStats::seedsWithMultipleOccurrences' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenomeIndex.h:270:16: note: Member variable 'IndexBuildStats::seedsWithMultipleOccurrences' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerContext.h:112:42: style:inconclusive: Member variable 'AlignerContext::argc' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:57:5: note: Member variable 'AlignerContext::argc' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerContext.h:112:42: note: Member variable 'AlignerContext::argc' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:256:9: style:inconclusive: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:50:36: note: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:256:9: note: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:258:9: style:inconclusive: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::occupied' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:60:9: note: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::occupied' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:258:9: note: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::occupied' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < DataBatch , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BigAlloc.h:86:6: warning:inconclusive: Class 'BigAllocator' which has virtual members does not have a virtual destructor. [virtualDestructor]
snap-1.0beta.18/SNAPLib/Compat.h:472:18: style:inconclusive: Technically the member function 'FileMapper::getFileSize' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BigAlloc.h:93:10: performance:inconclusive: Technically the member function 'BigAllocator::checkCanaries' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/BigAlloc.h:126:12: style:inconclusive: Technically the member function 'CountingBigAllocator::getMemoryUsed' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BigAlloc.h:161:10: style:inconclusive: Technically the member function 'ThreadHeap::free' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:460:14: style:inconclusive: Technically the member function 'VariableSizeMultiMap::valueIterator::hasValue' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/ParallelTask.h:277:9: style:inconclusive: Technically the member function 'ParallelWorker::getThreadNum' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/ParallelTask.h:278:9: style:inconclusive: Technically the member function 'ParallelWorker::getNumThreads' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/DataWriter.h:248:10: style:inconclusive: Technically the member function 'StdoutAsyncFile::isQueueEmpty' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:455:26: style:inconclusive: Technically the member function 'Read::getBatch' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:459:31: style:inconclusive: Technically the member function 'Read::getOriginalAlignedLocation' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:460:25: style:inconclusive: Technically the member function 'Read::getOriginalMAPQ' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:461:25: style:inconclusive: Technically the member function 'Read::getOriginalSAMFlags' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:462:25: style:inconclusive: Technically the member function 'Read::getOriginalFrontClipping' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:463:25: style:inconclusive: Technically the member function 'Read::getOriginalBackClipping' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:464:25: style:inconclusive: Technically the member function 'Read::getOriginalFrontHardClipping' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:465:25: style:inconclusive: Technically the member function 'Read::getOriginalBackHardClipping' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:466:28: style:inconclusive: Technically the member function 'Read::getOriginalRNEXT' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:467:25: style:inconclusive: Technically the member function 'Read::getOriginalRNEXTLength' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:468:25: style:inconclusive: Technically the member function 'Read::getOriginalPNEXT' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:557:14: style:inconclusive: Technically the member function 'Read::computeReverseCompliment' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Read.h:698:21: performance:inconclusive: Technically the member function 'Read::assureLocalBufferLargeEnough' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/Read.h:783:10: style:inconclusive: Technically the member function 'ReadWithOwnMemory::dispose' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Seed.h:140:16: style:inconclusive: Technically the member function 'Seed::getBase' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Seed.h:150:17: style:inconclusive: Technically the member function 'Seed::toString' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/ApproximateCounter.h:22:20: performance:inconclusive: Technically the member function 'ApproximateCounter::hash' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:35:19: style:inconclusive: Technically the member function 'GenomeIndex::getGenome' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/AlignerContext.h:60:10: performance:inconclusive: Technically the member function 'AlignerContext::printStatsHeader' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:209:17: note: Technically the member function 'AlignerContext::printStatsHeader' can be static (but you may consider moving to unnamed namespace).
snap-1.0beta.18/SNAPLib/AlignerContext.h:60:10: note: Technically the member function 'AlignerContext::printStatsHeader' can be static (but you may consider moving to unnamed namespace).
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:16:20: style:inconclusive: Technically the member function 'NumericHash::operator()' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:81:10: performance:inconclusive: Technically the member function 'FixedSizeMap::resize' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:168:16: style:inconclusive: Technically the member function 'FixedSizeMap::getSize' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:171:10: style:inconclusive: Technically the member function 'FixedSizeMap::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:197:7: performance:inconclusive: Technically the member function 'FixedSizeMap::key' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:202:8: performance:inconclusive: Technically the member function 'FixedSizeMap::value' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:283:10: performance:inconclusive: Technically the member function 'FixedSizeMap::isPowerOf2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:271:14: style:inconclusive: Technically the member function 'FixedSizeMap::Entry::operatordelete[]' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:33:17: style:inconclusive: Technically the member function 'LVResult::isValid' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BaseAligner.h:96:17: performance:inconclusive: Technically the member function 'BaseAligner::getName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/BaseAligner.h:98:17: style:inconclusive: Technically the member function 'BaseAligner::checkedAllSeeds' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BaseAligner.h:101:10: style:inconclusive: Technically the member function 'BaseAligner::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BaseAligner.h:104:10: style:inconclusive: Technically the member function 'BaseAligner::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BaseAligner.h:106:17: style:inconclusive: Technically the member function 'BaseAligner::getExplorePopularSeeds' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BaseAligner.h:109:17: style:inconclusive: Technically the member function 'BaseAligner::getStopOnFirstHit' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BaseAligner.h:164:10: performance:inconclusive: Technically the member function 'BaseAligner::decomposeGenomeLocation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:353:10: style:inconclusive: Technically the member function 'LandauVishkin < 1 >::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:356:10: style:inconclusive: Technically the member function 'LandauVishkin < 1 >::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:364:16: performance:inconclusive: Technically the member function 'LandauVishkin < 1 >::countPerfectMatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:353:10: style:inconclusive: Technically the member function 'LandauVishkin < -1 >::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:356:10: style:inconclusive: Technically the member function 'LandauVishkin < -1 >::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:364:16: performance:inconclusive: Technically the member function 'LandauVishkin < -1 >::countPerfectMatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:94:16: style:inconclusive: Technically the member function 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::size' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:97:16: style:inconclusive: Technically the member function 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::getCapacity' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BigAlloc.h:85:5: style: Class 'BigAllocator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/BigAlloc.h:121:5: style: Class 'CountingBigAllocator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/BigAlloc.h:147:5: style: Struct 'ThreadHeap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Util.h:447:5: style: Struct 'IdPair' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Util.h:478:5: style: Struct 'IdIntPair' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Util.h:482:5: style: Struct 'IdIntPair' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Util.h:529:2: style: Class 'NWaiter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:403:5: style: Class 'VariableSizeMapBig' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:432:5: style: Class 'VariableSizeMultiMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/DataReader.h:51:12: style: Struct 'DataBatch' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/DataReader.h:83:12: style: Struct 'DataBatch' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/DataReader.h:196:5: style: Class 'BatchTracker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Read.h:778:5: style: Class 'ReadWithOwnMemory' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/AlignerOptions.h:59:5: style: Struct 'AlignerOptions' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/AlignerStats.h:44:5: style: Struct 'AlignerStats' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:126:3: style: Class 'OverflowBackpointerAnchor' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:36:5: style: Class 'FixedSizeMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:92:5: style: Class 'ReadSupplierQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:105:5: style: Class 'ReadSupplierQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:182:5: style: Class 'ReadSupplierFromQueue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/PairedAligner.h:36:5: style: Class 'PairedAlignerContext' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/PairedAligner.h:77:5: style: Struct 'PairedAlignerOptions' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/ParallelTask.h:50:5: style: Class 'ParallelTask < WorkerContext >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:49:5: style: Class 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < DataBatch , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:41:17: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:45:17: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:41:17: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:42:14: style: The function 'getchar' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:50:17: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:42:14: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:43:16: style: The function 'gets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:55:16: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:43:16: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:44:14: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:58:14: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:44:14: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:45:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:61:15: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:45:15: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_map.h:34:17: style: The function 'prefetch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:68:17: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_map.h:34:17: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_map.h:35:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:45:15: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_map.h:35:15: note: Function in derived class
snap-1.0beta.18/SNAPLib/BigAlloc.h:124:19: style: The function 'allocate' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/BigAlloc.h:88:19: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/BigAlloc.h:124:19: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.h:222:10: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Compat.h:397:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.h:222:10: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.h:226:24: style: The function 'getWriter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Compat.h:414:21: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.h:226:24: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.h:227:24: style: The function 'getReader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Compat.h:431:21: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.h:227:24: note: Function in derived class
snap-1.0beta.18/SNAPLib/AlignerOptions.h:113:18: style: The function 'usageMessage' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerOptions.h:36:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/AlignerOptions.h:113:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/AlignerOptions.h:115:18: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerOptions.h:38:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/AlignerOptions.h:115:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:64:11: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:151:19: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:64:11: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:66:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:154:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:66:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:69:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:155:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:69:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:83:19: style: The function 'generateNewReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:170:27: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:83:19: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:84:20: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:171:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:84:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:100:18: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:161:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:100:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:102:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:164:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:102:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:105:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:165:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:105:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:120:25: style: The function 'generateNewPairedReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:177:33: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:120:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:121:20: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:178:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/RangeSplitter.h:121:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/AlignerStats.h:76:18: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerStats.h:35:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/AlignerStats.h:76:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/AlignerStats.h:78:18: style: The function 'printHistograms' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerStats.h:37:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/AlignerStats.h:78:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:111:19: style: The function 'generateNewReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:170:27: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:111:19: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:112:25: style: The function 'generateNewPairedReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:177:33: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:112:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:113:20: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:171:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:113:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:185:11: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:151:19: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:185:11: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:187:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:154:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:187:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:190:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:155:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:190:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:206:10: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:161:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:206:10: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:208:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:164:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:208:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:211:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:165:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:211:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:42:18: style: The function 'initialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:77:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:42:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:44:27: style: The function 'newStats' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:80:27: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:44:27: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:46:18: style: The function 'runTask' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:83:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:46:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:48:18: style: The function 'runIterationThread' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:86:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:48:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:54:10: style: The function 'isPaired' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:91:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:54:10: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:58:18: style: The function 'typeSpecificBeginIteration' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:88:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:58:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:59:18: style: The function 'typeSpecificNextIteration' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:89:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:59:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:79:18: style: The function 'usageMessage' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerOptions.h:113:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:79:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:81:18: style: The function 'parse' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerOptions.h:115:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:81:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.h:83:18: style: The function 'isPaired' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerOptions.h:128:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.h:83:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Read.h:750:37: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:346:9: warning: %f in format string (no. 7) requires 'double' but the argument type is 'signed long'. [invalidPrintfArgType_float]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:346:9: warning: %lld in format string (no. 8) requires 'long long' but the argument type is 'double'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:346:9: warning: %lld in format string (no. 9) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/BigAlloc.h:149:24: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BigAlloc.h:163:37: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.h:290:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.h:301:31: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.h:319:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.h:350:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.h:362:31: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.h:381:28: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.h:123:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.h:169:21: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.h:181:28: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.h:187:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.h:192:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.h:197:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Seed.h:181:32: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:183:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:199:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/FixedSizeMap.h:204:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:41:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:157:52: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:371:14: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:373:21: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:375:14: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/ParallelTask.h:179:6: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/ParallelTask.h:187:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:56:19: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:119:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:77:19: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:191:21: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Read.h:750:35: style: Unsigned expression 'i' can't be negative so it is unnecessary to test it. [unsignedPositive]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:72:95: style:inconclusive: Function 'runAlignment' argument 4 names different: declaration 'nArgsConsumed' definition 'argsConsumed'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignerContext.h:50:83: note: Function 'runAlignment' argument 4 names different: declaration 'nArgsConsumed' definition 'argsConsumed'.
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:72:95: note: Function 'runAlignment' argument 4 names different: declaration 'nArgsConsumed' definition 'argsConsumed'.
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:386:9: style:inconclusive: Function 'parseOptions' argument 1 names different: declaration 'argc' definition 'i_argc'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignerContext.h:74:38: note: Function 'parseOptions' argument 1 names different: declaration 'argc' definition 'i_argc'.
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:386:9: note: Function 'parseOptions' argument 1 names different: declaration 'argc' definition 'i_argc'.
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:387:18: style:inconclusive: Function 'parseOptions' argument 2 names different: declaration 'argv' definition 'i_argv'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignerContext.h:74:57: note: Function 'parseOptions' argument 2 names different: declaration 'argv' definition 'i_argv'.
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:387:18: note: Function 'parseOptions' argument 2 names different: declaration 'argv' definition 'i_argv'.
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:388:17: style:inconclusive: Function 'parseOptions' argument 3 names different: declaration 'version' definition 'i_version'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignerContext.h:74:75: note: Function 'parseOptions' argument 3 names different: declaration 'version' definition 'i_version'.
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:388:17: note: Function 'parseOptions' argument 3 names different: declaration 'version' definition 'i_version'.
snap-1.0beta.18/SNAPLib/ParallelTask.h:177:11: style:inconclusive: Function 'forkWorker' argument 1 names different: declaration 'threadContext' definition 'forkArg'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/ParallelTask.h:68:34: note: Function 'forkWorker' argument 1 names different: declaration 'threadContext' definition 'forkArg'.
snap-1.0beta.18/SNAPLib/ParallelTask.h:177:11: note: Function 'forkWorker' argument 1 names different: declaration 'threadContext' definition 'forkArg'.
snap-1.0beta.18/SNAPLib/ParallelTask.h:185:11: style:inconclusive: Function 'threadWorker' argument 1 names different: declaration 'threadContext' definition 'threadArg'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/ParallelTask.h:66:36: note: Function 'threadWorker' argument 1 names different: declaration 'threadContext' definition 'threadArg'.
snap-1.0beta.18/SNAPLib/ParallelTask.h:185:11: note: Function 'threadWorker' argument 1 names different: declaration 'threadContext' definition 'threadArg'.
snap-1.0beta.18/SNAPLib/HashTable.h:95:23: style: Local variable 'entry' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/HashTable.h:90:19: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/HashTable.h:95:23: note: Shadow variable
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:396:21: style: Local variable 'options' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/AlignerContext.h:101:42: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:396:21: note: Shadow variable
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:433:13: style: Local variable 'argsConsumed' shadows outer argument [shadowArgument]
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:389:15: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/AlignerContext.cpp:433:13: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.h:188:25: style: Local variable 'p' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:156:17: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.h:188:25: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.h:189:25: style: Local variable 't' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:157:17: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.h:189:25: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.h:191:21: style: Local variable 'end' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:158:9: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.h:191:21: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.h:192:29: style: Local variable 'pend' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:159:17: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.h:192:29: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.h:202:21: style: Local variable 'end' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:158:9: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.h:202:21: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.h:203:29: style: Local variable 'pend' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:159:17: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.h:203:29: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.h:217:21: style: Local variable 'end' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:158:9: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.h:217:21: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.h:218:29: style: Local variable 'pend' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:159:17: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.h:218:29: note: Shadow variable
snap-1.0beta.18/SNAPLib/Seed.h:107:33: style: Parameter 'peer' can be declared as reference to const [constParameter]
snap-1.0beta.18/SNAPLib/Seed.h:111:34: style: Parameter 'peer' can be declared as reference to const [constParameter]
snap-1.0beta.18/SNAPLib/Seed.h:115:33: style: Parameter 'peer' can be declared as reference to const [constParameter]
snap-1.0beta.18/SNAPLib/Seed.h:119:34: style: Parameter 'peer' can be declared as reference to const [constParameter]
snap-1.0beta.18/SNAPLib/Seed.h:123:34: style: Parameter 'peer' can be declared as reference to const [constParameter]
snap-1.0beta.18/SNAPLib/Seed.h:127:34: style: Parameter 'peer' can be declared as reference to const [constParameter]
snap-1.0beta.18/SNAPLib/Util.h:511:19: portability: Shifting signed 64-bit value by 63 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
snap-1.0beta.18/SNAPLib/Util.h:516:19: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
snap-1.0beta.18/SNAPLib/Read.h:809:27: style: Variable 'ownBufferUsed' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:192:34: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:203:34: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:218:34: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:159:17: style: Variable 'pend' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/AlignerStats.h:53:12: style:inconclusive: Member variable 'AlignerStats::lvCalls' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/AlignerStats.cpp:41:5: note: Member variable 'AlignerStats::lvCalls' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerStats.h:53:12: note: Member variable 'AlignerStats::lvCalls' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerStats.cpp:82:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignerStats.cpp:80:26: style:inconclusive: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignerStats.h:76:43: note: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'.
snap-1.0beta.18/SNAPLib/AlignerStats.cpp:80:26: note: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:33:42: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:34:43: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:55:42: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:56:43: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:72:42: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:73:43: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:94:42: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:95:43: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:29:60: style:inconclusive: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignmentResult.h:58:52: note: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:29:60: note: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:29:80: style:inconclusive: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignmentResult.h:58:71: note: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:29:80: note: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:53:55: style:inconclusive: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignmentResult.h:59:43: note: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:53:55: note: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:53:75: style:inconclusive: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignmentResult.h:59:62: note: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:53:75: note: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:68:60: style:inconclusive: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignmentResult.h:91:52: note: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:68:60: note: Function 'compareByContigAndScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:68:80: style:inconclusive: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignmentResult.h:91:71: note: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:68:80: note: Function 'compareByContigAndScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:92:51: style:inconclusive: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignmentResult.h:92:43: note: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:92:51: note: Function 'compareByScore' argument 1 names different: declaration 'first' definition 'first_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:92:71: style:inconclusive: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/AlignmentResult.h:92:62: note: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-1.0beta.18/SNAPLib/AlignmentResult.cpp:92:71: note: Function 'compareByScore' argument 2 names different: declaration 'second' definition 'second_'.
snap-1.0beta.18/SNAPLib/ApproximateCounter.h:13:14: style:inconclusive: Technically the member function 'ApproximateCounter::getCount' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/ApproximateCounter.cpp:29:30: note: Technically the member function 'ApproximateCounter::getCount' can be const.
snap-1.0beta.18/SNAPLib/ApproximateCounter.h:13:14: note: Technically the member function 'ApproximateCounter::getCount' can be const.
snap-1.0beta.18/SNAPLib/ApproximateCounter.cpp:34:45: portability: Shifting signed 64-bit value by 63 bits is implementation-defined behaviour. See condition at line 34. [shiftTooManyBitsSigned]
snap-1.0beta.18/SNAPLib/ApproximateCounter.cpp:34:18: note: Assuming that condition 'r<64' is not redundant
snap-1.0beta.18/SNAPLib/ApproximateCounter.cpp:34:45: note: Shift
snap-1.0beta.18/SNAPLib/Bam.cpp:1316:42: warning:inconclusive: The buffer 'bestReadId' may not be null-terminated after the call to strncpy(). [terminateStrncpy]
snap-1.0beta.18/SNAPLib/BufferedAsync.h:25:1: style: The class 'BufferedAsyncReader' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
snap-1.0beta.18/SNAPLib/BufferedAsync.h:48:1: style: The class 'BufferedAsyncWriter' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
snap-1.0beta.18/SNAPLib/Bam.cpp:42:12: warning: Member variable 'BAMReader::data' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Bam.cpp:42:12: warning: Member variable 'BAMReader::extraOffset' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Bam.cpp:1109:5: warning: Member variable 'BAMFilter::currentWriter' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Bam.cpp:1109:5: warning: Member variable 'BAMFilter::currentBuffer' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Bam.cpp:1109:5: warning: Member variable 'BAMFilter::currentBufferBytes' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/Bam.cpp:1109:5: warning: Member variable 'BAMFilter::currentOffset' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:57:16: style:inconclusive: Member variable 'GzipWriterFilterSupplier::multiThreaded' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:46:9: note: Member variable 'GzipWriterFilterSupplier::multiThreaded' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:57:16: note: Member variable 'GzipWriterFilterSupplier::multiThreaded' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Bam.cpp:1130:10: style:inconclusive: Member variable 'BAMFilter::header' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/Bam.cpp:1109:79: note: Member variable 'BAMFilter::header' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Bam.cpp:1130:10: note: Member variable 'BAMFilter::header' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Bam.cpp:1648:9: style:inconclusive: Member variable 'BAMIndexSupplier::lastRefId' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/Bam.cpp:1607:9: note: Member variable 'BAMIndexSupplier::lastRefId' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Bam.cpp:1648:9: note: Member variable 'BAMIndexSupplier::lastRefId' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < unsigned long , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < uint64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < DuplicateMateInfo * , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < DuplicateMateInfo * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < DuplicateMateInfo * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < DuplicateMateInfo * , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < DuplicateMateInfo * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < DuplicateMateInfo * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < BAMChunk , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BufferedAsync.h:33:25: style:inconclusive: Technically the member function 'BufferedAsyncReader::getWaitTimeInMillis' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BufferedAsync.h:55:25: style:inconclusive: Technically the member function 'BufferedAsyncWriter::getWaitTimeInMillis' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/Bam.h:182:17: performance:inconclusive: Technically the member function 'BAMAlignment::validate' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/Bam.cpp:1317:17: style:inconclusive: Technically the member function 'DuplicateMateInfo::getBestReadId' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/SAM.h:151:5: style: Class 'SAMFormat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Bam.h:367:9: style: Class 'BAMReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Bam.cpp:669:5: style: Class 'BAMFormat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Bam.cpp:1293:5: style: Struct 'DuplicateReadKey' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Bam.cpp:1323:5: style: Class 'BAMDupMarkFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Bam.cpp:1565:5: style: Class 'BAMDupMarkSupplier' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/Bam.cpp:1589:5: style: Class 'BAMIndexFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < DuplicateReadKey , DuplicateMateInfo , 150 , MapNumericHash < DuplicateReadKey > , 70 , 0 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < DuplicateReadKey , DuplicateMateInfo , 150 , MapNumericHash < DuplicateReadKey > , 70 , 0 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint32_t , VariableSizeVector < BAMChunk , 150 , false > , 150 , MapNumericHash < uint32_t > , 80 , -1 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < uint32_t , VariableSizeVector < BAMChunk , 150 , false > , 150 , MapNumericHash < uint32_t > , 80 , -1 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < unsigned long , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < uint64_t , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < DuplicateMateInfo * , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < BAMChunk , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/SAM.h:58:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:115:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:58:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/SAM.h:60:22: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:114:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:60:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/SAM.h:68:22: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:119:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:68:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/SAM.h:71:22: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:122:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:71:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/SAM.h:153:18: style: The function 'getSortInfo' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:48:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:153:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SAM.h:155:18: style: The function 'setupReaderContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:80:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:155:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SAM.h:158:33: style: The function 'getWriterSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:86:33: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:158:33: note: Function in derived class
snap-1.0beta.18/SNAPLib/SAM.h:160:18: style: The function 'writeHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:88:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:160:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SAM.h:164:18: style: The function 'writeRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:92:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SAM.h:164:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.h:373:22: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:114:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.h:373:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.h:392:14: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:136:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.h:392:14: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.h:397:14: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:139:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.h:397:14: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.h:400:14: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:140:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.h:400:14: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.h:403:32: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:142:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.h:403:32: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.h:410:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:137:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.h:410:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:59:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:81:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:59:33: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:61:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:84:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:61:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:62:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:85:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:62:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:671:18: style: The function 'getSortInfo' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:48:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:671:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:673:18: style: The function 'setupReaderContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:80:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:673:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:676:33: style: The function 'getWriterSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:86:33: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:676:33: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:678:18: style: The function 'writeHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:88:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:678:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:682:18: style: The function 'writeRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/FileFormat.h:92:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:682:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1113:15: style: The function 'inHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:57:16: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1113:15: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1116:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:60:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1116:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1118:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:66:24: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1118:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1345:18: style: The function 'onRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Bam.cpp:1121:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1345:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1568:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:81:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1568:33: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1571:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:84:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1571:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1572:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:85:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1572:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1593:18: style: The function 'onRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Bam.cpp:1121:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1593:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1614:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:81:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1614:33: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1617:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:84:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1617:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1618:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:85:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/Bam.cpp:1618:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/Bam.cpp:1820:19: style: Condition 'bsize==0' is always false [knownConditionTrueFalse]
snap-1.0beta.18/SNAPLib/Bam.cpp:1818:37: note: Assignment 'bsize=h->BSIZE()+1', assigned value is greater than 0
snap-1.0beta.18/SNAPLib/Bam.cpp:1820:19: note: Condition 'bsize==0' is always false
snap-1.0beta.18/SNAPLib/Bam.h:51:47: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:54:16: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:57:49: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:77:18: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:80:16: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:83:49: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:122:36: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:125:41: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:207:18: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:210:52: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:213:53: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:216:53: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:219:54: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:222:53: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:225:54: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:228:53: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:233:53: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:236:53: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:239:55: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:266:54: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:306:39: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:319:35: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:338:43: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:341:26: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:350:28: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.h:404:19: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:130:11: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:145:12: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:175:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:207:54: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:257:33: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:282:33: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:299:40: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:310:48: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:524:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:536:36: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:566:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:713:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:749:30: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:758:35: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:792:28: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:893:56: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:942:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:981:14: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:993:14: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1000:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1003:31: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1005:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1008:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1011:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1016:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1018:12: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1021:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1023:6: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1085:14: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1090:15: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1094:14: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1099:14: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1149:16: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1197:15: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1219:45: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1554:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:1817:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Bam.cpp:322:13: style: The scope of the variable 'lastOp' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/Bam.cpp:906:17: style: The scope of the variable 'warningPrinted' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/Bam.cpp:444:12: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
snap-1.0beta.18/SNAPLib/Bam.cpp:445:12: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
snap-1.0beta.18/SNAPLib/Bam.cpp:387:13: style:inconclusive: Function 'encodeSeq' argument 1 names different: declaration 'nibbles' definition 'encoded'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Bam.h:153:35: note: Function 'encodeSeq' argument 1 names different: declaration 'nibbles' definition 'encoded'.
snap-1.0beta.18/SNAPLib/Bam.cpp:387:13: note: Function 'encodeSeq' argument 1 names different: declaration 'nibbles' definition 'encoded'.
snap-1.0beta.18/SNAPLib/Bam.cpp:557:21: style:inconclusive: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Bam.h:426:41: note: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'.
snap-1.0beta.18/SNAPLib/Bam.cpp:557:21: note: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1174:12: style:inconclusive: Function 'getRead' argument 1 names different: declaration 'fileOffset' definition 'offset'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Bam.cpp:1123:34: note: Function 'getRead' argument 1 names different: declaration 'fileOffset' definition 'offset'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1174:12: note: Function 'getRead' argument 1 names different: declaration 'fileOffset' definition 'offset'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1194:19: style:inconclusive: Function 'getNextRead' argument 1 names different: declaration 'read' definition 'bam'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Bam.cpp:1125:45: note: Function 'getNextRead' argument 1 names different: declaration 'read' definition 'bam'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1194:19: note: Function 'getNextRead' argument 1 names different: declaration 'read' definition 'bam'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1195:13: style:inconclusive: Function 'getNextRead' argument 2 names different: declaration 'o_fileOffset' definition 'io_offset'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Bam.cpp:1125:59: note: Function 'getNextRead' argument 2 names different: declaration 'o_fileOffset' definition 'io_offset'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1195:13: note: Function 'getNextRead' argument 2 names different: declaration 'o_fileOffset' definition 'io_offset'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1365:40: style:inconclusive: Function 'onRead' argument 1 names different: declaration 'bam' definition 'lastBam'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Bam.cpp:1345:39: note: Function 'onRead' argument 1 names different: declaration 'bam' definition 'lastBam'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1365:40: note: Function 'onRead' argument 1 names different: declaration 'bam' definition 'lastBam'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1365:56: style:inconclusive: Function 'onRead' argument 2 names different: declaration 'fileOffset' definition 'lastOffset'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Bam.cpp:1345:51: note: Function 'onRead' argument 2 names different: declaration 'fileOffset' definition 'lastOffset'.
snap-1.0beta.18/SNAPLib/Bam.cpp:1365:56: note: Function 'onRead' argument 2 names different: declaration 'fileOffset' definition 'lastOffset'.
snap-1.0beta.18/SNAPLib/Bam.cpp:630:53: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:336:23: performance: Function parameter 'key' should be passed by const reference. [passedByValue]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:336:30: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:344:26: performance: Function parameter 'key' should be passed by const reference. [passedByValue]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:353:33: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:23:28: performance: Function parameter 'k' should be passed by const reference. [passedByValue]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:23:33: performance: Function parameter 'v' should be passed by const reference. [passedByValue]
snap-1.0beta.18/SNAPLib/Bam.cpp:388:11: style: Parameter 'ascii' can be declared as pointer to const [constParameter]
snap-1.0beta.18/SNAPLib/Bam.cpp:322:20: style: Variable 'lastOp' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/Bam.cpp:329:16: style: Variable 'lastOp' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/Bam.cpp:878:29: style: Variable 'newAddFrontClipping' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/Bam.cpp:1144:13: style: Variable 'ok' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/Bam.cpp:1199:22: style: Variable 'oldOffset' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/Bam.cpp:1148:88: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1404:71: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1415:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1463:71: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1472:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1507:130: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1521:71: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1530:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1741:84: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Bam.cpp:1755:91: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::highestUsedWeightList' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::lowestPossibleScoreOfAnyUnseenLocation' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::mostSeedsContainingAnyParticularBase' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::nSeedsApplied' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::bestScore' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::bestScoreGenomeLocation' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::secondBestScore' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::secondBestScoreGenomeLocation' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::secondBestScoreDirection' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::scoreLimit' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::lvScores' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::lvScoresAfterBestFound' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::probabilityOfAllCandidates' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::probabilityOfBestCandidate' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::firstPassSeedsNotSkipped' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::smallestSkippedSeed' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::highestWeightListChecked' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::totalProbabilityByDepth' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:47:14: warning: Member variable 'BaseAligner::popularSeedsSkipped' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.h:155:9: warning: Member variable 'Candidate::seedOffset' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:1361:32: warning: Member variable 'HashTableElement::candidatesScored' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:1361:32: warning: Member variable 'HashTableElement::bestScoreGenomeLocation' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BaseAligner.h:294:14: style:inconclusive: Member variable 'BaseAligner::extraSearchDepth' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:66:57: note: Member variable 'BaseAligner::extraSearchDepth' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BaseAligner.h:294:14: note: Member variable 'BaseAligner::extraSearchDepth' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BaseAligner.h:296:14: style:inconclusive: Member variable 'BaseAligner::noUkkonen' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:68:9: note: Member variable 'BaseAligner::noUkkonen' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BaseAligner.h:296:14: note: Member variable 'BaseAligner::noUkkonen' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BaseAligner.h:293:14: style:inconclusive: Member variable 'BaseAligner::minWeightToCheck' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:69:3: note: Member variable 'BaseAligner::minWeightToCheck' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/BaseAligner.h:293:14: note: Member variable 'BaseAligner::minWeightToCheck' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/SeedSequencer.h:35:21: style:inconclusive: Technically the member function 'SeedSequencer::SeedOffset' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/SeedSequencer.h:40:21: style:inconclusive: Technically the member function 'SeedSequencer::GetWrappedNextSeedToTest' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:123:13: warning: Class 'BaseAligner' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:123:13: warning: Class 'BaseAligner' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/SeedSequencer.h:33:5: style: Class 'SeedSequencer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:146:22: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:148:22: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:154:33: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:156:33: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:159:18: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:179:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:181:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:190:39: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:191:34: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:192:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:193:32: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:194:38: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:196:35: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:202:39: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:203:34: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:204:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:205:32: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:206:38: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:208:35: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:800:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:1235:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:877:33: style: The scope of the variable 'score2' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:967:32: style: The scope of the variable 'nearbyGenomeLocation' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:52:21: style:inconclusive: Function 'BaseAligner' argument 5 names different: declaration 'i_maxSeedsToUse' definition 'i_maxSeedsToUseFromCommandLine'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/BaseAligner.h:48:25: note: Function 'BaseAligner' argument 5 names different: declaration 'i_maxSeedsToUse' definition 'i_maxSeedsToUseFromCommandLine'.
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:52:21: note: Function 'BaseAligner' argument 5 names different: declaration 'i_maxSeedsToUse' definition 'i_maxSeedsToUseFromCommandLine'.
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:239:34: style:inconclusive: Function 'AlignRead' argument 1 names different: declaration 'read' definition 'inputRead'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/BaseAligner.h:67:34: note: Function 'AlignRead' argument 1 names different: declaration 'read' definition 'inputRead'.
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:239:34: note: Function 'AlignRead' argument 1 names different: declaration 'read' definition 'inputRead'.
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:1208:25: style:inconclusive: Function 'allocateNewCandidate' argument 1 names different: declaration 'genomeLoation' definition 'genomeLocation'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/BaseAligner.h:281:46: note: Function 'allocateNewCandidate' argument 1 names different: declaration 'genomeLoation' definition 'genomeLocation'.
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:1208:25: note: Function 'allocateNewCandidate' argument 1 names different: declaration 'genomeLoation' definition 'genomeLocation'.
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:833:26: style: Local variable 'score' shadows outer function [shadowFunction]
snap-1.0beta.18/SNAPLib/BaseAligner.h:268:5: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:833:26: note: Shadow variable
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:880:25: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/BaseAligner.h:287:14: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/BaseAligner.cpp:880:25: note: Shadow variable
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:391:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:407:7: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:416:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:417:30: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:457:19: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:559:21: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:569:12: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:524:39: style:inconclusive: Function 'allocate' argument 1 names different: declaration 'amountToAllocate' definition 'sizeToAllocate'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/BigAlloc.h:124:35: note: Function 'allocate' argument 1 names different: declaration 'amountToAllocate' definition 'sizeToAllocate'.
snap-1.0beta.18/SNAPLib/BigAlloc.cpp:524:39: note: Function 'allocate' argument 1 names different: declaration 'amountToAllocate' definition 'sizeToAllocate'.
snap-1.0beta.18/SNAPLib/BufferedAsync.h:30:25: style:inconclusive: Technically the member function 'BufferedAsyncReader::atEnd' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:80:22: note: Technically the member function 'BufferedAsyncReader::atEnd' can be const.
snap-1.0beta.18/SNAPLib/BufferedAsync.h:30:25: note: Technically the member function 'BufferedAsyncReader::atEnd' can be const.
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:46:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:47:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:113:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:151:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:152:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:178:10: style: The scope of the variable 'ok' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:33:12: style:inconclusive: Function 'open' argument 3 names different: declaration 'length' definition 'bytes'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/BufferedAsync.h:28:69: note: Function 'open' argument 3 names different: declaration 'length' definition 'bytes'.
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:33:12: note: Function 'open' argument 3 names different: declaration 'length' definition 'bytes'.
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:34:12: style:inconclusive: Function 'open' argument 4 names different: declaration 'bufferSize' definition 'i_bufferSize'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/BufferedAsync.h:28:84: note: Function 'open' argument 4 names different: declaration 'bufferSize' definition 'i_bufferSize'.
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:34:12: note: Function 'open' argument 4 names different: declaration 'bufferSize' definition 'i_bufferSize'.
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:144:12: style:inconclusive: Function 'open' argument 2 names different: declaration 'bufferSize' definition 'i_bufferSize'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/BufferedAsync.h:51:54: note: Function 'open' argument 2 names different: declaration 'bufferSize' definition 'i_bufferSize'.
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:144:12: note: Function 'open' argument 2 names different: declaration 'bufferSize' definition 'i_bufferSize'.
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:212:16: style: Local variable 'start' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:207:12: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:212:16: note: Shadow variable
snap-1.0beta.18/SNAPLib/BufferedAsync.cpp:178:13: style: Variable 'ok' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.h:89:17: style:inconclusive: Member variable 'ChimericPairedEndAligner::forceSpacing' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.cpp:58:62: note: Member variable 'ChimericPairedEndAligner::forceSpacing' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.h:89:17: note: Member variable 'ChimericPairedEndAligner::forceSpacing' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < util :: IdPair , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.h:63:10: style:inconclusive: Technically the member function 'ChimericPairedEndAligner::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.h:81:10: style:inconclusive: Technically the member function 'ChimericPairedEndAligner::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.cpp:61:5: warning: Class 'ChimericPairedEndAligner' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.cpp:61:5: warning: Class 'ChimericPairedEndAligner' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < util :: IdPair , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.h:65:18: style: The function 'align' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/PairedEndAligner.h:40:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.h:65:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.h:83:20: style: The function 'getLocationsScored' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/PairedEndAligner.h:61:20: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ChimericPairedEndAligner.h:83:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/SingleAligner.h:36:5: style: Class 'SingleAlignerContext' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/SingleAligner.h:43:27: style: The function 'newStats' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:80:27: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SingleAligner.h:43:27: note: Function in derived class
snap-1.0beta.18/SNAPLib/SingleAligner.h:45:18: style: The function 'runTask' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:83:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SingleAligner.h:45:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SingleAligner.h:47:18: style: The function 'runIterationThread' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:86:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SingleAligner.h:47:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SingleAligner.h:49:18: style: The function 'typeSpecificBeginIteration' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:88:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SingleAligner.h:49:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SingleAligner.h:50:18: style: The function 'typeSpecificNextIteration' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:89:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SingleAligner.h:50:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SingleAligner.h:62:10: style: The function 'isPaired' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerContext.h:91:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SingleAligner.h:62:10: note: Function in derived class
snap-1.0beta.18/SNAPLib/CommandProcessor.cpp:148:36: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/CommandProcessor.cpp:121:7: style: Local variable 'argc' shadows outer argument [shadowArgument]
snap-1.0beta.18/SNAPLib/CommandProcessor.cpp:91:24: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/CommandProcessor.cpp:121:7: note: Shadow variable
snap-1.0beta.18/SNAPLib/CommandProcessor.cpp:125:11: style: Local variable 'argv' shadows outer argument [shadowArgument]
snap-1.0beta.18/SNAPLib/CommandProcessor.cpp:91:43: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/CommandProcessor.cpp:125:11: note: Shadow variable
snap-1.0beta.18/SNAPLib/Compat.cpp:1029:0: error: #error "Don't know how to get time in nanos on your platform" [preprocessorErrorDirective]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1717:5: warning: Member variable 'DecompressManager::entry' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::batchSize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::fileName' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::fileSize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::currentMapStartSize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::currentMappedBase' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::offset' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::startBytes' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::validBytes' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2140:19: warning: Member variable 'MemMapDataReader::lock' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataReader.cpp:126:25: style:inconclusive: Member variable 'ReadBasedDataReader::maxBuffers' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:168:5: note: Member variable 'ReadBasedDataReader::maxBuffers' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:126:25: note: Member variable 'ReadBasedDataReader::maxBuffers' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:151:11: style:inconclusive: Member variable 'ReadBasedDataReader::headerBuffer' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:170:2: note: Member variable 'ReadBasedDataReader::headerBuffer' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:151:11: note: Member variable 'ReadBasedDataReader::headerBuffer' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:153:11: style:inconclusive: Member variable 'ReadBasedDataReader::headerExtra' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:171:2: note: Member variable 'ReadBasedDataReader::headerExtra' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:153:11: note: Member variable 'ReadBasedDataReader::headerExtra' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:128:10: style:inconclusive: Member variable 'ReadBasedDataReader::startedReadingHeader' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:171:41: note: Member variable 'ReadBasedDataReader::startedReadingHeader' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:128:10: note: Member variable 'ReadBasedDataReader::startedReadingHeader' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:127:10: style:inconclusive: Member variable 'ReadBasedDataReader::headerBuffersOutstanding' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:171:70: note: Member variable 'ReadBasedDataReader::headerBuffersOutstanding' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:127:10: note: Member variable 'ReadBasedDataReader::headerBuffersOutstanding' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:788:14: style:inconclusive: Member variable 'StdioDataReader::overflowBufferFilled' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:797:99: note: Member variable 'StdioDataReader::overflowBufferFilled' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:788:14: note: Member variable 'StdioDataReader::overflowBufferFilled' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:787:14: style:inconclusive: Member variable 'StdioDataReader::overflowBuffer' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:798:20: note: Member variable 'StdioDataReader::overflowBuffer' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:787:14: note: Member variable 'StdioDataReader::overflowBuffer' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1379:12: style:inconclusive: Member variable 'DecompressDataReader::offset' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1404:53: note: Member variable 'DecompressDataReader::offset' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1379:12: note: Member variable 'DecompressDataReader::offset' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1377:18: style:inconclusive: Member variable 'DecompressDataReader::totalExtra' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1405:5: note: Member variable 'DecompressDataReader::totalExtra' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1377:18: note: Member variable 'DecompressDataReader::totalExtra' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1375:18: style:inconclusive: Member variable 'DecompressDataReader::extraBytes' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1405:31: note: Member variable 'DecompressDataReader::extraBytes' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1375:18: note: Member variable 'DecompressDataReader::extraBytes' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2125:21: style:inconclusive: Member variable 'MemMapDataReader::extraUsed' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2147:9: note: Member variable 'MemMapDataReader::extraUsed' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2125:21: note: Member variable 'MemMapDataReader::extraUsed' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2119:21: style:inconclusive: Member variable 'MemMapDataReader::currentMap' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2148:9: note: Member variable 'MemMapDataReader::currentMap' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2119:21: note: Member variable 'MemMapDataReader::currentMap' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < int64_t , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataReader.cpp:181:5: warning: Class 'ReadBasedDataReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/DataReader.cpp:181:5: warning: Class 'ReadBasedDataReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1408:5: warning: Class 'DecompressDataReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1408:5: warning: Class 'DecompressDataReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2158:9: warning: Class 'MemMapDataReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2158:9: warning: Class 'MemMapDataReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1987:5: style: Class 'DecompressDataReaderSupplier' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < int64_t , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/DataReader.cpp:52:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:96:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:52:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:54:11: style: The function 'readHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:99:19: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:54:11: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:56:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:102:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:56:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:58:18: style: The function 'getData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:109:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:58:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:60:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:112:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:60:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:62:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:116:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:62:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:64:18: style: The function 'isEOF' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:119:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:64:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:66:23: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:122:23: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:66:23: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:68:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:127:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:68:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:70:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:133:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:70:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:72:20: style: The function 'getFileOffset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:136:20: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:72:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:74:18: style: The function 'getExtra' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:140:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:74:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:76:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:143:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:76:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:760:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.cpp:52:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:760:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:762:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.cpp:76:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:762:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:768:18: style: The function 'startIo' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.cpp:81:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:768:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:771:18: style: The function 'waitForBuffer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.cpp:84:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:771:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1300:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:96:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1300:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1302:19: style: The function 'readHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:99:19: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1302:19: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1304:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:102:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1304:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1306:18: style: The function 'getData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:109:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1306:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1308:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:112:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1308:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1310:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:116:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1310:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1312:18: style: The function 'isEOF' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:119:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1312:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1314:23: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:122:23: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1314:23: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1316:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:127:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1316:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1318:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:133:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1318:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1320:20: style: The function 'getFileOffset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:136:20: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1320:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1322:18: style: The function 'getExtra' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:140:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1322:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1324:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:143:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1324:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1707:18: style: The function 'step' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/ParallelTask.h:273:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1707:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1721:29: style: The function 'createWorker' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/ParallelTask.h:256:29: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1721:29: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1991:25: style: The function 'getDataReader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:157:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1991:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2050:25: style: The function 'getDataReader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:157:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2050:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2069:18: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:96:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2069:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2071:19: style: The function 'readHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:99:19: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2071:19: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2073:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:102:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2073:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2075:18: style: The function 'getData' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:109:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2075:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2077:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:112:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2077:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2079:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:116:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2079:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2081:18: style: The function 'isEOF' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:119:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2081:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2083:23: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:122:23: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2083:23: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2085:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:127:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2085:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2087:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:133:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2087:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2089:20: style: The function 'getFileOffset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:136:20: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2089:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2091:18: style: The function 'getExtra' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:140:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2091:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2093:25: style: The function 'getFilename' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataReader.h:143:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataReader.cpp:2093:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataReader.cpp:1812:71: style: Comparing expression of type 'unsigned short' against value 65536. Condition is always false. [compareValueOutOfTypeRangeError]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1685:13: portability: %lld in format string (no. 2) requires 'long long' but the argument type is 'ptrdiff_t {aka signed int}'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1689:13: portability: %lld in format string (no. 2) requires 'long long' but the argument type is 'ptrdiff_t {aka signed int}'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1693:13: warning: %lld in format string (no. 2) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1813:21: warning: %lld in format string (no. 1) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/DataReader.cpp:183:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:917:34: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1625:24: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1627:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1685:57: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1689:57: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1693:50: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1742:34: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1763:36: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1789:35: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1804:35: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1843:36: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1865:35: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2157:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2292:22: style: The scope of the variable 'found' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2475:9: style: The scope of the variable 'n' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/DataReader.cpp:166:12: style:inconclusive: Function 'ReadBasedDataReader' argument 4 names different: declaration 'bufferSpace' definition 'i_bufferSpace'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.cpp:48:97: note: Function 'ReadBasedDataReader' argument 4 names different: declaration 'bufferSpace' definition 'i_bufferSpace'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:166:12: note: Function 'ReadBasedDataReader' argument 4 names different: declaration 'bufferSpace' definition 'i_bufferSpace'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1400:12: style:inconclusive: Function 'DecompressDataReader' argument 3 names different: declaration 'totalExtra' definition 'i_totalExtra'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1296:67: note: Function 'DecompressDataReader' argument 3 names different: declaration 'totalExtra' definition 'i_totalExtra'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1400:12: note: Function 'DecompressDataReader' argument 3 names different: declaration 'totalExtra' definition 'i_totalExtra'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1614:12: style:inconclusive: Function 'decompress' argument 4 names different: declaration 'inputSize' definition 'inputBytes'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1329:85: note: Function 'decompress' argument 4 names different: declaration 'inputSize' definition 'inputBytes'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1614:12: note: Function 'decompress' argument 4 names different: declaration 'inputSize' definition 'inputBytes'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1615:13: style:inconclusive: Function 'decompress' argument 5 names different: declaration 'o_inputUsed' definition 'o_inputRead'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1329:104: note: Function 'decompress' argument 5 names different: declaration 'o_inputUsed' definition 'o_inputRead'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1615:13: note: Function 'decompress' argument 5 names different: declaration 'o_inputUsed' definition 'o_inputRead'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1617:12: style:inconclusive: Function 'decompress' argument 7 names different: declaration 'outputSize' definition 'outputBytes'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1330:30: note: Function 'decompress' argument 7 names different: declaration 'outputSize' definition 'outputBytes'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1617:12: note: Function 'decompress' argument 7 names different: declaration 'outputSize' definition 'outputBytes'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1618:13: style:inconclusive: Function 'decompress' argument 8 names different: declaration 'o_outputUsed' definition 'o_outputWritten'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1330:50: note: Function 'decompress' argument 8 names different: declaration 'o_outputUsed' definition 'o_outputWritten'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:1618:13: note: Function 'decompress' argument 8 names different: declaration 'o_outputUsed' definition 'o_outputWritten'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2193:17: style:inconclusive: Function 'init' argument 1 names different: declaration 'fileName' definition 'i_fileName'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2069:35: note: Function 'init' argument 1 names different: declaration 'fileName' definition 'i_fileName'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2193:17: note: Function 'init' argument 1 names different: declaration 'fileName' definition 'i_fileName'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2219:12: style:inconclusive: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2073:32: note: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2219:12: note: Function 'reinit' argument 1 names different: declaration 'startingOffset' definition 'i_startingOffset'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2489:15: style:inconclusive: Function 'releaseBatch' argument 1 names different: declaration 'batch' definition 'removed'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataReader.h:204:33: note: Function 'releaseBatch' argument 1 names different: declaration 'batch' definition 'removed'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:2489:15: note: Function 'releaseBatch' argument 1 names different: declaration 'batch' definition 'removed'.
snap-1.0beta.18/SNAPLib/DataReader.cpp:108:30: style: Parameter 'peer' can be declared as reference to const [constParameter]
snap-1.0beta.18/SNAPLib/DataReader.cpp:538:22: style: Variable 'nextStart' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:545:19: style: Variable 'nextStart' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1639:21: style: Variable 'multiBlock' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1777:19: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:1854:19: style: Variable 'index' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2226:22: style: Variable 'oldAmount' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2292:28: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2297:31: style: Variable 'found' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2475:11: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataReader.cpp:2477:11: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:117:14: warning: Member variable 'FileEncoder::writer' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:117:14: warning: Member variable 'FileEncoder::lock' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:117:14: warning: Member variable 'FileEncoder::encoderBatch' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/DataWriter.h:208:23: style:inconclusive: Member variable 'FileEncoder::coworker' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:123:5: note: Member variable 'FileEncoder::coworker' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataWriter.h:208:23: note: Member variable 'FileEncoder::coworker' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataWriter.cpp:109:30: style:inconclusive: Member variable 'AsyncDataWriter::supplier' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:269:5: note: Member variable 'AsyncDataWriter::supplier' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataWriter.cpp:109:30: note: Member variable 'AsyncDataWriter::supplier' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataWriter.cpp:107:15: style:inconclusive: Member variable 'AsyncDataWriter::count' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:270:5: note: Member variable 'AsyncDataWriter::count' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataWriter.cpp:107:15: note: Member variable 'AsyncDataWriter::count' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/DataWriter.h:193:10: style:inconclusive: Technically the member function 'FileEncoder::getOffsets' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:234:14: note: Technically the member function 'FileEncoder::getOffsets' can be const.
snap-1.0beta.18/SNAPLib/DataWriter.h:193:10: note: Technically the member function 'FileEncoder::getOffsets' can be const.
snap-1.0beta.18/SNAPLib/DataWriter.cpp:280:5: warning: Class 'AsyncDataWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:280:5: warning: Class 'AsyncDataWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:640:5: style: Class 'StdoutAsyncFileWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:37:25: style: The function 'getWriter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:132:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:37:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:39:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:135:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:39:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:78:18: style: The function 'getBuffer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:96:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:78:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:80:18: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:100:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:80:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:82:18: style: The function 'getBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:105:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:82:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:84:18: style: The function 'nextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:108:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:84:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:86:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:111:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:86:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:531:15: style: The function 'inHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:57:16: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:531:15: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:537:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:60:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:537:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:543:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:66:24: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:543:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:564:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:81:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:564:33: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:567:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:84:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:567:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:573:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:85:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:573:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:644:10: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Compat.h:404:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:644:10: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:647:10: style: The function 'beginWrite' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Compat.h:407:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:647:10: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:650:10: style: The function 'waitForCompletion' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Compat.h:410:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:650:10: note: Function in derived class
snap-1.0beta.18/SNAPLib/DataWriter.cpp:168:6: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:275:19: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:731:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:826:42: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/DataWriter.cpp:120:28: style:inconclusive: Function 'FileEncoder' argument 3 names different: declaration 'i_supplier' definition 'i_manager'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataWriter.h:168:79: note: Function 'FileEncoder' argument 3 names different: declaration 'i_supplier' definition 'i_manager'.
snap-1.0beta.18/SNAPLib/DataWriter.cpp:120:28: note: Function 'FileEncoder' argument 3 names different: declaration 'i_supplier' definition 'i_manager'.
snap-1.0beta.18/SNAPLib/Error.cpp:87:5: warning: %lld in format string (no. 2) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/Error.cpp:61:1: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
snap-1.0beta.18/SNAPLib/Error.cpp:75:1: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
snap-1.0beta.18/SNAPLib/FASTQ.cpp:40:14: warning: Member variable 'FASTQReader::fileName' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/FASTQ.cpp:339:31: warning: Member variable 'PairedInterleavedFASTQReader::fileName' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/FASTQ.h:202:13: warning: Class 'FASTQWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/FASTQ.h:202:13: warning: Class 'FASTQWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/FASTQ.h:200:9: style: Class 'FASTQWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/FASTQ.h:57:22: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:114:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:57:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:59:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:115:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:59:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:61:22: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:119:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:61:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:64:22: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:122:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:64:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:111:22: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:136:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:111:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:113:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:137:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:113:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:115:22: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:139:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:115:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:118:22: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:140:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:118:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:121:32: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:142:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:121:32: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:141:22: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:136:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:141:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:143:22: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:137:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:143:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:157:22: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:139:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:157:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:160:22: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:140:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:160:22: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.h:163:32: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:142:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/FASTQ.h:163:32: note: Function in derived class
snap-1.0beta.18/SNAPLib/FASTQ.cpp:258:40: warning: Either the condition 'NULL==newLine' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
snap-1.0beta.18/SNAPLib/FASTQ.cpp:241:18: note: Assuming that condition 'NULL==newLine' is not redundant
snap-1.0beta.18/SNAPLib/FASTQ.cpp:258:40: note: Null pointer subtraction
snap-1.0beta.18/SNAPLib/FASTQ.cpp:41:17: style:inconclusive: Function 'FASTQReader' argument 1 names different: declaration 'data' definition 'i_data'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/FASTQ.h:40:33: note: Function 'FASTQReader' argument 1 names different: declaration 'data' definition 'i_data'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:41:17: note: Function 'FASTQReader' argument 1 names different: declaration 'data' definition 'i_data'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:63:26: style:inconclusive: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/FASTQ.h:49:34: note: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:63:26: note: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:229:53: style:inconclusive: Function 'getReadFromBuffer' argument 2 names different: declaration 'bufferSize' definition 'validBytes'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/FASTQ.h:67:62: note: Function 'getReadFromBuffer' argument 2 names different: declaration 'bufferSize' definition 'validBytes'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:229:53: note: Function 'getReadFromBuffer' argument 2 names different: declaration 'bufferSize' definition 'validBytes'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:340:17: style:inconclusive: Function 'PairedInterleavedFASTQReader' argument 1 names different: declaration 'data' definition 'i_data'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/FASTQ.h:96:50: note: Function 'PairedInterleavedFASTQReader' argument 1 names different: declaration 'data' definition 'i_data'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:340:17: note: Function 'PairedInterleavedFASTQReader' argument 1 names different: declaration 'data' definition 'i_data'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:348:62: style:inconclusive: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/FASTQ.h:101:57: note: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:348:62: note: Function 'create' argument 6 names different: declaration 'i_context' definition 'context'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:482:30: style:inconclusive: Function 'writeRead' argument 1 names different: declaration 'readToWrite' definition 'read'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/FASTQ.h:184:30: note: Function 'writeRead' argument 1 names different: declaration 'readToWrite' definition 'read'.
snap-1.0beta.18/SNAPLib/FASTQ.cpp:482:30: note: Function 'writeRead' argument 1 names different: declaration 'readToWrite' definition 'read'.
snap-1.0beta.18/SNAPLib/GenericFile.cpp:37:14: warning: Member variable 'GenericFile::_mode' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:33:17: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:45:17: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:33:17: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:34:14: style: The function 'getchar' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:50:17: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:34:14: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:35:16: style: The function 'gets' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:55:16: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:35:16: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:36:14: style: The function 'advance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:58:14: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:36:14: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:38:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/GenericFile.h:61:15: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GenericFile_stdio.h:38:15: note: Function in derived class
snap-1.0beta.18/SNAPLib/GenericFile.cpp:47:44: style:inconclusive: Function 'open' argument 1 names different: declaration 'fileName' definition 'filename'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/GenericFile.h:41:42: note: Function 'open' argument 1 names different: declaration 'fileName' definition 'filename'.
snap-1.0beta.18/SNAPLib/GenericFile.cpp:47:44: note: Function 'open' argument 1 names different: declaration 'fileName' definition 'filename'.
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:63:14: style:inconclusive: Member variable 'GenericFile_Blob::blobEnd' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/GenericFile_Blob.cpp:27:144: note: Member variable 'GenericFile_Blob::blobEnd' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:63:14: note: Member variable 'GenericFile_Blob::blobEnd' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:45:15: style: Virtual function 'close' is called from destructor '~GenericFile_Blob()' at line 79. Dynamic binding is not used. [virtualCallInConstructor]
snap-1.0beta.18/SNAPLib/GenericFile_Blob.cpp:79:5: note: Calling close
snap-1.0beta.18/SNAPLib/GenericFile_Blob.h:45:15: note: close is a virtual function
snap-1.0beta.18/SNAPLib/GenericFile_Blob.cpp:27:76: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenericFile_Blob.cpp:89:24: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenericFile_map.h:35:15: style: Virtual function 'close' is called from destructor '~GenericFile_map()' at line 55. Dynamic binding is not used. [virtualCallInConstructor]
snap-1.0beta.18/SNAPLib/GenericFile_map.cpp:55:2: note: Calling close
snap-1.0beta.18/SNAPLib/GenericFile_map.h:35:15: note: close is a virtual function
snap-1.0beta.18/SNAPLib/GenericFile_map.cpp:38:141: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenericFile_map.cpp:67:13: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenericFile_map.cpp:62:15: style: Variable 'pageSize' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/AlignerOptions.cpp:36:17: warning: Member variable 'AlignerOptions::nInputs' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerOptions.cpp:36:17: warning: Member variable 'AlignerOptions::inputs' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/AlignerOptions.h:69:25: style:inconclusive: Member variable 'AlignerOptions::seedCountSpecified' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/AlignerOptions.cpp:63:5: note: Member variable 'AlignerOptions::seedCountSpecified' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerOptions.h:69:25: note: Member variable 'AlignerOptions::seedCountSpecified' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerOptions.h:67:25: style:inconclusive: Member variable 'AlignerOptions::numSeedsFromCommandLine' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/AlignerOptions.cpp:65:5: note: Member variable 'AlignerOptions::numSeedsFromCommandLine' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerOptions.h:67:25: note: Member variable 'AlignerOptions::numSeedsFromCommandLine' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerOptions.h:66:25: style:inconclusive: Member variable 'AlignerOptions::maxDistFraction' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/AlignerOptions.cpp:76:5: note: Member variable 'AlignerOptions::maxDistFraction' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerOptions.h:66:25: note: Member variable 'AlignerOptions::maxDistFraction' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/AlignerOptions.h:126:10: style:inconclusive: Technically the member function 'AlignerOptions::passFilter' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/AlignerOptions.cpp:740:17: note: Technically the member function 'AlignerOptions::passFilter' can be const.
snap-1.0beta.18/SNAPLib/AlignerOptions.h:126:10: note: Technically the member function 'AlignerOptions::passFilter' can be const.
snap-1.0beta.18/SNAPLib/AlignerOptions.cpp:483:29: style: Checking if unsigned expression 'writeBufferSize' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/SNAPLib/Genome.h:291:22: style:inconclusive: Member variable 'Genome::maxContigs' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/Genome.cpp:35:106: note: Member variable 'Genome::maxContigs' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Genome.h:291:22: note: Member variable 'Genome::maxContigs' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/Genome.cpp:51:5: warning: Class 'Genome' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/Genome.cpp:51:5: warning: Class 'Genome' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/Genome.cpp:143:5: warning: %lld in format string (no. 1) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/Genome.cpp:151:9: warning: %lld in format string (no. 1) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/Genome.cpp:239:14: warning: %lld in format string (no. 1) requires 'long long *' but the argument type is 'signed long *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/Genome.cpp:323:32: warning: %lld in format string (no. 1) requires 'long long *' but the argument type is 'signed long *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/Genome.cpp:323:32: warning: %d in format string (no. 2) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/Genome.cpp:45:18: warning: Either the condition 'NULL==bases' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
snap-1.0beta.18/SNAPLib/Genome.cpp:39:14: note: Assuming that condition 'NULL==bases' is not redundant
snap-1.0beta.18/SNAPLib/Genome.cpp:45:18: note: Null pointer subtraction
snap-1.0beta.18/SNAPLib/Genome.cpp:46:18: warning: Either the condition 'NULL==bases' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-1.0beta.18/SNAPLib/Genome.cpp:39:14: note: Assuming that condition 'NULL==bases' is not redundant
snap-1.0beta.18/SNAPLib/Genome.cpp:46:18: note: Null pointer addition
snap-1.0beta.18/SNAPLib/Genome.cpp:38:14: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Genome.cpp:263:33: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Genome.cpp:264:19: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Genome.cpp:221:12: style: The scope of the variable 'contigSize' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/Genome.cpp:222:11: style: The scope of the variable 'curName' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/Genome.cpp:34:111: style:inconclusive: Function 'Genome' argument 4 names different: declaration 'maxContigs' definition 'i_maxContigs'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Genome.h:174:37: note: Function 'Genome' argument 4 names different: declaration 'maxContigs' definition 'i_maxContigs'.
snap-1.0beta.18/SNAPLib/Genome.cpp:34:111: note: Function 'Genome' argument 4 names different: declaration 'maxContigs' definition 'i_maxContigs'.
snap-1.0beta.18/SNAPLib/Genome.cpp:180:87: style:inconclusive: Function 'loadFromFile' argument 3 names different: declaration 'i_minLocation' definition 'minLocation'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/Genome.h:196:108: note: Function 'loadFromFile' argument 3 names different: declaration 'i_minLocation' definition 'minLocation'.
snap-1.0beta.18/SNAPLib/Genome.cpp:180:87: note: Function 'loadFromFile' argument 3 names different: declaration 'i_minLocation' definition 'minLocation'.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::nChunks' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::encoder' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::input' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::inputSize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:39:5: warning: Member variable 'GzipCompressWorkerManager::inputUsed' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:293:19: warning: Member variable 'GzipWriterFilter::encoder' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:85:10: style: Unused private function: 'GzipWriterFilterSupplier::addTranslation' [unusedPrivateFunction]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:57:18: style:inconclusive: Member variable 'GzipCompressWorkerManager::chunkSize' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:41:9: note: Member variable 'GzipCompressWorkerManager::chunkSize' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:57:18: note: Member variable 'GzipCompressWorkerManager::chunkSize' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:39:5: style: Class 'GzipCompressWorkerManager' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:91:5: style: Class 'GzipWriterFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:46:18: style: The function 'initialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/ParallelTask.h:254:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:46:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:48:29: style: The function 'createWorker' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/ParallelTask.h:256:29: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:48:29: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:50:18: style: The function 'beginStep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/ParallelTask.h:258:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:50:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:52:18: style: The function 'finishStep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/ParallelTask.h:260:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:52:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:77:18: style: The function 'step' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/ParallelTask.h:273:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:77:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:93:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:60:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:93:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:95:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:66:24: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:95:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:117:15: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:139:18: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:170:43: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:205:10: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:240:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:242:24: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:288:11: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:326:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:115:11: style:inconclusive: Function 'initialize' argument 1 names different: declaration 'i_writer' definition 'i_encoder'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:46:35: note: Function 'initialize' argument 1 names different: declaration 'i_writer' definition 'i_encoder'.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:115:11: note: Function 'initialize' argument 1 names different: declaration 'i_writer' definition 'i_encoder'.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:395:50: style:inconclusive: Function 'addTranslations' argument 1 names different: declaration 'translation' definition 'moreTranslations'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:64:71: note: Function 'addTranslations' argument 1 names different: declaration 'translation' definition 'moreTranslations'.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:395:50: note: Function 'addTranslations' argument 1 names different: declaration 'translation' definition 'moreTranslations'.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:407:14: style:inconclusive: Function 'translate' argument 3 names different: declaration 'delta' definition 'o_logicalDelta'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/GzipDataWriter.h:66:67: note: Function 'translate' argument 3 names different: declaration 'delta' definition 'o_logicalDelta'.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:407:14: note: Function 'translate' argument 3 names different: declaration 'delta' definition 'o_logicalDelta'.
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:178:18: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/GzipDataWriter.cpp:229:25: style: Variable 'bamExtraData[5]' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/HashTable.cpp:249:35: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.cpp:252:88: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.cpp:335:16: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/HashTable.cpp:52:19: style: Checking if unsigned expression 'tableSize' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/SNAPLib/HashTable.cpp:165:26: style: Checking if unsigned expression 'table->tableSize' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/SNAPLib/HashTable.h:109:31: style: Local variable 'nProbesInGetEntryForKey' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/HashTable.cpp:263:8: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/HashTable.h:109:31: note: Shadow variable
snap-1.0beta.18/SNAPLib/FixedSizeSet.h:20:5: warning: Member variable 'FixedSizeSet::maxSize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:837:14: warning: Member variable 'GenomeIndex::seedLen' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:837:14: warning: Member variable 'GenomeIndex::hashTableKeySize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:837:14: warning: Member variable 'GenomeIndex::largeHashTable' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:837:14: warning: Member variable 'GenomeIndex::locationSize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:837:14: warning: Member variable 'GenomeIndex::overflowTableSize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1033:5: warning: Member variable 'PerCounterBatch::lowBases' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:99:15: style:inconclusive: Member variable 'GenomeIndex::overflowTable32' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:837:64: note: Member variable 'GenomeIndex::overflowTable32' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenomeIndex.h:99:15: note: Member variable 'GenomeIndex::overflowTable32' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenomeIndex.h:87:19: style:inconclusive: Member variable 'GenomeIndex::genome' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:837:110: note: Member variable 'GenomeIndex::genome' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenomeIndex.h:87:19: note: Member variable 'GenomeIndex::genome' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenomeIndex.h:101:19: style:inconclusive: Member variable 'GenomeIndex::mappedOverflowTable' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:837:142: note: Member variable 'GenomeIndex::mappedOverflowTable' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/GenomeIndex.h:101:19: note: Member variable 'GenomeIndex::mappedOverflowTable' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/FixedSizeSet.h:100:10: style:inconclusive: Technically the member function 'FixedSizeSet::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/FixedSizeSet.h:119:10: performance:inconclusive: Technically the member function 'FixedSizeSet::isPowerOf2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/FixedSizeSet.h:108:14: style:inconclusive: Technically the member function 'FixedSizeSet::Entry::operatordelete[]' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/FixedSizeVector.h:45:9: style:inconclusive: Technically the member function 'FixedSizeVector::size' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1438:2: warning: Class 'OverflowBackpointerAnchor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1438:2: warning: Class 'OverflowBackpointerAnchor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/FixedSizeSet.h:20:5: style: Class 'FixedSizeSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/FixedSizeVector.h:13:5: style: Class 'FixedSizeVector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:291:2: warning: %lld in format string (no. 1) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:473:4: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:551:4: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:676:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:676:17: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:679:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:679:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:679:9: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:679:9: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:731:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:731:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:731:5: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:731:5: warning: %lld in format string (no. 4) requires 'long long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:731:5: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:731:5: warning: %d in format string (no. 7) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:731:5: portability: %lld in format string (no. 8) requires 'long long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:731:5: warning: %d in format string (no. 10) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %d in format string (no. 2) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %d in format string (no. 3) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %lld in format string (no. 4) requires 'long long *' but the argument type is 'signed long *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %d in format string (no. 5) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %d in format string (no. 6) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %d in format string (no. 7) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: portability: %lld in format string (no. 8) requires 'long long *' but the argument type is 'size_t * {aka unsigned long *}'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %d in format string (no. 9) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1625:24: warning: %d in format string (no. 10) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/Histogram.cpp:36:5: warning: Class 'Histogram' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/Histogram.cpp:36:5: warning: Class 'Histogram' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/Histogram.cpp:95:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/Histogram.cpp:95:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:229:29: warning: Either the condition 'NULL==genome' is redundant or there is possible null pointer dereference: genome. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:223:14: note: Assuming that condition 'NULL==genome' is not redundant
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:229:29: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:558:4: warning: Either the condition 'NULL==file' is redundant or there is possible null pointer dereference: file. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:553:13: note: Assuming that condition 'NULL==file' is not redundant
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:558:4: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1676:4: warning: Either the condition 'NULL==overflowTableFile' is redundant or there is possible null pointer dereference: overflowTableFile. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1671:13: note: Assuming that condition 'NULL==overflowTableFile' is not redundant
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1676:4: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1677:4: warning: Either the condition 'NULL==overflowTableFile' is redundant or there is possible null pointer dereference: overflowTableFile. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1671:13: note: Assuming that condition 'NULL==overflowTableFile' is not redundant
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1677:4: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1750:4: warning: Either the condition 'NULL==hashTableFile' is redundant or there is possible null pointer dereference: hashTableFile. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1745:13: note: Assuming that condition 'NULL==hashTableFile' is not redundant
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1750:4: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1751:4: warning: Either the condition 'NULL==hashTableFile' is redundant or there is possible null pointer dereference: hashTableFile. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1745:13: note: Assuming that condition 'NULL==hashTableFile' is not redundant
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1751:4: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1773:23: warning: Either the condition 'NULL==tablesFile' is redundant or there is possible null pointer dereference: tablesFile. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1767:12: note: Assuming that condition 'NULL==tablesFile' is not redundant
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1773:23: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:508:34: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:510:34: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:563:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:564:30: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:700:53: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1058:46: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1151:45: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1260:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1261:21: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1389:11: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1391:18: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1401:11: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1403:18: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1473:41: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1508:15: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1519:15: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1689:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1691:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1703:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1704:22: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1707:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1708:22: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1855:34: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1881:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1967:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:2001:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:258:115: style:inconclusive: Function 'BuildIndexToDirectory' argument 5 names different: declaration 'directory' definition 'directoryName'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:152:69: note: Function 'BuildIndexToDirectory' argument 5 names different: declaration 'directory' definition 'directoryName'.
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:258:115: note: Function 'BuildIndexToDirectory' argument 5 names different: declaration 'directory' definition 'directoryName'.
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:880:57: style:inconclusive: Function 'ComputeBiasTable' argument 2 names different: declaration 'seedSize' definition 'seedLen'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:172:60: note: Function 'ComputeBiasTable' argument 2 names different: declaration 'seedSize' definition 'seedLen'.
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:880:57: note: Function 'ComputeBiasTable' argument 2 names different: declaration 'seedSize' definition 'seedLen'.
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1514:60: style:inconclusive: Function 'loadFromFile' argument 1 names different: declaration 'tripFile' definition 'file'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:131:27: note: Function 'loadFromFile' argument 1 names different: declaration 'tripFile' definition 'file'.
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1514:60: note: Function 'loadFromFile' argument 1 names different: declaration 'tripFile' definition 'file'.
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1160:19: style: Local variable 'genome' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:87:19: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1160:19: note: Shadow variable
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1161:14: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/GenomeIndex.h:84:9: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1161:14: note: Shadow variable
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1315:24: style: Local variable 'entryValue' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1301:20: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1315:24: note: Shadow variable
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1323:24: style: Local variable 'entryValue' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1301:20: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1323:24: note: Shadow variable
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:756:21: style: Parameter 'biasTable' can be declared as pointer to const [constParameter]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1016:26: style: Variable 'distinctSeeds' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1018:23: style: Variable 'distinctSeeds' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:1159:20: style: Variable 'countOfBases' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::countOfHashTableLookups' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::totalHashTableHits' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::largestHashTableHit' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::readWithMoreHits' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::readWithFewerHits' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::readLen' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::reads' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::localBestPairProbability' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::lowestFreeScoringCandidatePoolEntry' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::lowestFreeScoringMateCandidate' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:36:31: warning: Member variable 'IntersectingPairedEndAligner::firstFreeMergeAnchor' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::index' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::genome' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::genomeSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::maxReadSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::maxHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::maxBigHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::extraSearchDepth' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::maxK' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::numSeedsFromCommandLine' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::seedCoverage' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::minSpacing' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::maxSpacing' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::seedLen' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::doesGenomeIndexHave64BitLocations' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::nLocationsScored' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::noUkkonen' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::noOrderedEvaluation' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::noTruncation' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::hashTableHitSets' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::countOfHashTableLookups' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::totalHashTableHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::largestHashTableHit' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::readWithMoreHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::readWithFewerHits' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::rcReadData' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::rcReadQuality' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::readLen' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::reads' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::reversedRead' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::landauVishkin' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::reverseLandauVishkin' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::rcTranslationTable' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::nTable' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::seedUsed' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::localBestPairProbability' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::scoringCandidatePool' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::scoringCandidatePoolSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::lowestFreeScoringCandidatePoolEntry' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::scoringCandidates' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::scoringMateCandidates' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::lowestFreeScoringMateCandidate' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::mergeAnchorPool' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::firstFreeMergeAnchor' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::mergeAnchorPoolSize' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::hitsPerContigCounts' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::maxSecondaryAlignmentsPerContig' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:114:5: warning:inconclusive: Member variable 'IntersectingPairedEndAligner::contigCountEpoch' is not initialized in the constructor. [uninitMemberVarPrivate]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::currentDisjointHitSet' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::disjointHitSets' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::lookups32' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::lookups64' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::lookupListHead32' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::lookupListHead64' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::maxSeeds' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::nLookupsUsed' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::mostRecentLocationReturned' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::maxMergeDistance' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:197:9: warning: Member variable 'HashTableHitSet::doesGenomeIndexHave64BitLocations' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:127:21: style:inconclusive: Member variable 'IntersectingPairedEndAligner::maxBigHits' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:54:51: note: Member variable 'IntersectingPairedEndAligner::maxBigHits' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:127:21: note: Member variable 'IntersectingPairedEndAligner::maxBigHits' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:128:21: style:inconclusive: Member variable 'IntersectingPairedEndAligner::extraSearchDepth' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:55:5: note: Member variable 'IntersectingPairedEndAligner::extraSearchDepth' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:128:21: note: Member variable 'IntersectingPairedEndAligner::extraSearchDepth' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:102:10: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:105:10: style:inconclusive: Technically the member function 'IntersectingPairedEndAligner::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:72:11: style: The function 'setLandauVishkin' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/PairedEndAligner.h:55:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:72:11: note: Function in derived class
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:82:18: style: The function 'align' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/PairedEndAligner.h:40:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:82:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:107:20: style: The function 'getLocationsScored' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/PairedEndAligner.h:61:20: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:107:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:117:16: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:120:33: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:121:36: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:124:44: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:125:47: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:132:25: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:133:28: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:136:36: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:140:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:144:31: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:1062:21: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:1065:21: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:1068:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:1015:17: style: The scope of the variable 'score2' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:41:23: style:inconclusive: Function 'IntersectingPairedEndAligner' argument 5 names different: declaration 'maxSeedsFromCommandLine_' definition 'numSeedsFromCommandLine_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:43:23: note: Function 'IntersectingPairedEndAligner' argument 5 names different: declaration 'maxSeedsFromCommandLine_' definition 'numSeedsFromCommandLine_'.
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:41:23: note: Function 'IntersectingPairedEndAligner' argument 5 names different: declaration 'maxSeedsFromCommandLine_' definition 'numSeedsFromCommandLine_'.
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:91:159: style:inconclusive: Function 'getBigAllocatorReservation' argument 5 names different: declaration 'maxSeedsFromCommandLine' definition 'numSeedsFromCommandLine'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:97:147: note: Function 'getBigAllocatorReservation' argument 5 names different: declaration 'maxSeedsFromCommandLine' definition 'numSeedsFromCommandLine'.
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:91:159: note: Function 'getBigAllocatorReservation' argument 5 names different: declaration 'maxSeedsFromCommandLine' definition 'numSeedsFromCommandLine'.
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:198:10: style: Local variable 'rcReads' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:309:10: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:198:10: note: Shadow variable
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:744:60: style: Local variable 'result' shadows outer argument [shadowArgument]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:156:32: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:744:60: note: Shadow variable
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:783:60: style: Local variable 'result' shadows outer argument [shadowArgument]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:156:32: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:783:60: note: Shadow variable
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:1017:9: style: Local variable 'readLen' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:306:14: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:1017:9: note: Shadow variable
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:1018:9: style: Local variable 'seedLen' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.h:135:21: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:1018:9: note: Shadow variable
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:478:53: style: Variable 'previousMoreHitsLocation' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/IntersectingPairedEndAligner.cpp:505:42: style: Variable 'previousMoreHitsLocation' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:54:20: portability: Assigning an integer to a pointer is not portable. [AssignmentIntegerToAddress]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:520:27: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:15:25: warning: Member variable 'LandauVishkinWithCigar::A' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:15:25: warning: Member variable 'LandauVishkinWithCigar::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:15:25: warning: Member variable 'LandauVishkinWithCigar::backtraceMatched' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:15:25: warning: Member variable 'LandauVishkinWithCigar::backtraceD' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:172:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:243:39: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:520:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:528:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:727:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:731:29: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:216:6: style:inconclusive: Same expression used in consecutive assignments of 'lastBestIndels' and 'lastBestD'. [duplicateAssignExpression]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:217:9: note: Same expression used in consecutive assignments of 'lastBestIndels' and 'lastBestD'.
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:216:6: note: Same expression used in consecutive assignments of 'lastBestIndels' and 'lastBestD'.
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:512:10: style:inconclusive: Function 'computeEditDistanceNormalized' argument 11 names different: declaration 'o_textUsed' definition 'o_addFrontClipping'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:485:34: note: Function 'computeEditDistanceNormalized' argument 11 names different: declaration 'o_textUsed' definition 'o_addFrontClipping'.
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:512:10: note: Function 'computeEditDistanceNormalized' argument 11 names different: declaration 'o_textUsed' definition 'o_addFrontClipping'.
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:236:29: style: Local variable 'p' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:162:17: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:236:29: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:237:29: style: Local variable 't' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:163:17: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:237:29: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:239:25: style: Local variable 'end' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:169:9: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:239:25: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:240:33: style: Local variable 'pend' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:170:17: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:240:33: note: Shadow variable
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:656:11: style: Parameter 'sample' can be declared as pointer to const [constParameter]
snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:700:58: style: Parameter 'i_phredToProbability' can be declared as pointer to const [constParameter]
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.cpp:35:5: warning: Class 'MultiInputReadSupplier' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.cpp:35:5: warning: Class 'MultiInputReadSupplier' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.cpp:121:5: warning: Class 'MultiInputPairedReadSupplier' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.cpp:121:5: warning: Class 'MultiInputPairedReadSupplier' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:33:19: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:151:19: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:33:19: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:35:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:154:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:35:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:36:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:155:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:36:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:60:18: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:161:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:60:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:62:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:164:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:62:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:64:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:165:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:64:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:89:27: style: The function 'generateNewReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:170:27: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:89:27: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:90:28: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:171:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:90:28: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:104:33: style: The function 'generateNewPairedReadSupplier' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:177:33: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:104:33: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:105:28: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:178:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:105:28: note: Function in derived class
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.cpp:30:52: style:inconclusive: Function 'MultiInputReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:30:32: note: Function 'MultiInputReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'.
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.cpp:30:52: note: Function 'MultiInputReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'.
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.cpp:116:64: style:inconclusive: Function 'MultiInputPairedReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.h:57:38: note: Function 'MultiInputPairedReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'.
snap-1.0beta.18/SNAPLib/MultiInputReadSupplier.cpp:116:64: note: Function 'MultiInputPairedReadSupplier' argument 1 names different: declaration 'nReadSuppliers' definition 'i_nReadSuppliers'.
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:84:24: style:inconclusive: Member variable 'PairedReadMatcher::freeList' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:122:30: note: Member variable 'PairedReadMatcher::freeList' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:84:24: note: Member variable 'PairedReadMatcher::freeList' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:74:15: style:inconclusive: Member variable 'PairedReadMatcher::currentBatch' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:123:5: note: Member variable 'PairedReadMatcher::currentBatch' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:74:15: note: Member variable 'PairedReadMatcher::currentBatch' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , Read , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < uint64_t , Read , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , ReadWithOwnMemory * , 150 , MapNumericHash < uint64_t > , 80 , 0 , true , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < uint64_t , ReadWithOwnMemory * , 150 , MapNumericHash < uint64_t > , 80 , 0 , true , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , VariableSizeVector < ReadWithOwnMemory * , 150 , false > * , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeMap.h:276:5: style: Class 'VariableSizeMap < uint64_t , VariableSizeVector < ReadWithOwnMemory * , 150 , false > * , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:53:18: style: The function 'getNextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:136:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:53:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:55:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:137:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:55:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:58:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:139:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:58:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:61:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:140:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:61:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:63:28: style: The function 'getContext' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:142:28: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:63:28: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:150:40: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:165:44: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:179:10: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:266:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:270:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:366:61: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:136:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/PairedReadMatcher.cpp:413:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:117:34: error: Array 'nSmallHitsByTimeHistogram[32][32]' accessed at index nSmallHitsByTimeHistogram[32][*], which is out of bounds. [arrayIndexOutOfBounds]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:112:43: note: Assuming that condition 'nHitsBucket<nHitsBuckets' is not redundant
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:117:34: note: Array index out of bounds
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:126:32: error: Array 'nLVCallsByTimeHistogram[32][32]' accessed at index nLVCallsByTimeHistogram[32][*], which is out of bounds. [arrayIndexOutOfBounds]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:121:49: note: Assuming that condition 'nLVCallsBucket<nLVCallsBuckets' is not redundant
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:126:32: note: Array index out of bounds
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:129:32: error: Array 'mapqByNLVCallsHistogram[71][32]' accessed at index mapqByNLVCallsHistogram[*][32], which is out of bounds. [arrayIndexOutOfBounds]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:121:49: note: Assuming that condition 'nLVCallsBucket<nLVCallsBuckets' is not redundant
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:129:32: note: Array index out of bounds
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:132:34: error: Array 'mapqByNSmallHitsHistogram[71][32]' accessed at index mapqByNSmallHitsHistogram[*][32], which is out of bounds. [arrayIndexOutOfBounds]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:112:9: note: After for loop, nHitsBucket has value 32
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:122:32: note: Assuming condition is false
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:132:34: note: Array index out of bounds
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:369:39: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::pairedReadSupplierGenerator' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::minSpacing' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::maxSpacing' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::forceSpacing' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::intersectingAlignerMaxHits' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::maxCandidatePoolSize' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::fastqFile1' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::ignoreMismatchedIDs' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:303:23: warning: Member variable 'PairedAlignerContext::quicklyDropUnpairedReads' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/ParallelTask.h:50:5: style: Class 'ParallelTask' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/ParallelTask.cpp:113:22: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:68:27: warning: The struct 'PairedAlignerStats' defines member variable with name 'maxMapq' also defined in its parent struct 'AlignerStats'. [duplInheritedMember]
snap-1.0beta.18/SNAPLib/AlignerStats.h:54:27: note: Parent variable 'AlignerStats::maxMapq'
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:68:27: note: Derived variable 'PairedAlignerStats::maxMapq'
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:80:5: style: Struct 'PairedAlignerStats' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/ParallelTask.h:50:5: style: Class 'ParallelTask < PairedAlignerContext >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:137:18: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerStats.h:76:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:137:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:139:18: style: The function 'printHistograms' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/AlignerStats.h:78:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:139:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:150:22: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:154:19: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:190:33: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:311:38: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:369:31: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:438:38: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:439:53: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:562:21: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:187:52: style:inconclusive: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:137:44: note: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'.
snap-1.0beta.18/SNAPLib/PairedAligner.cpp:187:52: note: Function 'add' argument 1 names different: declaration 'other' definition 'i_other'.
snap-1.0beta.18/SNAPLib/ProbabilityDistance.cpp:24:22: warning: Member variable 'ProbabilityDistance::d' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/ProbabilityDistance.cpp:24:22: warning: Member variable 'ProbabilityDistance::prev' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/ProbabilityDistance.cpp:44:19: style: Condition 'q>=33' is always true [knownConditionTrueFalse]
snap-1.0beta.18/SNAPLib/ProbabilityDistance.cpp:32:15: note: Assuming that condition 'q<33' is not redundant
snap-1.0beta.18/SNAPLib/ProbabilityDistance.cpp:44:19: note: Condition 'q>=33' is always true
snap-1.0beta.18/SNAPLib/ProbabilityDistance.cpp:59:13: style:inconclusive: Function 'compute' argument 6 names different: declaration 'maxTotalShift' definition 'maxShift'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/ProbabilityDistance.h:26:17: note: Function 'compute' argument 6 names different: declaration 'maxTotalShift' definition 'maxShift'.
snap-1.0beta.18/SNAPLib/ProbabilityDistance.cpp:59:13: note: Function 'compute' argument 6 names different: declaration 'maxTotalShift' definition 'maxShift'.
snap-1.0beta.18/SNAPLib/RangeSplitter.h:90:15: style:inconclusive: Member variable 'RangeSplittingReadSupplierGenerator::numThreads' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:108:43: note: Member variable 'RangeSplittingReadSupplierGenerator::numThreads' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/RangeSplitter.h:90:15: note: Member variable 'RangeSplittingReadSupplierGenerator::numThreads' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/RangeSplitter.h:127:15: style:inconclusive: Member variable 'RangeSplittingPairedReadSupplierGenerator::numThreads' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:208:31: note: Member variable 'RangeSplittingPairedReadSupplierGenerator::numThreads' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/RangeSplitter.h:127:15: note: Member variable 'RangeSplittingPairedReadSupplierGenerator::numThreads' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:133:2: warning: Class 'RangeSplittingReadSupplierGenerator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:133:2: warning: Class 'RangeSplittingReadSupplierGenerator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:221:5: warning: Class 'RangeSplittingPairedReadSupplierGenerator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:221:5: warning: Class 'RangeSplittingPairedReadSupplierGenerator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:125:16: warning: Either the condition '!reader' is redundant or there is possible null pointer dereference: reader. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:121:7: note: Assuming that condition '!reader' is not redundant
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:125:16: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:36:74: style:inconclusive: Function 'RangeSplitter' argument 3 names different: declaration 'divisonSize_' definition 'divisionSize_'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/RangeSplitter.h:41:63: note: Function 'RangeSplitter' argument 3 names different: declaration 'divisonSize_' definition 'divisionSize_'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:36:74: note: Function 'RangeSplitter' argument 3 names different: declaration 'divisonSize_' definition 'divisionSize_'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:106:14: style:inconclusive: Function 'RangeSplittingReadSupplierGenerator' argument 3 names different: declaration 'numThreads' definition 'i_numThreads'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/RangeSplitter.h:80:88: note: Function 'RangeSplittingReadSupplierGenerator' argument 3 names different: declaration 'numThreads' definition 'i_numThreads'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:106:14: note: Function 'RangeSplittingReadSupplierGenerator' argument 3 names different: declaration 'numThreads' definition 'i_numThreads'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:107:26: style:inconclusive: Function 'RangeSplittingReadSupplierGenerator' argument 4 names different: declaration 'context' definition 'i_context'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/RangeSplitter.h:80:121: note: Function 'RangeSplittingReadSupplierGenerator' argument 4 names different: declaration 'context' definition 'i_context'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:107:26: note: Function 'RangeSplittingReadSupplierGenerator' argument 4 names different: declaration 'context' definition 'i_context'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:206:85: style:inconclusive: Function 'RangeSplittingPairedReadSupplierGenerator' argument 4 names different: declaration 'numThreads' definition 'i_numThreads'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/RangeSplitter.h:117:132: note: Function 'RangeSplittingPairedReadSupplierGenerator' argument 4 names different: declaration 'numThreads' definition 'i_numThreads'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:206:85: note: Function 'RangeSplittingPairedReadSupplierGenerator' argument 4 names different: declaration 'numThreads' definition 'i_numThreads'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:207:59: style:inconclusive: Function 'RangeSplittingPairedReadSupplierGenerator' argument 6 names different: declaration 'context' definition 'i_context'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/RangeSplitter.h:117:198: note: Function 'RangeSplittingPairedReadSupplierGenerator' argument 6 names different: declaration 'context' definition 'i_context'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:207:59: note: Function 'RangeSplittingPairedReadSupplierGenerator' argument 6 names different: declaration 'context' definition 'i_context'.
snap-1.0beta.18/SNAPLib/RangeSplitter.cpp:85:21: style: Variable 'oldPosition' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/Read.cpp:43:31: warning: Obsolete function 'alloca' called. [allocaCalled]
snap-1.0beta.18/SNAPLib/Read.cpp:43:23: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/ReadReader.cpp:44:5: error: Found a exit path from function with non-void return type that has missing return statement [missingReturn]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin::backtraceAction' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin::backtraceMatched' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:61:5: warning: Member variable 'LandauVishkin::backtraceD' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:353:10: style:inconclusive: Technically the member function 'LandauVishkin::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:356:10: style:inconclusive: Technically the member function 'LandauVishkin::operatordelete' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/LandauVishkin.h:364:16: performance:inconclusive: Technically the member function 'LandauVishkin::countPerfectMatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/ReadReader.cpp:36:18: style: The function 'reinit' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:115:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadReader.cpp:36:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadReader.cpp:38:18: style: The function 'getNextRead' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:114:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadReader.cpp:38:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadReader.cpp:46:18: style: The function 'holdBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:119:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadReader.cpp:46:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadReader.cpp:49:18: style: The function 'releaseBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:122:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadReader.cpp:49:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:194:25: style:inconclusive: Member variable 'ReadSupplierFromQueue::done' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:618:5: note: Member variable 'ReadSupplierFromQueue::done' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:194:25: note: Member variable 'ReadSupplierFromQueue::done' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:216:25: style:inconclusive: Member variable 'PairedReadSupplierFromQueue::done' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:652:43: note: Member variable 'PairedReadSupplierFromQueue::done' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:216:25: note: Member variable 'PairedReadSupplierFromQueue::done' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:151:10: style:inconclusive: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const. [functionConst]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:314:20: note: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:151:10: note: Technically the member function 'ReadSupplierQueue::areAnyReadsReady' can be const.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:413:26: style: Condition 'emptyQueue->next==emptyQueue' is always false [knownConditionTrueFalse]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:392:34: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:33:51: style:inconclusive: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_reader' definition 'reader'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:92:35: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_reader' definition 'reader'.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:33:51: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_reader' definition 'reader'.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:41:50: style:inconclusive: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_firstHalfReader' definition 'firstHalfReader'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:99:35: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_firstHalfReader' definition 'firstHalfReader'.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:41:50: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'i_firstHalfReader' definition 'firstHalfReader'.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:41:79: style:inconclusive: Function 'ReadSupplierQueue' argument 2 names different: declaration 'i_secondHalfReader' definition 'secondHalfReader'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:99:66: note: Function 'ReadSupplierQueue' argument 2 names different: declaration 'i_secondHalfReader' definition 'secondHalfReader'.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:41:79: note: Function 'ReadSupplierQueue' argument 2 names different: declaration 'i_secondHalfReader' definition 'secondHalfReader'.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:50:56: style:inconclusive: Function 'ReadSupplierQueue' argument 1 names different: declaration 'pairedReader' definition 'i_pairedReader'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.h:105:41: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'pairedReader' definition 'i_pairedReader'.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:50:56: note: Function 'ReadSupplierQueue' argument 1 names different: declaration 'pairedReader' definition 'i_pairedReader'.
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:532:26: style: Variable 'newBatch' can be declared as const array [constVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:109:17: style: Variable 'worked' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:277:22: style: Variable 'sizes' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:436:24: style: Variable 'balanceTime' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:437:27: style: Variable 'bufferWaitTime' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:438:27: style: Variable 'processingTime' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:453:28: style: Variable 'processingTime' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:459:25: style: Variable 'balanceTime' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:468:24: style: Variable 'processingTime' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:472:24: style: Variable 'bufferWaitTime' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:602:20: style: Variable 'processingTime' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:288:95: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:341:91: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:46:15: style: The function 'writeHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:188:15: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:46:15: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:48:18: style: The function 'writeReads' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:193:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:48:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:50:18: style: The function 'writePairs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:200:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:50:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:53:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:205:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:53:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:524:25: style: The function 'getWriter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:213:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:524:25: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:529:18: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/Read.h:215:18: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:529:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/ReadWriter.cpp:313:14: style: Variable 'fitInBuffer' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SAM.cpp:501:18: warning: Either the condition 'fieldLength[posfield]>=posBufferSize' is redundant or the array 'posBuffer[20]' is accessed at index 20, which is out of bounds. [arrayIndexOutOfBoundsCond]
snap-1.0beta.18/SNAPLib/SAM.cpp:496:35: note: Assuming that condition 'fieldLength[posfield]>=posBufferSize' is not redundant
snap-1.0beta.18/SNAPLib/SAM.cpp:501:18: note: Array index out of bounds
snap-1.0beta.18/SNAPLib/SAM.cpp:162:12: warning: Member variable 'SAMReader::didInitialSkip' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/SAM.cpp:377:14: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/SAM.cpp:502:18: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/SNAPLib/SAM.cpp:922:30: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-1.0beta.18/SNAPLib/SAM.cpp:1252:25: warning: %u in format string (no. 5) requires 'unsigned int' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-1.0beta.18/SNAPLib/SAM.cpp:1252:25: warning: %u in format string (no. 9) requires 'unsigned int' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-1.0beta.18/SNAPLib/SAM.cpp:1252:25: warning: %lld in format string (no. 10) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/SAM.cpp:1459:13: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-1.0beta.18/SNAPLib/SAM.cpp:1462:13: warning: %llu in format string (no. 1) requires 'unsigned long long' but the argument type is 'signed long'. [invalidPrintfArgType_uint]
snap-1.0beta.18/SNAPLib/SAM.cpp:603:32: warning: Either the condition 'NULL==newLine' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
snap-1.0beta.18/SNAPLib/SAM.cpp:590:18: note: Assuming that condition 'NULL==newLine' is not redundant
snap-1.0beta.18/SNAPLib/SAM.cpp:603:32: note: Null pointer addition
snap-1.0beta.18/SNAPLib/SAM.cpp:263:17: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/SAM.cpp:778:36: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/SAM.cpp:783:22: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/SAM.cpp:827:30: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/SAM.cpp:1228:40: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/SAM.cpp:1231:39: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/SAM.cpp:1141:10: style: The scope of the variable 'cigarBuf' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/SAM.cpp:1144:10: style: The scope of the variable 'cigarBufWithClipping' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/SAM.cpp:1219:17: style: The scope of the variable 'warningPrinted' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/SAM.cpp:119:26: style:inconclusive: Function 'create' argument 4 names different: declaration 'i_context' definition 'context'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/SAM.h:75:55: note: Function 'create' argument 4 names different: declaration 'i_context' definition 'context'.
snap-1.0beta.18/SNAPLib/SAM.cpp:119:26: note: Function 'create' argument 4 names different: declaration 'i_context' definition 'context'.
snap-1.0beta.18/SNAPLib/SAM.cpp:279:77: style:inconclusive: Function 'parseLine' argument 4 names different: declaration 'lineLength' definition 'linelength'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/SAM.h:116:21: note: Function 'parseLine' argument 4 names different: declaration 'lineLength' definition 'linelength'.
snap-1.0beta.18/SNAPLib/SAM.cpp:279:77: note: Function 'parseLine' argument 4 names different: declaration 'lineLength' definition 'linelength'.
snap-1.0beta.18/SNAPLib/SAM.cpp:331:26: style:inconclusive: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/SAM.h:128:41: note: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'.
snap-1.0beta.18/SNAPLib/SAM.cpp:331:26: note: Function 'getReadFromLine' argument 6 names different: declaration 'genomeLocation' definition 'out_genomeLocation'.
snap-1.0beta.18/SNAPLib/SAM.cpp:951:18: style:inconclusive: Function 'createSAMLine' argument 11 names different: declaration 'mateContigName' definition 'matecontigName'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/SAM.h:189:22: note: Function 'createSAMLine' argument 11 names different: declaration 'mateContigName' definition 'matecontigName'.
snap-1.0beta.18/SNAPLib/SAM.cpp:951:18: note: Function 'createSAMLine' argument 11 names different: declaration 'mateContigName' definition 'matecontigName'.
snap-1.0beta.18/SNAPLib/SAM.cpp:1419:33: style:inconclusive: Function 'computeCigarString' argument 12 names different: declaration 'frontHardClipped' definition 'frontHardClipping'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/SAM.h:225:18: note: Function 'computeCigarString' argument 12 names different: declaration 'frontHardClipped' definition 'frontHardClipping'.
snap-1.0beta.18/SNAPLib/SAM.cpp:1419:33: note: Function 'computeCigarString' argument 12 names different: declaration 'frontHardClipped' definition 'frontHardClipping'.
snap-1.0beta.18/SNAPLib/SAM.cpp:1420:33: style:inconclusive: Function 'computeCigarString' argument 13 names different: declaration 'backHardClipped' definition 'backHardClipping'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/SAM.h:225:45: note: Function 'computeCigarString' argument 13 names different: declaration 'backHardClipped' definition 'backHardClipping'.
snap-1.0beta.18/SNAPLib/SAM.cpp:1420:33: note: Function 'computeCigarString' argument 13 names different: declaration 'backHardClipped' definition 'backHardClipping'.
snap-1.0beta.18/SNAPLib/SAM.cpp:133:12: style: Local variable 'headerSize' shadows outer variable [shadowVariable]
snap-1.0beta.18/SNAPLib/SAM.h:140:29: note: Shadowed declaration
snap-1.0beta.18/SNAPLib/SAM.cpp:133:12: note: Shadow variable
snap-1.0beta.18/SNAPLib/SeedSequencer.cpp:38:5: warning: Class 'SeedSequencer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/SNAPLib/SeedSequencer.cpp:38:5: warning: Class 'SeedSequencer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/SNAPLib/SeedSequencer.cpp:38:5: warning: Class 'SeedSequencer' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
snap-1.0beta.18/SNAPLib/SeedSequencer.h:48:15: style: Class 'SeedSequencer' is unsafe, 'SeedSequencer::offsets' can leak by wrong usage. [unsafeClassCanLeak]
snap-1.0beta.18/SNAPLib/SAM.cpp:636:33: style: Variable 'splitter' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SAM.cpp:926:31: style: Variable 'bytesConsumed' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SAM.cpp:979:23: style: Variable 'cigar' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SAM.cpp:1031:22: style: Variable 'editDistance' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SingleAligner.cpp:43:23: warning: Member variable 'SingleAlignerContext::readSupplierGenerator' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/ParallelTask.h:50:5: style: Class 'ParallelTask < SingleAlignerContext >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/SingleAligner.cpp:151:28: warning: Either the condition 'supplier!=NULL' is redundant or there is possible null pointer dereference: supplier. [nullPointerRedundantCheck]
snap-1.0beta.18/SNAPLib/SingleAligner.cpp:235:18: note: Assuming that condition 'supplier!=NULL' is not redundant
snap-1.0beta.18/SNAPLib/SingleAligner.cpp:151:28: note: Null pointer dereference
snap-1.0beta.18/SNAPLib/SingleAligner.cpp:129:24: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:60:5: warning: Member variable 'SortBlock::data' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:78:12: warning: Member variable 'SortBlock::data' is not assigned a value in 'SortBlock::operator='. [operatorEqVarError]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:71:17: style:inconclusive: Member variable 'SortBlock::reader' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:60:63: note: Member variable 'SortBlock::reader' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:71:17: note: Member variable 'SortBlock::reader' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:164:37: style:inconclusive: Member variable 'SortedDataFilterSupplier::genome' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:129:9: note: Member variable 'SortedDataFilterSupplier::genome' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:164:37: note: Member variable 'SortedDataFilterSupplier::genome' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:166:37: style:inconclusive: Member variable 'SortedDataFilterSupplier::tempFileName' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:132:9: note: Member variable 'SortedDataFilterSupplier::tempFileName' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:166:37: note: Member variable 'SortedDataFilterSupplier::tempFileName' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:172:37: style:inconclusive: Member variable 'SortedDataFilterSupplier::blocks' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:137:9: note: Member variable 'SortedDataFilterSupplier::blocks' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:172:37: note: Member variable 'SortedDataFilterSupplier::blocks' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < SortEntry , 150 , true >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < SortBlock , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:30:36: note: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: style:inconclusive: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list. [initializerList]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:34:55: note: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:241:12: note: Member variable 'VariableSizeVector < SortEntry , 150 , false >::capacity' is in the wrong place in the initializer list.
snap-1.0beta.18/SNAPLib/PriorityQueue.h:31:17: performance:inconclusive: Technically the member function 'PriorityQueue < int64_t , int64_t >::check' can be static (but you may consider moving to unnamed namespace). [functionStatic]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:99:5: style: Class 'SortedDataFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < SortEntry , 150 , true >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < SortBlock , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < SortEntry , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:105:18: style: The function 'onAdvance' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:60:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:105:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:107:20: style: The function 'onNextBatch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:66:24: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:107:20: note: Function in derived class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:147:33: style: The function 'getFilter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:81:25: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:147:33: note: Function in derived class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:149:18: style: The function 'onClosing' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:84:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:149:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:150:18: style: The function 'onClosed' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
snap-1.0beta.18/SNAPLib/DataWriter.h:85:22: note: Virtual function in base class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:150:18: note: Function in derived class
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:393:20: style: The scope of the variable 'current' can be reduced. [variableScope]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:497:33: style:inconclusive: Function 'sorted' argument 7 names different: declaration 'sortedFilterSupplier' definition 'sortedFilterSuppler'. [funcArgNamesDifferent]
snap-1.0beta.18/SNAPLib/DataWriter.h:151:37: note: Function 'sorted' argument 7 names different: declaration 'sortedFilterSupplier' definition 'sortedFilterSuppler'.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:497:33: note: Function 'sorted' argument 7 names different: declaration 'sortedFilterSupplier' definition 'sortedFilterSuppler'.
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:220:26: style: Variable 'previous' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:242:12: style: Variable 'first' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:393:28: style: Variable 'current' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:394:16: style: Variable 'lastRefID' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:394:30: style: Variable 'lastPos' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:443:38: style: Variable 'oldBlocks[oldBlockIndex]' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:447:21: style: Variable 'current' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:458:37: style: Variable 'previous' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:221:95: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:336:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/SortedDataWriter.cpp:387:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
snap-1.0beta.18/SNAPLib/Util.cpp:164:4: warning: %lld in format string (no. 1) requires 'long long' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/Util.cpp:167:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned long'. [invalidPrintfArgType_sint]
snap-1.0beta.18/SNAPLib/Util.cpp:61:18: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.cpp:62:43: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.cpp:68:20: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.cpp:69:40: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/SNAPLib/Util.cpp:39:21: portability: Shifting signed 64-bit value by 63 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
snap-1.0beta.18/SNAPLib/Util.cpp:33:5: note: After for loop, highestBitSet has value 63
snap-1.0beta.18/SNAPLib/Util.cpp:39:21: note: Shift
snap-1.0beta.18/SNAPLib/Util.cpp:40:24: error: Shifting 64-bit value by 64 bits is undefined behaviour [shiftTooManyBits]
snap-1.0beta.18/SNAPLib/Util.cpp:33:5: note: After for loop, highestBitSet has value 63
snap-1.0beta.18/SNAPLib/Util.cpp:39:38: note: Assuming condition is false
snap-1.0beta.18/SNAPLib/Util.cpp:40:24: note: Shift
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:73:5: warning: Member variable 'ThreadContext::whichThread' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:74:9: performance: Variable 'nUnaligned' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:75:9: performance: Variable 'totalReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:121:17: style: Expression is always true because 'else if' condition is opposite to previous condition at line 119. [multiCondition]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:119:20: note: first condition
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:121:17: note: else if condition is opposite to first condition
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:110:20: style: Comparing expression of type 'unsigned int' against value 0. Condition is always false. [compareValueOutOfTypeRangeError]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:111:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:217:21: portability: %d in format string (no. 2) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:95:30: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:132:18: style: The scope of the variable 'matched' can be reduced. [variableScope]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:153:18: style: The scope of the variable 'badParse' can be reduced. [variableScope]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:154:20: style: The scope of the variable 'chrNameLen' can be reduced. [variableScope]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:156:25: style: The scope of the variable 'beginningOfFirstNumber' can be reduced. [variableScope]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:156:53: style: The scope of the variable 'stage' can be reduced. [variableScope]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:110:18: style: Checking if unsigned expression 'mapQ' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:156:59: style: Variable 'stage' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:170:27: style: Variable 'stage' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:184:31: style: Variable 'stage' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:196:39: style: Variable 'stage' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:222:29: style: Variable 'match0' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:223:29: style: Variable 'match1' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:231:32: style: Variable 'match0' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:234:32: style: Variable 'match1' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:238:36: style: Variable 'match0' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:240:36: style: Variable 'match1' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:288:47: style: Variable 'correctGenomeData' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:289:45: style: Variable 'correctLocation' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:290:45: style: Variable 'cigarForCorrect' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:292:47: style: Variable 'correctGenomeData' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:293:45: style: Variable 'correctLocation' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:294:45: style: Variable 'cigarForCorrect' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:261:37: style: Variable 'correctData' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ComputeROC/ComputeROC.cpp:425:29: style: Variable 'maxEditDistanceSeen' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/DistanceHist/DistanceHist.cpp:221:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/DistanceHist/DistanceHist.cpp:221:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/DistanceHist/DistanceHist.cpp:226:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/DistanceHist/DistanceHist.cpp:231:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/DistanceHist/DistanceHist.cpp:160:6: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/apps/ExtractReads/ExtractReads.cpp:86:67: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/apps/ExtractReads/ExtractReads.cpp:100:76: error: Uninitialized variable: isRC [legacyUninitvar]
snap-1.0beta.18/apps/ExtractReads/ExtractReads.cpp:91:10: style: Variable 'isRC' is not assigned a value. [unassignedVariable]
snap-1.0beta.18/apps/RandomizePIfastq/RandomizePIfastq.cpp:44:5: performance: Variable 'hFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
snap-1.0beta.18/apps/RandomizePIfastq/RandomizePIfastq.cpp:49:5: warning: Class 'IntermediateFile' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
snap-1.0beta.18/apps/RandomizePIfastq/RandomizePIfastq.cpp:49:5: warning: Class 'IntermediateFile' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
snap-1.0beta.18/apps/RandomizePIfastq/RandomizePIfastq.cpp:130:15: style: Variable 'done' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/ToFASTQ/ToFASTQ.cpp:57:5: warning: Member variable 'ThreadContext::whichThread' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/apps/ToFASTQ/ToFASTQ.cpp:58:9: performance: Variable 'totalReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
snap-1.0beta.18/apps/ToFASTQ/ToFASTQ.cpp:69:30: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/apps/stringz/stringz.cpp:169:11: portability: %lld in format string (no. 1) requires 'long long *' but the argument type is 'size_t * {aka unsigned long *}'. [invalidScanfArgType_int]
snap-1.0beta.18/apps/stringz/stringz.cpp:174:12: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/apps/stringz/stringz.cpp:176:13: portability: %d in format string (no. 1) requires 'int *' but the argument type is 'size_t * {aka unsigned long *}'. [invalidScanfArgType_int]
snap-1.0beta.18/apps/stringz/stringz.cpp:180:15: warning: %d in format string (no. 1) requires 'int *' but the argument type is 'unsigned int *'. [invalidScanfArgType_int]
snap-1.0beta.18/apps/stringz/stringz.cpp:237:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/stringz/stringz.cpp:237:3: portability: %lld in format string (no. 2) requires 'long long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/stringz/stringz.cpp:237:3: portability: %lld in format string (no. 3) requires 'long long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/stringz/stringz.cpp:241:2: portability: %lld in format string (no. 1) requires 'long long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-1.0beta.18/apps/stringz/stringz.cpp:155:27: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/apps/stringz/stringz.cpp:169:57: style: Checking if unsigned expression 'nStringz' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/apps/stringz/stringz.cpp:174:71: style: Checking if unsigned expression 'smallStringSize' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/apps/stringz/stringz.cpp:176:68: style: Checking if unsigned expression 'bigStringSize' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/apps/stringz/stringz.cpp:180:68: style: Checking if unsigned expression 'alphabetSize' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/apps/stringz/stringz.cpp:73:33: style: Parameter 'peer' can be declared as reference to const [constParameter]
snap-1.0beta.18/apps/stringz/stringz.cpp:107:21: style: Variable 'bestOffset' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/apps/wc/wc.cpp:31:5: warning: Member variable 'InputFile::fileName' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/apps/wc/wc.cpp:43:28: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/apps/wc/wc.cpp:215:36: style: Variable 'lastInputFile' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/import/pdclibhdfs/src/jni_helper.c:988:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
snap-1.0beta.18/import/pdclibhdfs/src/jni_helper.c:1006:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
snap-1.0beta.18/import/pdclibhdfs/src/jni_helper.c:1150:9: portability: %zd in format string (no. 1) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
snap-1.0beta.18/import/pdclibhdfs/src/jni_helper.c:937:30: style: Variable 'cnt' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/import/pdclibhdfs/src/jni_helper.c:791:16: style: Unused variable: jthr [unusedVariable]
snap-1.0beta.18/import/pdclibhdfs/src/jni_helper.c:940:29: style: Unused variable: savePtr [unusedVariable]
snap-1.0beta.18/import/pdclibhdfs/src/jni_helper.c:1100:13: style: Variable 'rv' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:1451:16: style: Condition 'length<0' is always false [knownConditionTrueFalse]
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:1439:16: note: Assuming that condition 'length<0' is not redundant
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:1445:17: note: Assuming condition is false
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:1451:16: note: Condition 'length<0' is always false
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:457:14: style: Variable 'cur' is reassigned a value before the old one has been used. [redundantAssignment]
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:456:9: note: cur is assigned
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:457:14: note: cur is overwritten
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:2998:12: warning: Size of pointer 'hdfsFileInfo' used instead of size of its data. [pointerSize]
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:65:13: style: struct member 'hdfsJniEnv::env' is never used. [unusedStructMember]
snap-1.0beta.18/import/pdclibhdfs/src/hdfs.c:2225:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:117:13: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:122:9: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:176:13: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:181:9: warning: %ld in format string (no. 1) requires 'long' but the argument type is 'signed int'. [invalidPrintfArgType_sint]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:267:14: style: Local variable 'buffer' shadows outer variable [shadowVariable]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:63:10: note: Shadowed declaration
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:267:14: note: Shadow variable
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:452:19: style: Local variable 'writePath' shadows outer variable [shadowVariable]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:65:17: note: Shadowed declaration
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:452:19: note: Shadow variable
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:453:13: style: Local variable 'buffer' shadows outer variable [shadowVariable]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:63:10: note: Shadowed declaration
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:453:13: note: Shadow variable
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:454:11: style: Local variable 'num_written_bytes' shadows outer variable [shadowVariable]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:64:9: note: Shadowed declaration
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:454:11: note: Shadow variable
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:535:15: style: Local variable 'buffer' shadows outer variable [shadowVariable]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:63:10: note: Shadowed declaration
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:535:15: note: Shadow variable
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:536:21: style: Local variable 'writePath' shadows outer variable [shadowVariable]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:65:17: note: Shadowed declaration
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:536:21: note: Shadow variable
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:538:13: style: Local variable 'num_written_bytes' shadows outer variable [shadowVariable]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:64:9: note: Shadowed declaration
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_ops.c:538:13: note: Shadow variable
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_threaded.c:88:19: style: Checking if unsigned expression 'blockSize' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/import/pdclibhdfs/src/test_libhdfs_threaded.c:99:19: style: Checking if unsigned expression 'blockSize' is less than zero. [unsignedLessThanZero]
snap-1.0beta.18/tests/EventTest.cpp:45:26: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/tests/EventTest.cpp:89:26: style: C-style pointer casting [cstyleCast]
snap-1.0beta.18/tests/EventTest.cpp:26:35: style:inconclusive: Function 'init' argument 1 names different: declaration 'parent' definition 'i_parent'. [funcArgNamesDifferent]
snap-1.0beta.18/tests/EventTest.cpp:12:24: note: Function 'init' argument 1 names different: declaration 'parent' definition 'i_parent'.
snap-1.0beta.18/tests/EventTest.cpp:26:35: note: Function 'init' argument 1 names different: declaration 'parent' definition 'i_parent'.
snap-1.0beta.18/tests/EventTest.cpp:56:51: style:inconclusive: Function 'testManyWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'. [funcArgNamesDifferent]
snap-1.0beta.18/tests/EventTest.cpp:22:42: note: Function 'testManyWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'.
snap-1.0beta.18/tests/EventTest.cpp:56:51: note: Function 'testManyWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'.
snap-1.0beta.18/tests/EventTest.cpp:101:53: style:inconclusive: Function 'testSingleWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'. [funcArgNamesDifferent]
snap-1.0beta.18/tests/EventTest.cpp:23:44: note: Function 'testSingleWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'.
snap-1.0beta.18/tests/EventTest.cpp:101:53: note: Function 'testSingleWaiters' argument 2 names different: declaration 'bind' definition 'i_bind'.
snap-1.0beta.18/tests/EventTest.cpp:32:41: style: Parameter 'variable' can be declared as pointer to const [constParameter]
snap-1.0beta.18/tests/ProbabilityDistanceTest.cpp:11:5: warning: Member variable 'ProbabilityDistanceTest::prob' is not initialized in the constructor. [uninitMemberVar]
snap-1.0beta.18/tests/TestLib.cpp:34:39: style: Variable 'e' can be declared as reference to const [constVariable]
diff:
head snap-1.0beta.18/SNAPLib/AlignerStats.h:44:5: style: Struct 'AlignerStats' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/Bam.cpp:388:11: style: Parameter 'ascii' can be declared as pointer to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/Bam.cpp:388:11: style: Parameter 'ascii' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/BigAlloc.h:121:5: style: Class 'CountingBigAllocator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/DataReader.cpp:108:30: style: Parameter 'peer' can be declared as reference to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/DataReader.cpp:108:30: style: Parameter 'peer' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/FixedSizeMap.h:36:5: style: Class 'FixedSizeMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/FixedSizeSet.h:20:5: style: Class 'FixedSizeSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/FixedSizeVector.h:13:5: style: Class 'FixedSizeVector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:756:21: style: Parameter 'biasTable' can be declared as pointer to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/GenomeIndex.cpp:756:21: style: Parameter 'biasTable' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:656:11: style: Parameter 'sample' can be declared as pointer to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:656:11: style: Parameter 'sample' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:700:58: style: Parameter 'i_phredToProbability' can be declared as pointer to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/LandauVishkin.cpp:700:58: style: Parameter 'i_phredToProbability' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/PairedAligner.cpp:80:5: style: Struct 'PairedAlignerStats' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/PairedAligner.h:36:5: style: Class 'PairedAlignerContext' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:532:26: style: Variable 'newBatch' can be declared as const array [constVariable]
2.8 snap-1.0beta.18/SNAPLib/ReadSupplierQueue.cpp:532:26: style: Variable 'newBatch' can be declared with const [constVariable]
2.8 snap-1.0beta.18/SNAPLib/ReadWriter.cpp:271:12: style: Variable 'staticUsedBuffer' can be declared with const [constVariable]
2.8 snap-1.0beta.18/SNAPLib/ReadWriter.cpp:272:20: style: Variable 'staticLocationBuffer' can be declared with const [constVariable]
2.8 snap-1.0beta.18/SNAPLib/SAM.cpp:279:40: style: Parameter 'endOfBuffer' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/Seed.h:107:33: style: Parameter 'peer' can be declared as reference to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/Seed.h:107:33: style: Parameter 'peer' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/Seed.h:111:34: style: Parameter 'peer' can be declared as reference to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/Seed.h:111:34: style: Parameter 'peer' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/Seed.h:115:33: style: Parameter 'peer' can be declared as reference to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/Seed.h:115:33: style: Parameter 'peer' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/Seed.h:119:34: style: Parameter 'peer' can be declared as reference to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/Seed.h:119:34: style: Parameter 'peer' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/Seed.h:123:34: style: Parameter 'peer' can be declared as reference to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/Seed.h:123:34: style: Parameter 'peer' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/Seed.h:127:34: style: Parameter 'peer' can be declared as reference to const [constParameter]
2.8 snap-1.0beta.18/SNAPLib/Seed.h:127:34: style: Parameter 'peer' can be declared with const [constParameter]
head snap-1.0beta.18/SNAPLib/SingleAligner.h:36:5: style: Class 'SingleAlignerContext' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < DuplicateReadKey , DuplicateMateInfo , 150 , MapNumericHash < DuplicateReadKey > , 70 , 0 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint32_t , VariableSizeVector < BAMChunk , 150 , false > , 150 , MapNumericHash < uint32_t > , 80 , -1 , -2 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , Read , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , ReadWithOwnMemory * , 150 , MapNumericHash < uint64_t > , 80 , 0 , true , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:272:5: style: Class 'VariableSizeMap < uint64_t , VariableSizeVector < ReadWithOwnMemory * , 150 , false > * , 150 , MapNumericHash < uint64_t > , 80 , 0 , -1 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:403:5: style: Class 'VariableSizeMapBig' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:432:5: style: Class 'VariableSizeMultiMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeMap.h:49:5: style: Class 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
2.8 snap-1.0beta.18/SNAPLib/VariableSizeMap.h:49:5: warning: Member variable 'VariableSizeMapBase < int64_t , unsigned int , 150 , MapNumericHash < int64_t > , 80 , 0 , -1 , false , false >::limit' is not initialized in the constructor. [uninitMemberVar]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < BAMChunk , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < DataBatch , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < DuplicateMateInfo * , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < ReadWithOwnMemory * , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < SortBlock , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < SortEntry , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < SortEntry , 150 , true >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < int64_t , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < std :: pair < uint64_t , uint64_t > , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < uint64_t , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < unsigned long , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector < util :: IdPair , 150 , false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/SNAPLib/VariableSizeVector.h:29:5: style: Class 'VariableSizeVector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head snap-1.0beta.18/apps/stringz/stringz.cpp:73:33: style: Parameter 'peer' can be declared as reference to const [constParameter]
2.8 snap-1.0beta.18/apps/stringz/stringz.cpp:73:33: style: Parameter 'peer' can be declared with const [constParameter]
head snap-1.0beta.18/tests/EventTest.cpp:32:41: style: Parameter 'variable' can be declared as pointer to const [constParameter]
2.8 snap-1.0beta.18/tests/EventTest.cpp:32:41: style: Parameter 'variable' can be declared with const [constParameter]
head snap-1.0beta.18/tests/TestLib.cpp:34:39: style: Variable 'e' can be declared as reference to const [constVariable]


DONE