2025-07-07 02:03
ftp://ftp.de.debian.org/debian/pool/main/b/bedtools/bedtools_2.31.1+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib --library=openssl --library=libcurl  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j6
platform: Linux-6.1.0-37-amd64-x86_64-with-glibc2.36
python: 3.11.2
client-version: 1.3.67
compiler: g++ (Debian 12.2.0-14+deb12u1) 12.2.0
cppcheck: head 2.17.0
head-info: 0eb4dd8 (2025-07-06 21:35:35 +0200)
count: 1951 1930
elapsed-time: 20.5 20.2
head-timing-info:

old-timing-info:

head results:
bedtools2-2.31.1/src/bed12ToBed6/bed12ToBed6.cpp:74:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bed12ToBed6/bed12ToBed6.cpp:98:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bed12ToBed6/bed12ToBed6.cpp:119:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bed12ToBed6/bed12ToBed6.cpp:140:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/annotateBed/annotateBed.cpp:121:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToFastq/bamToFastqMain.cpp:94:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToFastq/bamToFastqMain.cpp:123:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/annotateBed/annotateMain.cpp:112:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/annotateBed/annotateMain.cpp:141:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:40:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:71:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:120:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:255:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:167:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:235:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:288:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:324:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:363:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Type [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:389:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:421:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:555:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:616:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bed12ToBed6/bed12ToBed6.cpp:133:26: style: Parameter 'bedInput' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/bed12ToBed6/bed12ToBed6.cpp:39:38: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:175:17: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:207:17: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:91:21: style: Variable 'currName' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/annotateBed/annotateBed.cpp:27:5: warning: Class 'BedAnnotate' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/annotateBed/annotateBed.cpp:27:5: warning: Class 'BedAnnotate' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:115:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:150:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:200:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:218:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:107:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:142:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:178:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Compressed [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:262:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:312:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VERSION [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedpeToBam/bedpeToBam.cpp:105:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedpeToBam/bedpeToBam.cpp:140:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedpeToBam/bedpeToBam.cpp:172:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Compressed [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedpeToBam/bedpeToBam.cpp:300:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VERSION [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToFastq/bamToFastqMain.cpp:38:10: style: The scope of the variable 'haveFastq2' can be reduced. [variableScope]
bedtools2-2.31.1/src/bamToFastq/bamToFastqMain.cpp:31:37: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/bamToFastq/bamToFastqMain.cpp:38:24: style: Variable 'haveFastq2' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bamToFastq/bamToFastqMain.cpp:84:28: style: Variable 'haveFastq2' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bedtools.cpp:190:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedtools.cpp:217:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedtools.cpp:313:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedtools.cpp:356:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/closestFile/closestFile.h:24:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _sweep [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/closestFile/closestFile.cpp:24:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/closestFile/closestFile.cpp:34:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _sweep [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/closestFile/closestFile.h:18:5: style: Class 'ClosestFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/bedpeToBam/bedpeToBam.cpp:61:10: style: The scope of the variable 'haveMapQual' can be reduced. [variableScope]
bedtools2-2.31.1/src/bedpeToBam/bedpeToBam.cpp:48:37: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/bedpeToBam/bedpeToBam.cpp:61:26: style: Variable 'haveMapQual' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bedpeToBam/bedpeToBam.cpp:95:25: style: Variable 'haveMapQual' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/closestFile/closestHelp.cpp:12:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/clusterBed/clusterBed.cpp:46:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/clusterBed/clusterMain.cpp:75:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/clusterBed/clusterMain.cpp:105:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:194:45: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:194:58: performance: Function parameter 'sortType' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:194:75: performance: Function parameter 'session' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:195:61: performance: Function parameter 'imageType' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:214:57: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:214:70: performance: Function parameter 'sortType' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:214:87: performance: Function parameter 'session' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:215:54: performance: Function parameter 'imageType' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:214:26: style: Parameter 'bedInput' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/bedToIgv/bedToIgv.cpp:39:35: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/clusterBed/clusterBed.cpp:24:5: warning: Class 'BedCluster' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/clusterBed/clusterBed.cpp:24:5: warning: Class 'BedCluster' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/clusterBed/clusterBed.cpp:63:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
bedtools2-2.31.1/src/clusterBed/clusterBed.cpp:116:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
bedtools2-2.31.1/src/clusterBed/clusterBed.cpp:83:16: style: Variable 'chrom' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/complementFile/complementFile.cpp:16:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/complementFile/complementFile.cpp:66:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/complementFile/complementFile.cpp:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/complementFile/complementHelp.cpp:13:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/complementFile/complementFile.cpp:4:17: warning: Member variable 'ComplementFile::_frm' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/complementFile/complementFile.h:23:3: style: Class 'ComplementFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/coverageFile/coverageHelp.cpp:17:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:44:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:69:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:80:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:240:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/coverageFile/coverageFile.h:17:2: style: Class 'CoverageFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:234:1: error: Memory leak: coveredFractionString [memleak]
bedtools2-2.31.1/src/annotateBed/annotateMain.cpp:26:35: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:116:3: error: Common realloc mistake: '_depthArray' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:27:9: warning: If memory allocation fails, then there is a possible null pointer dereference: _depthArray [nullPointerOutOfMemory]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:26:32: note: Assuming allocation function fails
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:26:16: note: Assignment '_depthArray=(unsigned long*)malloc(newSize)', assigned value is 0
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:27:9: note: Null pointer dereference
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:26:16: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:116:17: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:85:91: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/coverageFile/coverageFile.cpp:197:89: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/expand/expand.cpp:84:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/expand/expand.cpp:129:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/expand/expand.cpp:196:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TAB_INVALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/clusterBed/clusterMain.cpp:38:10: style: The scope of the variable 'haveMaxDistance' can be reduced. [variableScope]
bedtools2-2.31.1/src/clusterBed/clusterMain.cpp:27:34: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/clusterBed/clusterMain.cpp:38:26: style: Variable 'haveMaxDistance' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/clusterBed/clusterMain.cpp:66:33: style: Variable 'haveMaxDistance' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/fastaFromBed/fastaFromBed.cpp:41:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fastaFromBed/fastaFromBed.cpp:77:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fastaFromBed/fastaFromBed.cpp:116:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fastaFromBed/fastaFromBedMain.cpp:122:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fastaFromBed/fastaFromBedMain.cpp:157:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fisher/fisher.cpp:24:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fisher/fisher.cpp:36:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _queryUnion [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fisher/fisher.cpp:57:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _dbUnion [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fisher/fisher.cpp:118:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fisher/fisher.h:18:5: style: Class 'Fisher' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/fisher/fisher.cpp:101:61: style:inconclusive: Function 'getTotalIntersection' argument 1 names different: declaration 'hits' definition 'recList'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/fisher/fisher.h:30:57: note: Function 'getTotalIntersection' argument 1 names different: declaration 'hits' definition 'recList'.
bedtools2-2.31.1/src/fisher/fisher.cpp:101:61: note: Function 'getTotalIntersection' argument 1 names different: declaration 'hits' definition 'recList'.
bedtools2-2.31.1/src/fastaFromBed/fastaFromBed.cpp:37:5: warning: Class 'Bed2Fa' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/fastaFromBed/fastaFromBed.cpp:37:5: warning: Class 'Bed2Fa' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/fisher/fisherHelp.cpp:5:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:53:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:79:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:135:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/expand/expand.cpp:46:33: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/expand/expand.cpp:50:31: style: Variable 'groupColumnsString' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/expand/expand.cpp:50:12: style: Variable 'groupColumnsString' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/expand/expand.cpp:175:12: style: Unused variable: inLine [unusedVariable]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:21:5: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:22:5: performance: Variable '_genomeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:29:5: warning: Class 'BedFlank' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:29:5: warning: Class 'BedFlank' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:65:36: style: Condition '_forceStrand==true' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/flankBed/flankBed.cpp:61:31: note: Assuming that condition '_forceStrand==false' is not redundant
bedtools2-2.31.1/src/flankBed/flankBed.cpp:65:36: note: Condition '_forceStrand==true' is always true
bedtools2-2.31.1/src/flankBed/flankBed.cpp:17:26: style:inconclusive: Function 'BedFlank' argument 4 names different: declaration 'leftSlop' definition 'leftFlank'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/flankBed/flankBed.h:34:20: note: Function 'BedFlank' argument 4 names different: declaration 'leftSlop' definition 'leftFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:17:26: note: Function 'BedFlank' argument 4 names different: declaration 'leftSlop' definition 'leftFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:17:43: style:inconclusive: Function 'BedFlank' argument 5 names different: declaration 'rightSlop' definition 'rightFlank'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/flankBed/flankBed.h:34:36: note: Function 'BedFlank' argument 5 names different: declaration 'rightSlop' definition 'rightFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:17:43: note: Function 'BedFlank' argument 5 names different: declaration 'rightSlop' definition 'rightFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:75:39: style:inconclusive: Function 'AddFlank' argument 2 names different: declaration 'leftSlop' definition 'leftFlank'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/flankBed/flankBed.h:61:33: note: Function 'AddFlank' argument 2 names different: declaration 'leftSlop' definition 'leftFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:75:39: note: Function 'AddFlank' argument 2 names different: declaration 'leftSlop' definition 'leftFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:75:54: style:inconclusive: Function 'AddFlank' argument 3 names different: declaration 'rightSlop' definition 'rightFlank'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/flankBed/flankBed.h:61:47: note: Function 'AddFlank' argument 3 names different: declaration 'rightSlop' definition 'rightFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:75:54: note: Function 'AddFlank' argument 3 names different: declaration 'rightSlop' definition 'rightFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:131:47: style:inconclusive: Function 'AddStrandedFlank' argument 2 names different: declaration 'leftSlop' definition 'leftFlank'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/flankBed/flankBed.h:65:41: note: Function 'AddStrandedFlank' argument 2 names different: declaration 'leftSlop' definition 'leftFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:131:47: note: Function 'AddStrandedFlank' argument 2 names different: declaration 'leftSlop' definition 'leftFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:131:62: style:inconclusive: Function 'AddStrandedFlank' argument 3 names different: declaration 'rightSlop' definition 'rightFlank'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/flankBed/flankBed.h:65:55: note: Function 'AddStrandedFlank' argument 3 names different: declaration 'rightSlop' definition 'rightFlank'.
bedtools2-2.31.1/src/flankBed/flankBed.cpp:131:62: note: Function 'AddStrandedFlank' argument 3 names different: declaration 'rightSlop' definition 'rightFlank'.
bedtools2-2.31.1/src/flankBed/flankBedMain.cpp:109:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/flankBed/flankBedMain.cpp:147:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:60:10: style: The scope of the variable 'haveMapQual' can be reduced. [variableScope]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:216:9: style: The scope of the variable 'bedLength' can be reduced. [variableScope]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:282:33: style: Local variable 'cOp' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:276:29: note: Shadowed declaration
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:282:33: note: Shadow variable
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:47:35: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:60:26: style: Variable 'haveMapQual' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bedToBam/bedToBam.cpp:94:25: style: Variable 'haveMapQual' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:77:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:109:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:137:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable starts [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:165:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:237:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable starts [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:261:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:385:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:479:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:495:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageMain.cpp:138:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageMain.cpp:243:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:75:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:115:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:148:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:190:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:44:10: style: The scope of the variable 'haveColumns' can be reduced. [variableScope]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:143:29: style: Parameter 'inFile' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:159:45: style: Parameter 's1Col' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:159:59: style: Parameter 'e1Col' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:159:73: style: Parameter 's2Col' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:159:87: style: Parameter 'e2Col' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:35:37: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:44:22: style: Variable 'haveColumns' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/getOverlap/getOverlap.cpp:70:25: style: Variable 'haveColumns' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:27:5: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:28:5: performance: Variable '_genomeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:40:5: performance: Variable '_requestedStrand' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:48:5: performance: Variable '_gb_track_line_opts' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:49:5: performance: Variable '_currChromName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:50:5: performance: Variable '_currChromSize' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:68:25: style:inconclusive: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const. [functionConst]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.h:109:10: note: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const.
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:68:25: note: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const.
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:60:9: warning: Class 'BedGenomeCoverage' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:60:9: warning: Class 'BedGenomeCoverage' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:98:53: style:inconclusive: Function 'StartNewChrom' argument 1 names different: declaration 'chrom' definition 'newChrom'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.h:104:39: note: Function 'StartNewChrom' argument 1 names different: declaration 'chrom' definition 'newChrom'.
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:98:53: note: Function 'StartNewChrom' argument 1 names different: declaration 'chrom' definition 'newChrom'.
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:431:17: style: Local variable 'depth' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:410:13: note: Shadowed declaration
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:431:17: note: Shadow variable
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:21:66: performance: Function parameter 'requestedStrand' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:25:69: performance: Function parameter 'gb_track_line_opts' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/groupBy/groupBy.cpp:29:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/groupBy/groupBy.cpp:89:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/groupBy/groupBy.cpp:146:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:268:12: style: Variable 'header' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/groupBy/groupBy.h:16:5: style: Class 'GroupBy' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/groupBy/groupBy.cpp:41:13: style: Local variable 'i' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/groupBy/groupBy.cpp:31:11: note: Shadowed declaration
bedtools2-2.31.1/src/groupBy/groupBy.cpp:41:13: note: Shadow variable
bedtools2-2.31.1/src/groupBy/groupByHelp.cpp:5:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/htsutil.cpp:66:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/htsutil.cpp:96:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/htsutil.cpp:110:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/htsutil.cpp:121:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/htsutil.cpp:137:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sam [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/intersectFile/intersectFile.cpp:39:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/intersectFile/intersectFile.cpp:55:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/intersectFile/intersectFile.cpp:81:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/intersectFile/intersectFile.cpp:117:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/intersectFile/intersectFile.cpp:122:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/intersectFile/intersectFile.h:26:5: style: Class 'IntersectFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/intersectFile/intersectFile.cpp:120:50: style:inconclusive: Function 'checkSplits' argument 1 names different: declaration 'hits' definition 'hitSet'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/intersectFile/intersectFile.h:43:44: note: Function 'checkSplits' argument 1 names different: declaration 'hits' definition 'hitSet'.
bedtools2-2.31.1/src/intersectFile/intersectFile.cpp:120:50: note: Function 'checkSplits' argument 1 names different: declaration 'hits' definition 'hitSet'.
bedtools2-2.31.1/src/htsutil.cpp:145:27: error: Invalid index() argument nr 2. A non-boolean value is required. [invalidFunctionArgBool]
bedtools2-2.31.1/src/htsutil.cpp:147:27: error: Invalid index() argument nr 2. A non-boolean value is required. [invalidFunctionArgBool]
bedtools2-2.31.1/src/htsutil.cpp:153:28: error: Invalid index() argument nr 2. A non-boolean value is required. [invalidFunctionArgBool]
bedtools2-2.31.1/src/intersectFile/intersectHelp.cpp:17:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/jaccard/jaccard.cpp:48:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/jaccard/jaccard.cpp:69:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/jaccard/jaccard.h:17:2: style: Class 'Jaccard' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/jaccard/jaccardHelp.cpp:16:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:43:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:95:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:19:5: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:36:16: style:inconclusive: Technically the member function 'BedLinks::WriteURL' can be const. [functionConst]
bedtools2-2.31.1/src/linksBed/linksBed.h:42:10: note: Technically the member function 'BedLinks::WriteURL' can be const.
bedtools2-2.31.1/src/linksBed/linksBed.cpp:36:16: note: Technically the member function 'BedLinks::WriteURL' can be const.
bedtools2-2.31.1/src/linksBed/linksBed.cpp:20:5: warning: Class 'BedLinks' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:20:5: warning: Class 'BedLinks' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:18:45: style: Parameter 'base' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:18:59: style: Parameter 'org' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:18:72: style: Parameter 'db' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:36:30: style: Parameter 'bed' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/linksBed/linksBed.cpp:36:43: style: Parameter 'base' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/linksBed/linksMain.cpp:82:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/linksBed/linksMain.cpp:105:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/mapFile/mapFile.h:17:5: style: Class 'MapFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/mapFile/mapHelp.cpp:13:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/linksBed/linksMain.cpp:27:32: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:45:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBedMain.cpp:94:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBedMain.cpp:129:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:20:5: performance: Variable '_fastaInFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:21:5: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:22:5: performance: Variable '_fastaOutFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:149:24: performance:inconclusive: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.h:55:10: note: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:149:24: note: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:25:5: warning: Class 'MaskFastaFromBed' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:25:5: warning: Class 'MaskFastaFromBed' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:149:63: performance: Function parameter 'chrom' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:72:13: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/mergeFile/mergeFile.cpp:21:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/mergeFile/mergeFile.cpp:38:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/mergeFile/mergeFile.cpp:10:12: warning: Member variable 'MergeFile::_frm' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/mergeFile/mergeFile.h:21:5: style: Class 'MergeFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/mergeFile/mergeHelp.cpp:18:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:112:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:233:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBedMain.cpp:27:43: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:52:19: style:inconclusive: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const. [functionConst]
bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:68:10: note: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const.
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:52:19: note: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const.
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:228:19: performance:inconclusive: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:71:10: note: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:228:19: note: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:39:2: warning: Class 'MultiCovBam' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:39:2: warning: Class 'MultiCovBam' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:20:72: performance: Function parameter 'bed_file' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:125:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:149:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBed.cpp:69:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBed.cpp:94:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBed.cpp:130:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBed.cpp:147:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBed.cpp:154:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBed.cpp:181:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBed.cpp:238:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable START [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBed.cpp:286:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable START [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/flankBed/flankBedMain.cpp:27:32: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:142:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:171:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:206:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:293:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/nekSandbox1/nekSandboxMain.cpp:42:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/nekSandbox1/nekSandboxMain.cpp:43:80: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:56:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:104:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:21:5: performance: Variable '_dbFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:22:5: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:25:5: performance: Variable '_pattern' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:68:14: style:inconclusive: Technically the member function 'NucBed::PrintHeader' can be const. [functionConst]
bedtools2-2.31.1/src/nucBed/nucBed.h:53:10: note: Technically the member function 'NucBed::PrintHeader' can be const.
bedtools2-2.31.1/src/nucBed/nucBed.cpp:68:14: note: Technically the member function 'NucBed::PrintHeader' can be const.
bedtools2-2.31.1/src/nucBed/nucBed.cpp:29:5: warning: Class 'NucBed' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:29:5: warning: Class 'NucBed' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:16:24: style: Parameter 'dbFile' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:16:40: style: Parameter 'bedFile' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/nucBed/nucBed.cpp:117:12: style: Unused variable: sequence [unusedVariable]
bedtools2-2.31.1/src/nucBed/nucBedMain.cpp:99:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/nucBed/nucBedMain.cpp:123:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/nucBed/nucBedMain.cpp:27:30: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/pairToBed/pairToBed.h:106:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:356:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_INVALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:387:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:45:10: style: The scope of the variable 'haveFiles' can be reduced. [variableScope]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:47:10: style: The scope of the variable 'haveGenome' can be reduced. [variableScope]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:48:10: style: The scope of the variable 'haveFiller' can be reduced. [variableScope]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:43:41: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:294:18: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:45:28: style: Variable 'haveFiles' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:47:28: style: Variable 'haveGenome' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:48:28: style: Variable 'haveFiller' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:84:27: style: Variable 'haveFiles' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:112:28: style: Variable 'haveGenome' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:119:33: style: Variable 'haveFiller' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiIntersectBed/multiIntersectBedMain.cpp:54:12: style: Unused variable: basePath [unusedVariable]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:40:5: performance: Variable '_bedAFilePE' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:41:5: performance: Variable '_bedBFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:46:5: performance: Variable '_searchType' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/pairToBed/pairToBed.h:82:10: style:inconclusive: Technically the member function 'BedIntersectPE::ConvertBamToBedPE' can be const. [functionConst]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:51:5: warning: Class 'BedIntersectPE' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:51:5: warning: Class 'BedIntersectPE' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:288:16: style: Local variable 'spanLength' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:257:12: note: Shadowed declaration
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:288:16: note: Shadow variable
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:37:39: performance: Function parameter 'searchType' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:409:14: style: Variable 'prevName' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/pairToBed/pairToBed.cpp:409:25: style: Variable 'currName' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/pairToBed/pairToBedMain.cpp:123:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToBed/pairToBedMain.cpp:173:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:57:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_INVALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:160:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:195:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:22:5: performance: Variable '_bedAFilePE' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:23:5: performance: Variable '_bedBFilePE' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:25:5: performance: Variable '_searchType' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:31:5: warning: Class 'PairToPair' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:31:5: warning: Class 'PairToPair' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:112:14: style: The scope of the variable 'found1' can be reduced. [variableScope]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:113:14: style: The scope of the variable 'found2' can be reduced. [variableScope]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:20:35: performance: Function parameter 'searchType' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:19:71: style: Parameter 'overlapFraction' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:112:21: style: Variable 'found1' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:113:21: style: Variable 'found2' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:115:20: style: Variable 'found1' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/pairToPair/pairToPair.cpp:117:20: style: Variable 'found2' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:38:10: style: The scope of the variable 'haveBed' can be reduced. [variableScope]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:39:10: style: The scope of the variable 'haveBams' can be reduced. [variableScope]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:47:10: style: The scope of the variable 'haveFraction' can be reduced. [variableScope]
bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:34:63: performance: Function parameter 'bed_file' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:27:38: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:38:28: style: Variable 'haveBed' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:39:28: style: Variable 'haveBams' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:47:29: style: Variable 'haveFraction' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:71:25: style: Variable 'haveBed' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:78:26: style: Variable 'haveBams' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/multiBamCov/multiBamCovMain.cpp:95:30: style: Variable 'haveFraction' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/pairToPair/pairToPairMain.cpp:113:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToPair/pairToPairMain.cpp:151:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/randomBed/randomBed.cpp:68:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/randomBed/randomBed.cpp:18:5: performance: Variable '_genomeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/randomBed/randomBed.cpp:20:5: performance: Variable '_length' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/randomBed/randomBed.cpp:48:10: style: The scope of the variable 'strand' can be reduced. [variableScope]
bedtools2-2.31.1/src/randomBed/randomBed.cpp:16:30: style: Parameter 'genomeFile' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/randomBed/randomBedMain.cpp:85:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/randomBed/randomBedMain.cpp:109:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/randomBed/randomBedMain.cpp:27:33: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/randomBed/randomBedMain.cpp:33:20: style: Variable 'bedFile' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/randomBed/randomBedMain.cpp:33:12: style: Variable 'bedFile' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:44:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:109:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:133:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:150:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:188:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:269:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:402:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:453:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:565:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:586:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:598:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/fastaFromBed/fastaFromBedMain.cpp:27:39: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/regressTest/regressTestMain.cpp:47:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/reldist/reldist.cpp:60:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/reldist/reldist.cpp:101:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:88:10: style: The scope of the variable 'useAlignmentScore' can be reduced. [variableScope]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:601:14: style: The scope of the variable 'minMapQuality' can be reduced. [variableScope]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:532:24: performance: Function parameter 'color' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:72:35: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:88:28: style: Variable 'useAlignmentScore' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:141:31: style: Variable 'useAlignmentScore' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:293:19: style: Variable 'header' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:293:12: style: Variable 'header' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:329:19: style: Variable 'header' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:329:12: style: Variable 'header' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/reldist/reldist.cpp:22:5: performance: Variable '_bedAFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/reldist/reldist.cpp:23:5: performance: Variable '_bedBFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/reldist/reldist.cpp:69:9: portability: %lu in format string (no. 3) requires 'unsigned long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
bedtools2-2.31.1/src/reldist/reldist.cpp:20:41: style:inconclusive: Function 'RelativeDistance' argument 3 names different: declaration '_summary' definition 'summary'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/reldist/reldist.h:41:27: note: Function 'RelativeDistance' argument 3 names different: declaration '_summary' definition 'summary'.
bedtools2-2.31.1/src/reldist/reldist.cpp:20:41: note: Function 'RelativeDistance' argument 3 names different: declaration '_summary' definition 'summary'.
bedtools2-2.31.1/src/reldist/reldist.cpp:18:43: performance: Function parameter 'bedAFile' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/reldist/reldist.cpp:19:43: performance: Function parameter 'bedBFile' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/reldist/reldistMain.cpp:78:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/reldist/reldistMain.cpp:116:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sampleFile/sampleFile.cpp:63:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sampleFile/sampleFile.cpp:102:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sampleFile/sampleFile.cpp:8:13: warning: Member variable 'SampleFile::_seed' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/sampleFile/sampleFile.h:17:5: style: Class 'SampleFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/sampleFile/sampleHelp.cpp:12:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shiftBed/shiftBed.cpp:42:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shiftBed/shiftBed.cpp:16:3: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/shiftBed/shiftBed.cpp:17:3: performance: Variable '_genomeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/shiftBed/shiftBed.cpp:23:3: warning: Class 'BedShift' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/shiftBed/shiftBed.cpp:23:3: warning: Class 'BedShift' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/shiftBed/shiftBedMain.cpp:103:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shiftBed/shiftBedMain.cpp:135:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/reldist/reldistMain.cpp:27:34: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:22:14: warning: Member variable 'RegressTest::_fpReportFile' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:149:19: performance:inconclusive: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/regressTest/RegressTest.h:77:7: note: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:149:19: note: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:27:2: warning: Class 'RegressTest' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:27:2: warning: Class 'RegressTest' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:633:4: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:573:21: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:570:18: note: Assuming allocation function fails
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:570:18: note: Assignment 'fp=std::fopen(pidFilename.c_str(),"r")', assigned value is 0
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:573:21: note: Null pointer dereference
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:574:9: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:570:18: note: Assuming allocation function fails
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:570:18: note: Assignment 'fp=std::fopen(pidFilename.c_str(),"r")', assigned value is 0
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:574:9: note: Null pointer dereference
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:611:6: style: The scope of the variable 'currMem' can be reduced. [variableScope]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:313:37: style:inconclusive: Function 'performTests' argument 1 names different: declaration 'correctness' definition 'isCorrectnessTest'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/regressTest/RegressTest.h:83:25: note: Function 'performTests' argument 1 names different: declaration 'correctness' definition 'isCorrectnessTest'.
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:313:37: note: Function 'performTests' argument 1 names different: declaration 'correctness' definition 'isCorrectnessTest'.
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:401:68: style:inconclusive: Function 'executeAndCompareCorrectness' argument 1 names different: declaration 'cmdAndOutput' definition 'fileList'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/regressTest/RegressTest.h:84:56: note: Function 'executeAndCompareCorrectness' argument 1 names different: declaration 'cmdAndOutput' definition 'fileList'.
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:401:68: note: Function 'executeAndCompareCorrectness' argument 1 names different: declaration 'cmdAndOutput' definition 'fileList'.
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:452:68: style:inconclusive: Function 'executeAndComparePerformance' argument 1 names different: declaration 'cmdAndOutput' definition 'fileList'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/regressTest/RegressTest.h:85:56: note: Function 'executeAndComparePerformance' argument 1 names different: declaration 'cmdAndOutput' definition 'fileList'.
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:452:68: note: Function 'executeAndComparePerformance' argument 1 names different: declaration 'cmdAndOutput' definition 'fileList'.
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:345:10: style: Local variable 'inFilesCmd' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:320:9: note: Shadowed declaration
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:345:10: note: Shadow variable
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:479:13: style: Variable 'oldRunTimeInfo' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:503:13: style: Variable 'newRunTimeInfo' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:514:14: style: Variable 'diffRunTimeInfo' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:528:15: style: Variable 'diffRunTimeInfo' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:209:4: performance: Assigning the result of c_str() to a std::string is slow and redundant. [stlcstrAssignment]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:268:9: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:272:38: performance: Concatenating the result of c_str() and a std::string is slow and redundant. [stlcstrConcat]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:320:9: style: Unused variable: inFilesCmd [unusedVariable]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:322:9: style: Unused variable: allOptsCmd [unusedVariable]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:324:9: style: Unused variable: oldVerionFinalCmd [unusedVariable]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:325:9: style: Unused variable: newVersionFinalCmd [unusedVariable]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:611:14: style: Variable 'currMem' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:621:11: style: Variable 'currMem' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/regressTest/RegressTest.cpp:173:88: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:109:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:150:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:250:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:280:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:354:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shuffleBed/shuffleBedMain.cpp:132:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shuffleBed/shuffleBedMain.cpp:162:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:26:5: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:27:5: performance: Variable '_genomeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:28:5: performance: Variable '_excludeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:29:5: performance: Variable '_includeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:56:9: warning: Class 'BedShuffle' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:56:9: warning: Class 'BedShuffle' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:22:63: style:inconclusive: Function 'BedShuffle' argument 13 names different: declaration '_maxTries' definition 'maxTries'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/shuffleBed/shuffleBed.h:42:23: note: Function 'BedShuffle' argument 13 names different: declaration '_maxTries' definition 'maxTries'.
bedtools2-2.31.1/src/shuffleBed/shuffleBed.cpp:22:63: note: Function 'BedShuffle' argument 13 names different: declaration '_maxTries' definition 'maxTries'.
bedtools2-2.31.1/src/slopBed/slopBed.cpp:52:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/slopBed/slopBed.cpp:82:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/slopBed/slopBed.cpp:20:5: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/slopBed/slopBed.cpp:21:5: performance: Variable '_genomeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/slopBed/slopBed.cpp:28:5: warning: Class 'BedSlop' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/slopBed/slopBed.cpp:28:5: warning: Class 'BedSlop' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/pairToPair/pairToPairMain.cpp:44:10: style: The scope of the variable 'haveFraction' can be reduced. [variableScope]
bedtools2-2.31.1/src/pairToPair/pairToPairMain.cpp:26:37: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/pairToPair/pairToPairMain.cpp:44:23: style: Variable 'haveFraction' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/pairToPair/pairToPairMain.cpp:91:30: style: Variable 'haveFraction' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/slopBed/slopBedMain.cpp:109:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/slopBed/slopBedMain.cpp:149:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:56:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:136:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortBySizeAsc [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:163:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortBySizeDesc [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:178:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortBySizeAsc [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:195:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortBySizeDesc [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:212:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortByScoreAsc [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:234:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortByScoreDesc [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:20:5: performance: Variable '_bedFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:21:5: warning: Class 'BedSort' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/sortBed/sortBed.cpp:21:5: warning: Class 'BedSort' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/sortBed/sortMain.cpp:114:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/sortBed/sortMain.cpp:174:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shiftBed/shiftBedMain.cpp:25:32: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/spacingFile/spacingFile.cpp:9:14: warning: Member variable 'SpacingFile::_inputFile' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/spacingFile/spacingFile.h:18:5: style: Class 'SpacingFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/spacingFile/spacingHelp.cpp:12:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/split/splitBed.cpp:81:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/split/splitBed.cpp:157:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/split/splitBed.cpp:180:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/split/splitBed.cpp:192:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/split/splitBed.cpp:217:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FOPEN_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/split/splitBed.cpp:285:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortBySizeDesc [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/split/splitBed.cpp:341:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/split/splitBed.cpp:67:11: warning: Member variable 'BedSplit::bedType' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/split/splitBed.cpp:339:16: performance:inconclusive: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/split/splitBed.h:35:10: note: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/split/splitBed.cpp:339:16: note: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/split/splitBed.cpp:168:29: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/split/splitBed.cpp:126:19: style: Checking if unsigned expression 'num_chuncks' is less than zero. [unsignedLessThanZero]
bedtools2-2.31.1/src/split/splitBed.cpp:147:49: style:inconclusive: Function 'saveFileChunk' argument 1 names different: declaration 'name' definition 'filename'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/split/splitBed.h:36:43: note: Function 'saveFileChunk' argument 1 names different: declaration 'name' definition 'filename'.
bedtools2-2.31.1/src/split/splitBed.cpp:147:49: note: Function 'saveFileChunk' argument 1 names different: declaration 'name' definition 'filename'.
bedtools2-2.31.1/src/split/splitBed.cpp:77:11: style: Variable 'algorithm' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/split/splitBed.cpp:79:30: style: Variable 'long_options' can be declared as const array [constVariable]
bedtools2-2.31.1/src/split/splitBed.cpp:306:28: style: Unused variable: stdevs [unusedVariable]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:10:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:62:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:133:28: style: Array index 'i' is used before limits check. [arrayIndexThenCheck]
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: style: Virtual function 'upCast' is called from constructor 'SubtractFile(ContextSubtract*context)' at line 10. Dynamic binding is not used. [virtualCallInConstructor]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:10:31: note: Calling upCast
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: note: upCast is a virtual function
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: style: Virtual function 'upCast' is called from constructor 'SubtractFile(ContextSubtract*context)' at line 10. Dynamic binding is not used. [virtualCallInConstructor]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:10:72: note: Calling upCast
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: note: upCast is a virtual function
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: style: Virtual function 'upCast' is called from constructor 'SubtractFile(ContextSubtract*context)' at line 15. Dynamic binding is not used. [virtualCallInConstructor]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:15:6: note: Calling upCast
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: note: upCast is a virtual function
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: style: Virtual function 'upCast' is called from constructor 'SubtractFile(ContextSubtract*context)' at line 16. Dynamic binding is not used. [virtualCallInConstructor]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:16:3: note: Calling upCast
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: note: upCast is a virtual function
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: style: Virtual function 'upCast' is called from constructor 'SubtractFile(ContextSubtract*context)' at line 16. Dynamic binding is not used. [virtualCallInConstructor]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:16:41: note: Calling upCast
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: note: upCast is a virtual function
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: style: Virtual function 'upCast' is called from constructor 'SubtractFile(ContextSubtract*context)' at line 17. Dynamic binding is not used. [virtualCallInConstructor]
bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:17:6: note: Calling upCast
bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: note: upCast is a virtual function
bedtools2-2.31.1/src/subtractFile/subtractFile.h:18:5: style: Class 'SubtractFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/subtractFile/subtractHelp.cpp:12:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/summaryFile/summaryFile.cpp:32:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _context [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/summaryFile/summaryFile.cpp:70:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/summaryFile/summaryFile.cpp:17:14: warning: Member variable 'SummaryFile::_frm' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/summaryFile/summaryFile.cpp:17:14: warning: Member variable 'SummaryFile::_inputFile' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/summaryFile/summaryFile.h:23:5: style: Class 'SummaryFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/summaryFile/summaryFile.cpp:88:23: style: Local variable 'chromDataIt' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/summaryFile/summaryFile.cpp:77:55: note: Shadowed declaration
bedtools2-2.31.1/src/summaryFile/summaryFile.cpp:88:23: note: Shadow variable
bedtools2-2.31.1/src/summaryFile/summaryHelp.cpp:12:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/shuffleBed/shuffleBedMain.cpp:27:34: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/tagBam/tagBam.cpp:67:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/tagBam/tagBamMain.cpp:137:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/tagBam/tagBamMain.cpp:202:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/slopBed/slopBedMain.cpp:27:31: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/tagBam/tagBam.cpp:17:35: style:inconclusive: Function 'TagBam' argument 3 names different: declaration 'annoLabels' definition 'annoLables'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/tagBam/tagBam.h:42:39: note: Function 'TagBam' argument 3 names different: declaration 'annoLabels' definition 'annoLables'.
bedtools2-2.31.1/src/tagBam/tagBam.cpp:17:35: note: Function 'TagBam' argument 3 names different: declaration 'annoLabels' definition 'annoLables'.
bedtools2-2.31.1/src/tagBam/tagBam.cpp:114:33: style: Local variable 'i' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/tagBam/tagBam.cpp:97:25: note: Shadowed declaration
bedtools2-2.31.1/src/tagBam/tagBam.cpp:114:33: note: Shadow variable
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphs.cpp:81:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coord [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphs.cpp:101:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coord [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphs.cpp:138:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphs.cpp:153:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphs.cpp:165:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphs.cpp:172:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphs.cpp:203:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphs.cpp:220:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chrom [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:139:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:165:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:199:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:288:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/BamTools-Ancillary/BamAncillary.cpp:65:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/BamTools-Ancillary/BamAncillary.cpp:104:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/BamTools-Ancillary/BamAncillary.cpp:34:51: error: Same iterator is used with containers '(std::vector<CigarOp>)bam.CigarData' that are temporaries or defined in different scopes. [iterators3]
bedtools2-2.31.1/src/utils/BamTools-Ancillary/BamAncillary.cpp:36:17: note: Same iterator is used with containers '(std::vector<CigarOp>)bam.CigarData' that are temporaries or defined in different scopes.
bedtools2-2.31.1/src/utils/BamTools-Ancillary/BamAncillary.cpp:34:51: note: Same iterator is used with containers '(std::vector<CigarOp>)bam.CigarData' that are temporaries or defined in different scopes.
bedtools2-2.31.1/src/sortBed/sortMain.cpp:27:31: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:28:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:108:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/BlockedIntervals/BlockedIntervals.cpp:61:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/BlockedIntervals/BlockedIntervals.cpp:80:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/BlockedIntervals/BlockedIntervals.cpp:22:17: style: Unused variable: lengths [unusedVariable]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:104:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:135:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SINGLE_LINE_DELIM_TEXT_FILE_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:265:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_POS_PLUS_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:367:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FILE_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:701:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNTESTED [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:735:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNTESTED [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:743:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNTESTED [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:753:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:759:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:787:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:805:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_FILE_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:14:14: warning: Member variable 'ContextBase::_runToQueryEnd' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:14:14: warning: Member variable 'ContextBase::_isCram' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:14:14: warning: Member variable 'ContextBase::_argc' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:14:14: warning: Member variable 'ContextBase::_argv' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:14:14: warning: Member variable 'ContextBase::_i' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:763:19: performance:inconclusive: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:312:10: note: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:763:19: note: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:92:3: warning: Class 'ContextBase' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:92:3: warning: Class 'ContextBase' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:147:18: style: Virtual function 'hasColumnOpsMethods' is called from constructor 'ContextBase()' at line 91. Dynamic binding is not used. [virtualCallInConstructor]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:91:6: note: Calling hasColumnOpsMethods
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:147:18: note: hasColumnOpsMethods is a virtual function
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:147:18: style: Virtual function 'hasColumnOpsMethods' is called from destructor '~ContextBase()' at line 113. Dynamic binding is not used. [virtualCallInConstructor]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:113:6: note: Calling hasColumnOpsMethods
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:147:18: note: hasColumnOpsMethods is a virtual function
bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:124:30: performance:inconclusive: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/BinTree/BinTree.h:66:13: note: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:124:30: note: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/BinTree/BinTree.h:32:2: style: Class 'BinTree' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:72:19: style: Variable 'bin' can be declared as reference to const [constVariableReference]
bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:74:72: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:86:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL_TIES [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:144:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REF_DIST [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:208:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL_TIES [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:235:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EACH_DB [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.cpp:10:20: warning: Member variable 'ContextComplement::_onlyChromsWithBedRecords' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.h:17:11: style: The destructor '~ContextComplement' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:33:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.h:17:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.h:18:16: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:243:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.h:18:16: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.h:19:7: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:78:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.h:19:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.cpp:39:11: style: Condition '!handle_limit_chroms()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.cpp:39:31: note: Calling function 'handle_limit_chroms' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextComplement.cpp:39:11: note: Condition '!handle_limit_chroms()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:10:17: warning: Member variable 'ContextClosest::_forceUpstream' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:10:17: warning: Member variable 'ContextClosest::_forceDownstream' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:107:7: style:inconclusive: Technically the member function 'ContextIntersect::shouldRunToDbEnd' can be const. [functionConst]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:16:11: style: The destructor '~ContextIntersect' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:33:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:16:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:17:15: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:78:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:17:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:19:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:243:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:19:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:20:15: style: The function 'determineOutputType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:54:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:20:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:142:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:121:15: style: The function 'handle_c' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:288:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:121:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:17:11: style: The destructor '~ContextClosest' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:16:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:17:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:18:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:19:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:18:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:19:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:19:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:20:18: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:17:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:20:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:19:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is identical to the overridden function [uselessOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.h:19:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:45:16: style: Condition '!handle_d()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:45:25: note: Calling function 'handle_d' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:45:16: note: Condition '!handle_d()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:51:14: style: Condition '!handle_io()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:51:24: note: Calling function 'handle_io' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:51:14: note: Condition '!handle_io()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:54:14: style: Condition '!handle_iu()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:54:24: note: Calling function 'handle_iu' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:54:14: note: Condition '!handle_iu()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:57:14: style: Condition '!handle_id()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:57:24: note: Calling function 'handle_id' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:57:14: note: Condition '!handle_id()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:60:14: style: Condition '!handle_fu()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:60:24: note: Calling function 'handle_fu' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:60:14: note: Condition '!handle_fu()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:63:14: style: Condition '!handle_fd()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:63:24: note: Calling function 'handle_fd' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:63:14: note: Condition '!handle_fd()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:66:14: style: Condition '!handle_N()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:66:23: note: Calling function 'handle_N' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextClosest.cpp:66:14: note: Condition '!handle_N()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:10:18: warning: Member variable 'ContextCoverage::_mean' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:17:11: style: The destructor '~ContextCoverage' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:16:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:17:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:18:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:19:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:18:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:19:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:19:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:20:18: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:17:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:20:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:32:7: style: The function 'handle_c' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:121:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:32:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:19:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is identical to the overridden function [uselessOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.h:19:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:30:8: style: Condition '!handle_d()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:30:17: note: Calling function 'handle_d' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:30:8: note: Condition '!handle_d()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:36:8: style: Condition '!handle_hist()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:36:20: note: Calling function 'handle_hist' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:36:8: note: Condition '!handle_hist()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:39:8: style: Condition '!handle_mean()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:39:20: note: Calling function 'handle_mean' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextCoverage.cpp:39:8: note: Condition '!handle_mean()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:16:3: style: The destructor '~ContextGroupBy' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:33:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:16:3: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:17:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:243:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:17:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:18:15: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:78:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:18:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:31:7: style: The function 'handle_g' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:275:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:31:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:34:7: style: The function 'handle_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:277:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.h:34:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:43:8: style: Condition '!handle_inheader()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:43:24: note: Calling function 'handle_inheader' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:43:8: note: Condition '!handle_inheader()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:46:8: style: Condition '!handle_outheader()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:46:25: note: Calling function 'handle_outheader' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:46:8: note: Condition '!handle_outheader()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:52:8: style: Condition '!handle_full()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:52:20: note: Calling function 'handle_full' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:52:8: note: Condition '!handle_full()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:55:8: style: Condition '!handle_ignorecase()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:55:26: note: Calling function 'handle_ignorecase' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextGroupBy.cpp:55:8: note: Condition '!handle_ignorecase()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.h:20:9: style:inconclusive: Technically the member function 'ContextFisher::getExcludeFile' can be const. [functionConst]
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:16:4: style: The destructor '~ContextJaccard' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:16:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:16:4: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:17:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:19:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:17:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:18:15: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:17:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:18:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:21:7: style: The function 'handle_s' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:128:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:21:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:22:7: style: The function 'handle_S' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:129:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:22:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.h:17:4: style: The destructor '~ContextFisher' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:16:4: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.h:17:4: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.h:18:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:17:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.h:18:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.h:19:15: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.h:18:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.h:19:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.cpp:26:8: style: Condition '!handle_m()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.cpp:26:17: note: Calling function 'handle_m' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextFisher.cpp:26:8: note: Condition '!handle_m()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.cpp:114:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FILE_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.cpp:46:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAME_STRAND_EITHER [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextJaccard.cpp:55:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAME_STRAND_FORWARD [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.cpp:10:19: warning: Member variable 'ContextIntersect::_splitBlockMgr' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.cpp:10:19: warning: Member variable 'ContextIntersect::_shouldRunToDbEnd' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:16:11: style: The destructor '~ContextMap' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:16:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:16:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:17:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:19:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:17:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:18:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:18:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:19:18: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:17:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:19:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:18:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is identical to the overridden function [uselessOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMap.h:18:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:86:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ANY_STRAND [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:135:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAME_STRAND_EITHER [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:144:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAME_STRAND_FORWARD [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.h:17:3: style: The destructor '~ContextMerge' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:33:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.h:17:3: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.h:18:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:243:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.h:18:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.h:19:15: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:78:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.h:19:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.h:23:7: style: The function 'handle_n' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:279:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.h:23:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:40:8: style: Condition '!handle_nms()' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:40:19: note: Calling function 'handle_nms' returns 0
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:40:8: note: Condition '!handle_nms()' is always true
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:43:8: style: Condition '!handle_scores()' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:43:22: note: Calling function 'handle_scores' returns 0
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:43:8: note: Condition '!handle_scores()' is always true
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:52:8: style: Condition '!handle_s()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:52:17: note: Calling function 'handle_s' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextMerge.cpp:52:8: note: Condition '!handle_s()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextSample.h:16:3: style: The destructor '~ContextSample' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:33:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSample.h:16:3: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSample.h:17:7: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:78:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSample.h:17:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSample.h:19:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:243:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSample.h:19:15: note: Function in derived class
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:46:10: style: The scope of the variable 'haveFiles' can be reduced. [variableScope]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:48:10: style: The scope of the variable 'haveGenome' can be reduced. [variableScope]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:49:10: style: The scope of the variable 'haveFiller' can be reduced. [variableScope]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:44:41: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:289:18: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:46:28: style: Variable 'haveFiles' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:48:28: style: Variable 'haveGenome' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:49:28: style: Variable 'haveFiller' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:84:27: style: Variable 'haveFiles' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:112:28: style: Variable 'haveGenome' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:119:33: style: Variable 'haveFiller' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/unionBedGraphs/unionBedGraphsMain.cpp:54:12: style: Unused variable: basePath [unusedVariable]
bedtools2-2.31.1/src/utils/Contexts/ContextSpacing.h:16:3: style: The destructor '~ContextSpacing' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:33:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSpacing.h:16:3: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSpacing.h:19:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:243:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSpacing.h:19:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSummary.h:16:3: style: The destructor '~ContextSummary' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:33:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSummary.h:16:3: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSummary.h:17:7: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:78:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSummary.h:17:7: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSummary.h:19:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:243:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSummary.h:19:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:42:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:69:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:106:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:123:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/Fasta/split.cpp:22:11: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
bedtools2-2.31.1/src/utils/Fasta/split.cpp:25:15: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:31:13: warning: Member variable 'FastaIndex::faidx' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Fasta/Fasta.h:64:9: warning: Member variable 'FastaReference::filesize' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Fasta/Fasta.h:64:9: warning: Member variable 'FastaReference::index' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:84:20: performance:inconclusive: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static. [functionStatic]
bedtools2-2.31.1/src/utils/Fasta/Fasta.h:54:16: note: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static.
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:84:20: note: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static.
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:17:11: style: The destructor '~ContextSubtract' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:16:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:17:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:18:15: style: The function 'parseCmdArgs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:19:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:18:15: note: Function in derived class
bedtools2-2.31.1/src/utils/Fasta/Fasta.h:45:9: style: Class 'FastaIndex' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:19:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:19:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:20:18: style: The function 'isValidState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:17:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:20:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:19:18: style: The function 'hasIntersectMethods' overrides a function in a base class but is identical to the overridden function [uselessOverride]
bedtools2-2.31.1/src/utils/Contexts/ContextIntersect.h:105:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.h:19:18: note: Function in derived class
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.cpp:34:8: style: Condition '!handle_A()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.cpp:34:17: note: Calling function 'handle_A' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.cpp:34:8: note: Condition '!handle_A()' is always false
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.cpp:37:8: style: Condition '!handle_N()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.cpp:37:17: note: Calling function 'handle_N' returns 1
bedtools2-2.31.1/src/utils/Contexts/ContextSubtract.cpp:37:8: note: Condition '!handle_N()' is always false
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:66:42: style:inconclusive: Function 'entry' argument 1 names different: declaration 'key' definition 'name'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/Fasta/Fasta.h:51:38: note: Function 'entry' argument 1 names different: declaration 'key' definition 'name'.
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:66:42: note: Function 'entry' argument 1 names different: declaration 'key' definition 'name'.
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:35:39: performance: Function parameter 'fname' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:86:34: performance: Function parameter 'reffilename' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:99:43: performance: Function parameter 'seqname' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:119:46: performance: Function parameter 'seqname' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:142:46: performance: Function parameter 'seqname' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:56:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RefName [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.cpp:108:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RefName [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:45:7: style:inconclusive: Technically the member function 'InputStreamMgr::getEofHit' can be const. [functionConst]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.h:24:2: style: Class 'InputStreamMgr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.h:18:2: style: Class 'BufferedStreamMgr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:19:11: style: The destructor '~BamFileReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:17:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:19:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:20:15: style: The function 'open' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:27:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:20:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:21:15: style: The function 'isOpen' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:28:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:21:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:22:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:29:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:22:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:23:15: style: The function 'eof' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:30:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:33:15: style: The function 'readEntry' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:31:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:33:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:35:15: style: The function 'hasHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:33:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:35:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:36:24: style: The function 'getHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:34:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:36:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:50:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:35:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BamFileReader.h:50:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.cpp:22:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:80:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_FILE_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:111:25: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:111:45: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:113:26: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:116:15: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:147:43: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:79:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:160:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:236:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:136:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:65:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:13:2: warning: Class 'SingleLineDelimTransferBuffer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:13:2: warning: Class 'SingleLineDelimTransferBuffer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h:13:2: style: Class 'SingleLineDelimTransferBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:36:26: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:37:26: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:9:82: style:inconclusive: Function 'SingleLineDelimTransferBuffer' argument 2 names different: declaration 'delim' definition 'delimChar'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.h:13:52: note: Function 'SingleLineDelimTransferBuffer' argument 2 names different: declaration 'delim' definition 'delimChar'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:9:82: note: Function 'SingleLineDelimTransferBuffer' argument 2 names different: declaration 'delim' definition 'delimChar'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:148:39: style:inconclusive: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const. [functionConst]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:55:9: note: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:148:39: note: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:17:2: warning: Class 'SingleLineDelimTextFileReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:17:2: warning: Class 'SingleLineDelimTextFileReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:24:2: style: Class 'SingleLineDelimTextFileReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:25:3: style: The destructor '~SingleLineDelimTextFileReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:17:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:25:3: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:27:15: style: The function 'readEntry' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:31:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:27:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:28:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:35:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:28:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:33:24: style: The function 'getHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:34:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:33:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:34:15: style: The function 'hasHeader' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/FileReader.h:33:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:34:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:74:10: warning: Identical condition and return expression 'wasHeader', return value is always false [identicalConditionAfterEarlyExit]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:44:19: note: 'wasHeader' is assigned value 'false' here.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:69:6: note: If condition 'wasHeader' is true, the function will return/exit
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:74:10: note: Returning identical expression 'wasHeader'
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:73:6: style: Condition '!findDelimiters()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:73:21: note: Calling function 'findDelimiters' returns 1
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:73:6: note: Condition '!findDelimiters()' is always false
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:80:50: style:inconclusive: Function 'getField' argument 1 names different: declaration 'numField' definition 'fieldNum'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:29:28: note: Function 'getField' argument 1 names different: declaration 'numField' definition 'fieldNum'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:80:50: note: Function 'getField' argument 1 names different: declaration 'numField' definition 'fieldNum'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:80:68: style:inconclusive: Function 'getField' argument 2 names different: declaration 'val' definition 'str'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:29:46: note: Function 'getField' argument 2 names different: declaration 'val' definition 'str'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:80:68: note: Function 'getField' argument 2 names different: declaration 'val' definition 'str'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:87:50: style:inconclusive: Function 'getField' argument 1 names different: declaration 'numField' definition 'fieldNum'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:30:28: note: Function 'getField' argument 1 names different: declaration 'numField' definition 'fieldNum'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:87:50: note: Function 'getField' argument 1 names different: declaration 'numField' definition 'fieldNum'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:60:28: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.cpp:48:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORWARD [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.cpp:169:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORWARD [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:17:17: warning: Member variable 'InputStreamMgr::_finalInputStream' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:152:6: style: The scope of the variable 'currChar' can be reduced. [variableScope]
bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/InputStreamMgr.cpp:152:15: style: Variable 'currChar' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMgr.cpp:53:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMgr.cpp:133:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_POS_PLUS_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMgr.cpp:207:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMgr.cpp:248:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FILE_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMgr.cpp:255:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FILE_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMgr.h:33:2: style: Class 'FileRecordMgr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.h:17:2: style: Class 'FileRecordMergeMgr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.h:30:10: style: The function 'getNextRecord' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMgr.h:46:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.h:30:10: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.h:33:7: style: The function 'eof' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMgr.h:37:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.h:33:7: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.cpp:27:60: style:inconclusive: Function 'getNextRecord' argument 1 names different: declaration 'keyList' definition 'recList'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.h:30:41: note: Function 'getNextRecord' argument 1 names different: declaration 'keyList' definition 'recList'.
bedtools2-2.31.1/src/utils/FileRecordTools/FileRecordMergeMgr.cpp:27:60: note: Function 'getNextRecord' argument 1 names different: declaration 'keyList' definition 'recList'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:131:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:30:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED3_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:26:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED6_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:52:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:249:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:295:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Length [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:316:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Type [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.cpp:36:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.cpp:91:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.cpp:6:15: warning: Member variable 'Bed3Interval::_skipFirstThreeFieldsWhenPrinting' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:24:7: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:67:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:24:7: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:26:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:69:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:26:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:27:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:70:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:27:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:28:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:71:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:28:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:29:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:73:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:29:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:30:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:131:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:30:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:32:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:128:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:32:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:33:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:129:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:33:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:36:11: style: The destructor '~Bed3Interval' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:63:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:36:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:46:37: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:52:23: error: va_list 'ap_copy' was opened but not closed by va_end(). [va_end_missing]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:28:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED12_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp:62:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:27:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED4_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.cpp:24:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp:16:37: warning:inconclusive: Member variable 'Bed12Interval::_thickStartStr' is not assigned a value in 'Bed12Interval::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp:16:37: warning:inconclusive: Member variable 'Bed12Interval::_thickEndStr' is not assigned a value in 'Bed12Interval::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp:16:37: warning:inconclusive: Member variable 'Bed12Interval::_blockCountStr' is not assigned a value in 'Bed12Interval::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: warning: The class 'Bed6Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Derived function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp:142:21: warning: The class 'Bed12Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed6Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Parent function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp:142:21: note: Derived function 'Bed12Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp:142:21: warning: The class 'Bed12Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.cpp:142:21: note: Derived function 'Bed12Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:21:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:21:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:22:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:26:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:22:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:23:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:27:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:24:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:28:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:25:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:29:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:26:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:30:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:26:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:28:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:32:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:28:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:29:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:33:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:29:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:34:11: style: The destructor '~Bed6Interval' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:36:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:34:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:22:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:21:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:22:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:23:15: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:68:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:24:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:22:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:25:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:23:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:26:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:24:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:26:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:27:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:27:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:28:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:26:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:28:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:53:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:28:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:53:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:54:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:29:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:54:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:56:9: style: The function 'getLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:192:17: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:56:9: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:60:11: style: The destructor '~Bed12Interval' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:34:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:60:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.cpp:64:20: warning: The class 'Bed4Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.cpp:64:20: note: Derived function 'Bed4Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:22:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:22:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:23:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:26:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:24:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:27:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:25:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:28:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:26:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:29:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:26:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:27:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:30:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:27:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:29:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:32:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:29:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:30:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:33:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:30:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:35:11: style: The destructor '~Bed4Interval' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:36:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:35:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.h:51:10: style:inconclusive: Technically the member function 'RecordKeyVector::allClear' can be const. [functionConst]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:261:17: warning: The class 'BamRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed6Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Parent function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:261:17: note: Derived function 'BamRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:261:17: warning: The class 'BamRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:261:17: note: Derived function 'BamRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.h:24:5: style: Class 'RecordKeyVector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:34:7: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:24:7: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:34:7: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:36:15: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:68:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:36:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:48:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:48:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:50:15: style: The function 'printUnmapped' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:149:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:50:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:52:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:26:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:52:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:59:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:28:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:59:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:60:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:29:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:60:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:63:9: style: The function 'getLength' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:192:17: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:63:9: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:77:11: style: The destructor '~BamRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:34:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:77:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:284:12: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:26:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED5_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.cpp:25:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.cpp:27:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.cpp:71:20: warning: The class 'Bed5Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.cpp:71:20: note: Derived function 'Bed5Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.cpp:77:20: warning: The class 'Bed6Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.cpp:77:20: note: Derived function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:21:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:21:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:22:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:26:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:22:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:23:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:27:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:24:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:28:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:25:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:29:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:26:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:30:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:26:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:28:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:32:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:28:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:29:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:33:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:29:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:34:11: style: The destructor '~Bed5Interval' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:36:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:34:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:26:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BEDGRAPH_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.cpp:24:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.cpp:64:24: warning: The class 'BedGraphInterval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.cpp:64:24: note: Derived function 'BedGraphInterval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:21:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:21:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:22:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:26:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:22:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:23:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:27:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:24:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:28:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:25:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:29:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:26:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:30:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:26:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:28:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:32:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:28:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:29:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:33:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:29:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:34:11: style: The destructor '~BedGraphInterval' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:36:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:34:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:29:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_PLUS_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.cpp:87:23: warning: The class 'BedPlusInterval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.cpp:87:23: note: Derived function 'BedPlusInterval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:21:11: style: The destructor '~BedPlusInterval' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:36:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:21:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:23:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:24:15: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:68:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:25:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:26:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:26:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:27:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:26:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:27:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:28:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:27:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:28:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:29:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:28:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:29:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:30:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:29:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:31:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:32:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:31:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:32:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:33:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:32:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/EmptyRecord.h:22:3: style: The destructor '~EmptyRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:63:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/EmptyRecord.h:22:3: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/EmptyRecord.h:24:7: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:67:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/EmptyRecord.h:24:7: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/EmptyRecord.h:26:6: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:129:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/EmptyRecord.h:26:6: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:26:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VCF_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:27:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:28:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GFF_PLUS_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:26:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_POS_PLUS_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BlockMgr.cpp:66:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BlockMgr.cpp:88:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Type [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:35:14: warning: The class 'GffRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed6Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Parent function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:35:14: note: Derived function 'GffRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:35:14: warning: The class 'GffRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:35:14: note: Derived function 'GffRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.cpp:63:21: warning: The class 'GffPlusRecord' defines member function with name 'isNumericField' also defined in its parent class 'GffRecord'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:35:14: note: Parent function 'GffRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.cpp:63:21: note: Derived function 'GffPlusRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.cpp:63:21: warning: The class 'GffPlusRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed6Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Parent function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.cpp:63:21: note: Derived function 'GffPlusRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.cpp:63:21: warning: The class 'GffPlusRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.cpp:63:21: note: Derived function 'GffPlusRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:20:11: style: The destructor '~GffRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:34:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:20:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:21:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:21:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:21:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:22:15: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:68:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:22:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:23:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:22:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:24:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:23:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:25:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:24:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:26:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:26:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:27:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:26:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:27:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:31:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:29:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:31:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:34:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:28:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:34:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:36:15: style: The function 'isZeroBased' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:78:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:36:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:21:11: style: The destructor '~GffPlusRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:20:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:21:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:22:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:21:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:22:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:23:15: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:22:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:23:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:24:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:23:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:25:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:24:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:26:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:26:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:27:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:26:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:27:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:28:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:27:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:28:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:30:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:34:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:30:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:31:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:31:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:31:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:36:15: style: The function 'isZeroBased' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:36:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:36:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.cpp:5:12: warning: Member variable 'GffRecord::_numFields' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.cpp:160:17: warning: The class 'GffRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed6Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Parent function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.cpp:160:17: note: Derived function 'GffRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.cpp:160:17: warning: The class 'GffRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.cpp:160:17: note: Derived function 'GffRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.cpp:103:46: style:inconclusive: Function 'printRemainingFields' argument 1 names different: declaration 'outbuf' definition 'outBuf'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:39:36: note: Function 'printRemainingFields' argument 1 names different: declaration 'outbuf' definition 'outBuf'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.cpp:103:46: note: Function 'printRemainingFields' argument 1 names different: declaration 'outbuf' definition 'outBuf'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BlockMgr.cpp:24:2: warning: Class 'BlockMgr' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BlockMgr.cpp:24:2: warning: Class 'BlockMgr' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:31:14: warning: The class 'Bed4Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed4Interval.h:31:14: note: Derived function 'Bed4Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:30:14: warning: The class 'Bed5Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed5Interval.h:30:14: note: Derived function 'Bed5Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:31:14: warning: The class 'BedGraphInterval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedGraphInterval.h:31:14: note: Derived function 'BedGraphInterval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:36:14: warning: The class 'BedPlusInterval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:36:14: note: Derived function 'BedPlusInterval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:55:14: warning: The class 'Bed12Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed6Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Parent function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:55:14: note: Derived function 'Bed12Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:55:14: warning: The class 'Bed12Interval' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed12Interval.h:55:14: note: Derived function 'Bed12Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:61:14: warning: The class 'BamRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed6Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Parent function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:61:14: note: Derived function 'BamRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:61:14: warning: The class 'BamRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.h:61:14: note: Derived function 'BamRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:29:14: warning: The class 'VcfRecord' defines member function with name 'isNumericField' also defined in its parent class 'BedPlusInterval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:36:14: note: Parent function 'BedPlusInterval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:29:14: note: Derived function 'VcfRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:29:14: warning: The class 'VcfRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:29:14: note: Derived function 'VcfRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:35:14: warning: The class 'GffPlusRecord' defines member function with name 'isNumericField' also defined in its parent class 'GffRecord'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffRecord.h:35:14: note: Parent function 'GffRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:35:14: note: Derived function 'GffPlusRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:35:14: warning: The class 'GffPlusRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed6Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed6Interval.h:30:14: note: Parent function 'Bed6Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:35:14: note: Derived function 'GffPlusRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:35:14: warning: The class 'GffPlusRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/GffPlusRecord.h:35:14: note: Derived function 'GffPlusRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BlockMgr.h:25:2: style: Class 'BlockMgr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.h:33:2: style: Class 'RecordMgr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:20:15: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:23:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:20:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:21:15: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:24:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:21:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:22:7: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:25:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:22:7: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:23:7: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:26:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:23:7: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:24:7: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:27:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:24:7: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:25:15: style: The function 'printNull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:28:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:26:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:29:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:26:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:28:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:31:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:28:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:31:15: style: The function 'isZeroBased' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:78:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.h:31:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:21:11: style: The destructor '~NoPosPlusRecord' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:63:11: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:21:11: note: Destructor in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:22:7: style: The function 'initFromFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:67:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:22:7: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:24:15: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:68:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:24:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:25:15: style: The function 'print' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:69:15: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:25:15: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:26:45: style: The function 'getType' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:131:45: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:26:45: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:28:24: style: The function 'getField' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:128:24: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:28:24: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:29:14: style: The function 'getNumFields' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:129:14: note: Virtual function in base class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/NoPosPlusRecord.h:29:14: note: Function in derived class
bedtools2-2.31.1/src/utils/FileRecordTools/Records/PlusFields.cpp:4:13: warning: Member variable 'PlusFields::_numOffsetFields' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BlockMgr.cpp:231:17: style: Unused variable: overlappingStarts [unusedVariable]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BlockMgr.cpp:232:17: style: Unused variable: overlappingEnd [unusedVariable]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:37:2: warning: Member variable 'RecordListNode::_val' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.cpp:16:2: performance: Variable '_list' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:76:24: performance:inconclusive: Technically the member function 'RecordList::end' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.cpp:38:51: style:inconclusive: Technically the member function 'RecordKeyList::end' can be const. [functionConst]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.h:27:25: note: Technically the member function 'RecordKeyList::end' can be const.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.cpp:38:51: note: Technically the member function 'RecordKeyList::end' can be const.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.h:46:10: style:inconclusive: Technically the member function 'RecordKeyList::allClear' can be const. [functionConst]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:38:2: style: Class 'RecordListNode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.h:20:5: style: Class 'RecordKeyList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.cpp:13:55: style: Parameter 'list' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:44:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:168:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:269:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.cpp:46:41: warning: Member variable 'RecordKeyVector::_key' is not assigned a value in 'RecordKeyVector::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.cpp:46:41: warning: Member variable 'RecordKeyVector::_currPos' is not assigned a value in 'RecordKeyVector::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.cpp:46:41: warning:inconclusive: Member variable 'RecordKeyVector::_mustDeleteVec' is not assigned a value in 'RecordKeyVector::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.cpp:32:2: warning: Class 'RecordKeyVector' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.cpp:28:58: style:inconclusive: Function 'RecordKeyVector' argument 2 names different: declaration 'vector' definition 'vec'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.h:25:45: note: Function 'RecordKeyVector' argument 2 names different: declaration 'vector' definition 'vec'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyVector.cpp:28:58: note: Function 'RecordKeyVector' argument 2 names different: declaration 'vector' definition 'vec'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:109:25: warning:inconclusive: Member variable 'RecordList::_dontDelete' is not assigned a value in 'RecordList::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:150:29: performance:inconclusive: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:106:18: note: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:150:29: note: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:173:18: performance:inconclusive: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:112:7: note: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:173:18: note: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:120:43: style: Parameter 'other' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:218:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED6_PLUS_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:80:4: warning: Class 'RecordMgr' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:80:4: warning: Class 'RecordMgr' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:176:23: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:182:25: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:189:25: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:196:25: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:203:29: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:210:25: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:217:28: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:226:27: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:232:25: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:239:25: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:246:22: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:252:27: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:258:29: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:275:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:281:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:287:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:293:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:299:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:305:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:311:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:316:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:321:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:327:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:332:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:337:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordMgr.cpp:342:5: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/StrandQueue.cpp:101:11: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/StrandQueue.cpp:108:29: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::block_starts' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::block_ends' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::_startPosStr' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::_endPosStr' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::_score' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::_zeroLength' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::_isUnmapped' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::_isMateUnmapped' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning:inconclusive: Member variable 'Record::_isValidHit' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:22:23: warning: Member variable 'Record::_frm' is not assigned a value in 'Record::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:23:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RefName [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:43:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:131:39: style:inconclusive: Function 'intersects' argument 1 names different: declaration 'otherRecord' definition 'record'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:167:40: note: Function 'intersects' argument 1 names different: declaration 'otherRecord' definition 'record'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:131:39: note: Function 'intersects' argument 1 names different: declaration 'otherRecord' definition 'record'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:150:48: style:inconclusive: Function 'sameChromIntersects' argument 1 names different: declaration 'otherRecord' definition 'record'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.h:179:49: note: Function 'sameChromIntersects' argument 1 names different: declaration 'otherRecord' definition 'record'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Record.cpp:150:48: note: Function 'sameChromIntersects' argument 1 names different: declaration 'otherRecord' definition 'record'.
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.cpp:121:17: warning: The class 'VcfRecord' defines member function with name 'isNumericField' also defined in its parent class 'BedPlusInterval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/BedPlusInterval.h:36:14: note: Parent function 'BedPlusInterval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.cpp:121:17: note: Derived function 'VcfRecord::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.cpp:121:17: warning: The class 'VcfRecord' defines member function with name 'isNumericField' also defined in its parent class 'Bed3Interval'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/FileRecordTools/Records/Bed3Interval.h:35:14: note: Parent function 'Bed3Interval::isNumericField'
bedtools2-2.31.1/src/utils/FileRecordTools/Records/VcfRecord.cpp:121:17: note: Derived function 'VcfRecord::isNumericField'
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:29:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RefName [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:52:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:137:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:149:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:164:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:21:13: warning: Member variable 'GenomeFile::_genomeLength' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:17:5: performance: Variable '_genomeFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:107:22: style:inconclusive: Technically the member function 'GenomeFile::getGenomeSize' can be const. [functionConst]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:54:14: note: Technically the member function 'GenomeFile::getGenomeSize' can be const.
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:107:22: note: Technically the member function 'GenomeFile::getGenomeSize' can be const.
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:111:28: style:inconclusive: Technically the member function 'GenomeFile::getChromList' can be const. [functionConst]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:55:20: note: Technically the member function 'GenomeFile::getChromList' can be const.
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:111:28: note: Technically the member function 'GenomeFile::getChromList' can be const.
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:115:17: style:inconclusive: Technically the member function 'GenomeFile::getNumberOfChroms' can be const. [functionConst]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:56:9: note: Technically the member function 'GenomeFile::getNumberOfChroms' can be const.
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:115:17: note: Technically the member function 'GenomeFile::getNumberOfChroms' can be const.
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:119:20: style:inconclusive: Technically the member function 'GenomeFile::getGenomeFileName' can be const. [functionConst]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:57:12: note: Technically the member function 'GenomeFile::getGenomeFileName' can be const.
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:119:20: note: Technically the member function 'GenomeFile::getGenomeFileName' can be const.
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:40:5: style: Class 'GenomeFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:43:5: style: Class 'GenomeFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:55:20: performance: Function 'getChromList()' should return member '_chromList' by const reference. [returnByReference]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:57:12: performance: Function 'getGenomeFileName()' should return member '_genomeFile' by const reference. [returnByReference]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:56:17: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:62:24: style: Variable 'c2' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:17:16: warning: Member variable 'NewGenomeFile::_currChromId' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:24:16: warning: Member variable 'NewGenomeFile::_genomeFile' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:24:16: warning: Member variable 'NewGenomeFile::_currChromId' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:20:5: performance: Variable '_genomeFileName' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.h:28:6: style: Class 'NewGenomeFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.h:29:6: style: Class 'NewGenomeFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:17:44: style:inconclusive: Function 'NewGenomeFile' argument 1 names different: declaration 'genomeFileName' definition 'genomeFilename'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.h:28:34: note: Function 'NewGenomeFile' argument 1 names different: declaration 'genomeFileName' definition 'genomeFilename'.
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:17:44: note: Function 'NewGenomeFile' argument 1 names different: declaration 'genomeFileName' definition 'genomeFilename'.
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:24:57: style:inconclusive: Function 'NewGenomeFile' argument 1 names different: declaration 'genome' definition 'refVector'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.h:29:47: note: Function 'NewGenomeFile' argument 1 names different: declaration 'genome' definition 'refVector'.
bedtools2-2.31.1/src/utils/GenomeFile/NewGenomeFile.cpp:24:57: note: Function 'NewGenomeFile' argument 1 names different: declaration 'genome' definition 'refVector'.
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.cpp:107:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.cpp:172:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.cpp:346:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:41:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:52:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:60:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:73:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:87:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:141:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:154:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:167:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:179:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:358:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.h:38:16: style:inconclusive: Technically the member function 'KeyListOps::getColumns' can be const. [functionConst]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.h:39:16: style:inconclusive: Technically the member function 'KeyListOps::getOperations' can be const. [functionConst]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.h:40:16: style:inconclusive: Technically the member function 'KeyListOps::getNullValue' can be const. [functionConst]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.h:41:16: style:inconclusive: Technically the member function 'KeyListOps::getDelimStr' can be const. [functionConst]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.h:22:2: style: Class 'KeyListOpsMethods' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:52:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:56:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:58:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:43:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:66:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:112:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:130:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:199:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REF_DIST [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:217:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORWARD [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:280:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORWARD [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:424:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:449:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALL_DBS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:643:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORWARD [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:667:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.cpp:152:31: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:25:20: warning: Member variable 'KeyListOpsMethods::_nonNumErrFlag' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:25:20: warning: Member variable 'KeyListOpsMethods::_isBam' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:219:58: style:inconclusive: Function 'getDistinctSortNum' argument 1 names different: declaration 'ascending' definition 'asc'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.h:62:43: note: Function 'getDistinctSortNum' argument 1 names different: declaration 'ascending' definition 'asc'.
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:219:58: note: Function 'getDistinctSortNum' argument 1 names different: declaration 'ascending' definition 'asc'.
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:112:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:130:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:199:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:211:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:227:75: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:282:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:288:79: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:305:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/KeyListOps/KeyListOpsMethods.cpp:312:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:371:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:469:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:62:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FILE_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:90:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MERGE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:112:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:165:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:227:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:254:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTERSECT [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:341:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GROUP_BY [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:506:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNKNOWN_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:572:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:581:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:590:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_RECORD_TYPE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:598:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:51:19: style:inconclusive: Technically the member function 'NewChromSweep::getQueryTotalRecordLength' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:52:19: style:inconclusive: Technically the member function 'NewChromSweep::getDatabaseTotalRecordLength' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:54:19: style:inconclusive: Technically the member function 'NewChromSweep::getQueryTotalRecords' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:55:19: style:inconclusive: Technically the member function 'NewChromSweep::getDatabaseTotalRecords' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:327:21: style:inconclusive: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:108:10: note: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:327:21: note: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:431:21: style:inconclusive: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:128:10: note: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:431:21: note: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:34:5: style: Class 'NewChromSweep' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:87:21: style: Condition 'testChromOrderVal' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:83:9: note: Assuming that condition 'testChromOrderVal' is not redundant
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:87:21: note: Condition 'testChromOrderVal' is always true
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:72:35: style:inconclusive: Function 'closeOut' argument 1 names different: declaration 'testChromOrder' definition 'testChromOrderVal'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:48:24: note: Function 'closeOut' argument 1 names different: declaration 'testChromOrder' definition 'testChromOrderVal'.
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:72:35: note: Function 'closeOut' argument 1 names different: declaration 'testChromOrder' definition 'testChromOrderVal'.
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:320:34: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:329:37: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:464:95: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:38:2: warning: Class 'RecordOutputMgr' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/RecordOutputMgr/RecordOutputMgr.cpp:38:2: warning: Class 'RecordOutputMgr' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:22:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:33:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:224:21: style:inconclusive: Technically the member function 'VectorOps::GetCount' can be const. [functionConst]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:69:14: note: Technically the member function 'VectorOps::GetCount' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:224:21: note: Technically the member function 'VectorOps::GetCount' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:236:19: style:inconclusive: Technically the member function 'VectorOps::GetCollapse' can be const. [functionConst]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:73:12: note: Technically the member function 'VectorOps::GetCollapse' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:236:19: note: Technically the member function 'VectorOps::GetCollapse' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:247:19: style:inconclusive: Technically the member function 'VectorOps::GetConcat' can be const. [functionConst]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:75:12: note: Technically the member function 'VectorOps::GetConcat' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:247:19: note: Technically the member function 'VectorOps::GetConcat' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:295:19: style:inconclusive: Technically the member function 'VectorOps::GetFreqDesc' can be const. [functionConst]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:81:12: note: Technically the member function 'VectorOps::GetFreqDesc' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:295:19: note: Technically the member function 'VectorOps::GetFreqDesc' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:331:19: style:inconclusive: Technically the member function 'VectorOps::GetFreqAsc' can be const. [functionConst]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:83:12: note: Technically the member function 'VectorOps::GetFreqAsc' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:331:19: note: Technically the member function 'VectorOps::GetFreqAsc' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:367:19: style:inconclusive: Technically the member function 'VectorOps::GetFirst' can be const. [functionConst]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:85:12: note: Technically the member function 'VectorOps::GetFirst' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:367:19: note: Technically the member function 'VectorOps::GetFirst' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:373:19: style:inconclusive: Technically the member function 'VectorOps::GetLast' can be const. [functionConst]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:87:12: note: Technically the member function 'VectorOps::GetLast' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:373:19: note: Technically the member function 'VectorOps::GetLast' can be const.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:38:5: style: Class 'VectorOps' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:271:43: style:inconclusive: Function 'GetDistinctSortNum' argument 1 names different: declaration 'asc' definition 'ascending'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:79:36: note: Function 'GetDistinctSortNum' argument 1 names different: declaration 'asc' definition 'ascending'.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:271:43: note: Function 'GetDistinctSortNum' argument 1 names different: declaration 'asc' definition 'ascending'.
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:236:38: performance: Function parameter 'delimiter' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:306:23: style: Unused variable: freqPair [unusedVariable]
bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:342:23: style: Unused variable: freqPair [unusedVariable]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:54:16: performance:inconclusive: Technically the member function 'RecDistList::begin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:85:24: style:inconclusive: Technically the member function 'CloseSweep::getDistances' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:723:18: style:inconclusive: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:122:7: note: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:723:18: note: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:634:18: style:inconclusive: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:149:10: note: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:634:18: note: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:731:44: style:inconclusive: Technically the member function 'CloseSweep::purgePointException' can be const. [functionConst]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:154:24: note: Technically the member function 'CloseSweep::purgePointException' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:731:44: note: Technically the member function 'CloseSweep::purgePointException' can be const.
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:23:2: warning: Class 'RecDistList' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:23:2: warning: Class 'RecDistList' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:88:20: warning: The class 'CloseSweep' defines member variable with name '_context' also defined in its parent class 'NewChromSweep'. [duplInheritedMember]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:59:23: note: Parent variable 'NewChromSweep::_context'
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:88:20: note: Derived variable 'CloseSweep::_context'
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:37:2: style: Class 'RecDistList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:82:2: style: Class 'CloseSweep' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:83:3: style: The destructor '~CloseSweep' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:37:14: note: Virtual destructor in base class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:83:3: note: Destructor in derived class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:84:7: style: The function 'init' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:38:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:84:7: note: Function in derived class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:134:7: style: The function 'masterScan' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:95:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:134:7: note: Function in derived class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:135:10: style: The function 'scanCache' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:99:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:135:10: note: Function in derived class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:136:10: style: The function 'chromChange' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:101:18: note: Virtual function in base class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:136:10: note: Function in derived class
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:478:39: style: Local variable 'i' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:461:9: note: Shadowed declaration
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:478:39: note: Shadow variable
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:333:15: style: Variable 'upRecs' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:334:15: style: Variable 'downRecs' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:335:15: style: Variable 'overlaps' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:614:16: style: Variable 'upRecs' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:615:16: style: Variable 'downRecs' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:326:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:636:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:674:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:795:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:865:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:939:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1025:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1092:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1115:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1199:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:120:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:146:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:202:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:247:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:624:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable starts [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedGraphFile/bedGraphFile.h:134:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedGraphFile/bedGraphFile.h:167:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedGraphFile/bedGraphFile.cpp:31:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedGraphFile/bedGraphFile.h:162:24: style:inconclusive: Technically the member function 'BedGraphFile::parseLine' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedGraphFile/bedGraphFile.h:108:5: style: Class 'BedGraphFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:30:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:81:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_INVALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:94:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:141:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId_CHRPOS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:182:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_BLANK [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:286:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:412:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _binFirstShift [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:479:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_INVALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:48:13: warning: Member variable 'ChromSweep::_overlapFraction' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:48:13: warning: Member variable 'ChromSweep::_sameStrand' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:48:13: warning: Member variable 'ChromSweep::_diffStrand' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:48:13: warning: Member variable 'ChromSweep::_reciprocal' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:48:13: warning: Member variable 'ChromSweep::_useMergedIntervals' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:140:18: style:inconclusive: Technically the member function 'ChromSweep::IsValidHit' can be const. [functionConst]
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.h:101:10: note: Technically the member function 'ChromSweep::IsValidHit' can be const.
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:140:18: note: Technically the member function 'ChromSweep::IsValidHit' can be const.
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:52:5: warning: Class 'ChromSweep' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:52:5: warning: Class 'ChromSweep' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/utils/driver/BedtoolsDriver.cpp:126:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/driver/BedtoolsDriver.cpp:164:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:196:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_NOW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:308:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable IGNORE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:6:24: warning: Member variable 'FileRecordTypeChecker::_numBytesInBuffer' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:404:11: style: Condition 'validLinesFound' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:95:52: style:inconclusive: Function 'scanBuffer' argument 1 names different: declaration 'buf' definition 'buffer'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.h:39:30: note: Function 'scanBuffer' argument 1 names different: declaration 'buf' definition 'buffer'.
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:95:52: note: Function 'scanBuffer' argument 1 names different: declaration 'buf' definition 'buffer'.
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:418:59: style: Parameter 'counts' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:367:25: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/fileType/fileType.cpp:28:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/CommonHelp.cpp:10:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/CommonHelp.cpp:51:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/CommonHelp.cpp:56:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/CommonHelp.cpp:92:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/CommonHelp.cpp:104:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/tagBam/tagBamMain.cpp:26:33: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/utils/general/CompressionTools.cpp:36:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_WBITS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/CompressionTools.cpp:36:2: warning: Return value of function inflateInit2() is not used. [ignoredReturnValue]
bedtools2-2.31.1/src/utils/general/CompressionTools.cpp:37:2: warning: Return value of function inflate() is not used. [ignoredReturnValue]
bedtools2-2.31.1/src/utils/general/BTlist.h:215:19: warning:inconclusive: Member variable 'BTlist < int >::_dontDelete' is not assigned a value in 'BTlist < int >::operator='. [operatorEqVarError]
bedtools2-2.31.1/src/utils/general/BTlist.h:41:2: warning: Member variable 'BTlistNode < int >::_val' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/general/BTlist.h:131:23: performance:inconclusive: Technically the member function 'BTlist < int >::end' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/general/FreeList.h:20:2: style: Class 'FreeList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/general/BTlist.h:71:2: style: Class 'BTlist < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/general/BTlist.h:42:2: style: Class 'BTlistNode < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/general/CompressionTools.cpp:31:22: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/general/CompressionTools.cpp:33:23: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/general/BTlist.h:50:10: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/general/CompressionTools.cpp:11:54: style:inconclusive: Function 'inflateGzippedArray' argument 1 names different: declaration 'inbuf' definition 'inList'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/general/CompressionTools.h:16:55: note: Function 'inflateGzippedArray' argument 1 names different: declaration 'inbuf' definition 'inList'.
bedtools2-2.31.1/src/utils/general/CompressionTools.cpp:11:54: note: Function 'inflateGzippedArray' argument 1 names different: declaration 'inbuf' definition 'inList'.
bedtools2-2.31.1/src/utils/general/BTlist.h:226:31: style: Parameter 'other' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:76:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/PushBackStreamBuf.h:19:2: style: Class 'PushBackStreamBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/general/PushBackStreamBuf.cpp:36:53: style:inconclusive: Function 'pushBack' argument 1 names different: declaration 'vec' definition 'newBuf'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/general/PushBackStreamBuf.h:21:35: note: Function 'pushBack' argument 1 names different: declaration 'vec' definition 'newBuf'.
bedtools2-2.31.1/src/utils/general/PushBackStreamBuf.cpp:36:53: note: Function 'pushBack' argument 1 names different: declaration 'vec' definition 'newBuf'.
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:20:12: warning: Member variable 'BedFilePE::bedType' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:20:12: warning: Member variable 'BedFilePE::_bedStream' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:91:17: style:inconclusive: Technically the member function 'BedFilePE::reportBedPETab' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:72:10: note: Technically the member function 'BedFilePE::reportBedPETab' can be const.
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:91:17: note: Technically the member function 'BedFilePE::reportBedPETab' can be const.
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:138:17: style:inconclusive: Technically the member function 'BedFilePE::reportBedPENewLine' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:73:10: note: Technically the member function 'BedFilePE::reportBedPENewLine' can be const.
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:138:17: note: Technically the member function 'BedFilePE::reportBedPENewLine' can be const.
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:504:17: performance:inconclusive: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:75:10: note: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:504:17: note: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:55:5: style: Class 'BedFilePE' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:504:49: style:inconclusive: Function 'splitBedPEIntoBeds' argument 1 names different: declaration 'a' definition 'bedpeEntry'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:75:42: note: Function 'splitBedPEIntoBeds' argument 1 names different: declaration 'a' definition 'bedpeEntry'.
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:504:49: note: Function 'splitBedPEIntoBeds' argument 1 names different: declaration 'a' definition 'bedpeEntry'.
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:408:53: performance: Function parameter 'chrom' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:408:93: performance: Function parameter 'name' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:408:106: performance: Function parameter 'strand' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:20:30: style: Parameter 'bedFile' can be declared as reference to const [constParameterReference]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:28:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currCapacity [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:37:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currCapacity [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:45:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currCapacity [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:57:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _buffer [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:62:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _buffer [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:66:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _buffer [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:71:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _buffer [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:177:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currSize [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:187:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currSize [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:198:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currSize [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:211:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currSize [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:226:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _buffer [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:230:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _buffer [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:236:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _buffer [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:242:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currCapacity [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:260:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currSize [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:267:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currSize [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:303:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currSize [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:315:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _currSize [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:19:13: style:inconclusive: Boolean expression 'hasDigits' is used in bitwise operation. [bitwiseOnBoolean]
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:32:13: style:inconclusive: Boolean expression 'hasDigits' is used in bitwise operation. [bitwiseOnBoolean]
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:49:55: style:inconclusive: Function 'str2chrPos' argument 2 names different: declaration 'len' definition 'ulen'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/general/ParseTools.h:33:43: note: Function 'str2chrPos' argument 2 names different: declaration 'len' definition 'ulen'.
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:49:55: note: Function 'str2chrPos' argument 2 names different: declaration 'len' definition 'ulen'.
bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:24:16: performance:inconclusive: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/general/Tokenizer.h:38:6: note: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:24:16: note: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace).
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:69:10: style: Local variable 'endpos' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:55:14: note: Shadowed declaration
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:69:10: note: Shadow variable
bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:111:19: style:inconclusive: Technically the member function 'Tokenizer::fetchElem' can be const. [functionConst]
bedtools2-2.31.1/src/utils/general/Tokenizer.h:48:9: note: Technically the member function 'Tokenizer::fetchElem' can be const.
bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:111:19: note: Technically the member function 'Tokenizer::fetchElem' can be const.
bedtools2-2.31.1/src/utils/general/ParseTools.cpp:52:8: style: Variable 'ulen' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:19:41: style:inconclusive: Function 'setNumExpectedItems' argument 1 names different: declaration 'val' definition 'newSize'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/general/Tokenizer.h:24:31: note: Function 'setNumExpectedItems' argument 1 names different: declaration 'val' definition 'newSize'.
bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:19:41: note: Function 'setNumExpectedItems' argument 1 names different: declaration 'val' definition 'newSize'.
bedtools2-2.31.1/src/utils/general/QuickString.cpp:57:12: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/general/QuickString.cpp:246:13: style: C-style pointer casting [cstyleCast]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:48:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mode [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:71:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable opened [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:82:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mode [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:108:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:114:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mode [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:130:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:141:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable buf [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:151:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable badbit [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:157:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable badbit [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/gzstream/gzstream.C:142:5: error: Return value of allocation function 'open' is not stored. [leakReturnValNotUsed]
bedtools2-2.31.1/src/utils/htslib/htslib/khash_str2int.h:30:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:51:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:58:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:73:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:127:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:391:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_EXTERNAL [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:464:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_EXTERNAL [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:538:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_BETA [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:622:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_BETA [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:731:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_INT [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:795:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_INT [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:861:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable symbol [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:876:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:909:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable symbol [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:926:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable len [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:966:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_BYTE_ARRAY_BLOCK [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1119:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_HUFF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1156:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_HUFF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1220:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable symbol [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1250:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_HUFFMAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1462:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_BYTE_ARRAY_LEN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1567:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_BYTE_ARRAY_LEN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1679:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_BYTE_ARRAY_STOP [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1769:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_BYTE_ARRAY_STOP [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1939:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable E_HUFFMAN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/hts.h:840:12: style: Return value '!(*((char*)(&one)))' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/htslib/hts.h:839:15: note: Assignment 'one=1', assigned value is 1
bedtools2-2.31.1/src/utils/htslib/htslib/hts.h:840:12: note: Return value '!(*((char*)(&one)))' is always false
bedtools2-2.31.1/src/utils/htslib/bgzip.c:184:24: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:183:36: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/bgzip.c:183:36: note: Assignment 'name=malloc(strlen(argv[optind])+5)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/bgzip.c:184:24: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/bgzip.c:185:24: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:183:36: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/bgzip.c:183:36: note: Assignment 'name=malloc(strlen(argv[optind])+5)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/bgzip.c:185:24: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/bgzip.c:316:17: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:315:30: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/bgzip.c:315:30: note: Assignment 'name=strdup(argv[optind])', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/bgzip.c:316:17: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/bgzip.c:316:29: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:315:30: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/bgzip.c:315:30: note: Assignment 'name=strdup(argv[optind])', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/bgzip.c:316:29: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/bgzip.c:317:30: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/bgzip.c:315:30: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/bgzip.c:315:30: note: Assignment 'name=strdup(argv[optind])', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/bgzip.c:317:30: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/htslib/hfile.h:257:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bufsiz [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:193:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:291:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:318:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:340:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:356:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:677:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRId64 [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1229:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1455:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1887:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1914:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1981:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:2021:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1119:17: style: Condition 'sym>=-1' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1118:19: note: Assignment 'sym=*syms++', assigned value is greater than -1
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1119:17: note: Condition 'sym>=-1' is always true
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:545:9: error: Memory leak: c [memleak]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1258:13: error: Common realloc mistake: 'vals' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1259:13: error: Common realloc mistake: 'freqs' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1283:17: error: Common realloc mistake: 'vals' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1284:17: error: Common realloc mistake: 'freqs' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1300:5: error: Common realloc mistake: 'freqs' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1939:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1939:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1940:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1940:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1941:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1941:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1942:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1942:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1943:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1943:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1944:25: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1944:25: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1945:27: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1945:27: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1962:15: warning:inconclusive: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1938:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1962:15: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1981:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1981:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1982:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1982:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1983:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1983:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1984:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1984:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1985:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1985:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1986:9: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1986:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1987:44: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1987:44: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1988:44: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1988:44: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1995:15: warning: If memory allocation fails, then there is a possible null pointer dereference: t [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1980:31: note: Assignment 't=malloc(sizeof(*t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1987:81: note: Assuming condition is false
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1995:15: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1276:17: style: Local variable 'k' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1243:61: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1276:17: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:337:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:483:92: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_beta_decode_int' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1971:26: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:483:92: note: Parameter 'out_size' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:501:93: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_beta_decode_char' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1973:31: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:501:93: note: Parameter 'out_size' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:585:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:597:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:760:89: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_gamma_decode' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:807:17: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:760:89: note: Parameter 'out_size' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:847:42: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1014:21: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:847:42: note: Parameter 'slice' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:847:61: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1014:21: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:847:61: note: Parameter 'c' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:848:42: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1014:21: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:848:42: note: Parameter 'in' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:848:52: style: Parameter 'out' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'out' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1014:21: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:848:52: note: Parameter 'out' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:848:62: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_null' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1014:21: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:848:62: note: Parameter 'out_size' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:853:63: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_char0' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1950:26: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:853:63: note: Parameter 'out_size' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:867:62: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_char' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1952:31: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:867:62: note: Parameter 'out_size' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:902:62: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_int0' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1954:31: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:902:62: note: Parameter 'out_size' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:915:61: style: Parameter 'out_size' can be declared as pointer to const. However it seems that 'cram_huffman_decode_int' is a callback function, if 'out_size' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1956:31: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:915:61: note: Parameter 'out_size' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1107:43: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_huffman_encode_char0' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1951:25: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1107:43: note: Parameter 'slice' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1107:62: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_huffman_encode_char0' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1951:25: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1107:62: note: Parameter 'c' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1108:37: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_huffman_encode_char0' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1951:25: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1108:37: note: Parameter 'in' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1115:20: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1143:42: style: Parameter 'slice' can be declared as pointer to const. However it seems that 'cram_huffman_encode_int0' is a callback function, if 'slice' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1955:25: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1143:42: note: Parameter 'slice' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1143:61: style: Parameter 'c' can be declared as pointer to const. However it seems that 'cram_huffman_encode_int0' is a callback function, if 'c' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1955:25: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1143:61: note: Parameter 'c' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1144:36: style: Parameter 'in' can be declared as pointer to const. However it seems that 'cram_huffman_encode_int0' is a callback function, if 'in' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1955:25: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1144:36: note: Parameter 'in' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1151:10: style: Variable 'syms' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1591:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_codecs.c:1629:25: style: Variable 'cp_end' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_encode.c:48:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_STR is a macro then please configure it. [unknownMacro]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:139:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:698:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAM_QNAME [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:998:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DS_END [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1039:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DS_QS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1077:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1207:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CMATCH [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1940:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DS_TC [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1990:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CRAM_TL [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2046:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAM_RNEXT [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2237:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CRAM_RL [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2853:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAM_QNAME [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2987:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPRESSION_HEADER [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:3113:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMPRESSION_HEADER [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:3285:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref_id [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:131:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable codec [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:152:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DS_RG [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:170:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DS_END [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:389:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cram [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:337:8: style: Redundant initialization for 'op'. The initialized value is overwritten before it is read. [redundantInitialization]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:328:14: note: op is initialized
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:337:8: note: op is overwritten
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:50:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:53:34: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:59:32: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:67:51: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:76:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:88:55: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:104:38: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:186:61: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:195:47: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:196:46: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:197:48: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:198:42: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:201:64: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_external.c:298:49: style: Parameter 'out_rg' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_index.c:372:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable e [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_index.c:451:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nslice [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_index.c:476:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HTS_IDX_NONE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_index.c:544:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref_id [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_index.c:592:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SAM_POS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_index.c:472:50: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::bedType' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::isBed12' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::isZeroBased' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::_status' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::_lineNum' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::_fileType' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::_bedStream' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::_firstLine' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::_numFields' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:85:10: warning: Member variable 'BedFile::_total_flattened_length' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::bedType' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::isBed12' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::isZeroBased' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::_status' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::_lineNum' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::_fileType' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::_bedStream' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::_firstLine' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::_numFields' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_index.c:473:13: style: Variable 'ret' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:98:10: warning: Member variable 'BedFile::_total_flattened_length' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:158:15: style:inconclusive: Technically the member function 'BedFile::Empty' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:395:10: note: Technically the member function 'BedFile::Empty' can be const.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:158:15: note: Technically the member function 'BedFile::Empty' can be const.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:201:15: style:inconclusive: Technically the member function 'BedFile::PrintHeader' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:404:10: note: Technically the member function 'BedFile::PrintHeader' can be const.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:201:15: note: Technically the member function 'BedFile::PrintHeader' can be const.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:329:24: style:inconclusive: Technically the member function 'BedFile::getTotalLength' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:477:19: note: Technically the member function 'BedFile::getTotalLength' can be const.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:329:24: note: Technically the member function 'BedFile::getTotalLength' can be const.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:333:24: style:inconclusive: Technically the member function 'BedFile::getTotalFlattenedLength' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:481:19: note: Technically the member function 'BedFile::getTotalFlattenedLength' can be const.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:333:24: note: Technically the member function 'BedFile::getTotalFlattenedLength' can be const.
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:663:17: style:inconclusive: Technically the member function 'BedFile::parseBedLine' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:769:17: style:inconclusive: Technically the member function 'BedFile::parseVcfLine' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:841:17: style:inconclusive: Technically the member function 'BedFile::parseGffLine' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:924:17: style:inconclusive: Technically the member function 'BedFile::reportBedTab' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1010:17: style:inconclusive: Technically the member function 'BedFile::reportToFileBedNewLine' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1104:17: style:inconclusive: Technically the member function 'BedFile::reportBedRangeTab' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1187:17: style:inconclusive: Technically the member function 'BedFile::reportBedRangeNewLine' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1265:10: style:inconclusive: Technically the member function 'BedFile::reportNullBedTab' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:1301:10: style:inconclusive: Technically the member function 'BedFile::reportNullBedNewLine' can be const. [functionConst]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:381:5: style: Class 'BedFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:71:22: style: Expression is always true because 'else if' condition is opposite to previous condition at line 70. [multiCondition]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:70:17: note: first condition
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:71:22: note: else if condition is opposite to first condition
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:746:30: style: Condition '_numFields!=this->bedType' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:817:30: style: Condition '_numFields!=this->bedType' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:771:24: note: Assuming that condition '_numFields>=this->bedType' is not redundant
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:817:30: note: Condition '_numFields!=this->bedType' is always true
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:824:50: style: Condition '_numFields!=0' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:809:29: note: Assuming that condition '_numFields==1' is not redundant
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:824:50: note: Condition '_numFields!=0' is always false
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:895:30: style: Condition '_numFields!=this->bedType' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:255:21: style: Condition 'bed.chrom!=_prev_chrom' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:513:49: style:inconclusive: Function 'countSplitHits' argument 1 names different: declaration 'bedBlock' definition 'bedBlocks'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:465:44: note: Function 'countSplitHits' argument 1 names different: declaration 'bedBlock' definition 'bedBlocks'.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:513:49: note: Function 'countSplitHits' argument 1 names different: declaration 'bedBlock' definition 'bedBlocks'.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:647:28: style:inconclusive: Function 'setGff' argument 1 names different: declaration 'isGff' definition 'gff'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:525:23: note: Function 'setGff' argument 1 names different: declaration 'isGff' definition 'gff'.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:647:28: note: Function 'setGff' argument 1 names different: declaration 'isGff' definition 'gff'.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:649:28: style:inconclusive: Function 'setVcf' argument 1 names different: declaration 'isVcf' definition 'vcf'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:526:23: note: Function 'setVcf' argument 1 names different: declaration 'isVcf' definition 'vcf'.
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:649:28: note: Function 'setVcf' argument 1 names different: declaration 'isVcf' definition 'vcf'.
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:714:35: style: Local variable 'i' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:671:20: note: Shadowed declaration
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:714:35: note: Shadow variable
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:338:42: performance: Function parameter 'strand' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:398:30: performance: Function parameter 'chrom' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:398:70: performance: Function parameter 'strand' should be passed by const reference. [passedByValue]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:552:15: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:553:15: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:554:15: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:597:29: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:598:29: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:175:15: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:176:15: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:177:15: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:182:17: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
bedtools2-2.31.1/src/utils/bedFile/bedFile.h:338:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:789:19: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
bedtools2-2.31.1/src/utils/htslib/cram/cram_samtools.c:145:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1498:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:2060:27: style: Expression is always true because 'else if' condition is opposite to previous condition at line 2059. [multiCondition]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:2059:22: note: first condition
bedtools2-2.31.1/src/utils/htslib/bgzf.c:2060:27: note: else if condition is opposite to first condition
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:47:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cram_stats [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:62:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_i2i [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:84:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_i2i [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:138:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_STAT_VAL [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:198:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_i2i [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1539:16: style: Condition 'ret' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1537:19: note: Assignment 'ret=0', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1539:16: note: Condition 'ret' is always false
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1863:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/htslib/hts.h:839:15: note: Assignment 'one=1', assigned value is 1
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1863:18: note: Calling function 'ed_is_big' returns 0
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1863:18: note: Condition 'ed_is_big()' is always false
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1955:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/htslib/hts.h:839:15: note: Assignment 'one=1', assigned value is 1
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1955:18: note: Calling function 'ed_is_big' returns 0
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1955:18: note: Condition 'ed_is_big()' is always false
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:143:13: error: Common realloc mistake: 'vals' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:144:13: error: Common realloc mistake: 'freqs' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:168:17: error: Common realloc mistake: 'vals' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:169:17: error: Common realloc mistake: 'freqs' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:160:13: style: Local variable 'i' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:130:16: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/cram_stats.c:160:13: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/bgzf.c:991:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:346:25: style:inconclusive: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/bgzf.h:121:36: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'.
bedtools2-2.31.1/src/utils/htslib/bgzf.c:346:25: note: Function 'bgzf_hopen' argument 1 names different: declaration 'fp' definition 'hfp'.
bedtools2-2.31.1/src/utils/htslib/bgzf.c:421:25: style:inconclusive: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/bgzf.h:316:29: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'.
bedtools2-2.31.1/src/utils/htslib/bgzf.c:421:25: note: Function 'bgzf_compress' argument 1 names different: declaration 'dst' definition '_dst'.
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1674:40: style:inconclusive: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/bgzf.h:255:44: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'.
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1674:40: note: Function 'bgzf_set_cache_size' argument 2 names different: declaration 'size' definition 'cache_size'.
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1699:46: style:inconclusive: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/bgzf.h:212:50: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'.
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1699:46: note: Function 'bgzf_seek' argument 3 names different: declaration 'whence' definition 'where'.
bedtools2-2.31.1/src/utils/htslib/bgzf.c:931:17: style: Local variable 'ret' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:888:13: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/bgzf.c:931:17: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/bgzf.c:995:18: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1803:24: style: Variable 'buf' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:2085:23: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:2091:39: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/htslib/hfile.h:116:33: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/htslib/hfile.h:136:34: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1199:10: style: Variable 'size' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/bgzf.c:1213:10: style: Variable 'size' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:148:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fp [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:157:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:173:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fp [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:189:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fp [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:208:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MF_READ [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:268:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MF_READ [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:381:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MF_MMAP [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:450:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:515:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MF_WRITE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:613:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MF_WRITE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:189:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:507:13: style: Condition 'len!=size*nmemb' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:498:9: note: len is assigned 'size*nmemb<=mf->size-mf->offset?size*nmemb:mf->size-mf->offset' here.
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:501:9: note: Assuming condition is false
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:507:13: note: Condition 'len!=size*nmemb' is always true
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:98:13: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:458:20: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:481:18: style: Parameter 'mf' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/mFILE.c:514:22: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/pooled_alloc.c:105:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pool [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:763:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:801:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:863:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:874:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:939:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1105:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1442:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAW [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1538:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable refs [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1568:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable refs [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1592:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1626:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1775:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1823:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable refs [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1861:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable refs [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1917:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2048:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2256:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2274:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2585:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2732:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DS_RN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2788:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DS_RN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2882:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3226:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3255:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CORE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3283:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable map [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3397:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_s2i [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3427:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cram_record [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3511:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable content_type [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3740:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3791:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3983:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CRAM_FPAIRED [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4150:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQS_PER_SLICE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4350:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DS_END [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4412:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4627:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:319:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable freq [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:669:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RANS_BYTE_L [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:123:31: style: Condition 'i>0' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:123:20: note: Assuming that condition 'i==0' is not redundant
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:123:31: note: Condition 'i>0' is always true
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:122:22: style: The comparison 'path_sep == ':'' is always true because 'path_sep' and '':'' represent the same value. [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:103:21: note: 'path_sep' is assigned value '':'' here.
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:122:22: note: The comparison 'path_sep == ':'' is always true because 'path_sep' and '':'' represent the same value.
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:96:34: style: Parameter 'searchpath' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:171:28: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:218:44: style: Parameter 'dirname' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:221:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/open_trace_file.c:315:54: style: Parameter 'relative_to' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:82:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable prev_id [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:113:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:292:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:444:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:581:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_s2i [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:644:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZER [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:765:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ORDER_UNKNOWN [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:795:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KS_INITIALIZER [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:868:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sam_hdr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:1014:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sam_hdr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:1077:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_s2i [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:1088:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_s2i [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:1124:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tag [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:1162:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable m_s2i [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:127:21: style: Condition '!rle' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:123:17: note: Assuming that condition 'rle' is not redundant
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:127:21: note: Condition '!rle' is always true
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:460:25: style: Condition '!rle_j' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:456:21: note: Assuming that condition 'rle_j' is not redundant
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:460:25: note: Condition '!rle_j' is always true
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:508:8: style: Redundant initialization for 'l3'. The initialized value is overwritten before it is read. [redundantInitialization]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:505:22: note: l3 is initialized
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:508:8: note: l3 is overwritten
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:679:18: style: Argument '0*isz4' to init list { is always 0. Constant literal calculation disable/hide variable expression 'isz4'. [knownArgumentHiddenVariableExpression]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:72:25: style: Variable 'out_end' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:290:18: style: Variable 'm' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:294:17: style: Variable 'c' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:692:18: style: Variable 'm' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/cram/rANS_static.c:697:17: style: Variable 'c' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1877:16: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1874:13: note: outer condition: ds&CRAM_QS
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1877:16: note: identical inner condition: ds&CRAM_QS
bedtools2-2.31.1/src/utils/htslib/cram/string_alloc.c:100:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable str [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/string_alloc.c:114:16: style: Checking if unsigned expression 'length' is less than zero. [unsignedLessThanZero]
bedtools2-2.31.1/src/utils/htslib/cram/string_alloc.c:146:48: style: Parameter 'instr' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:999:21: style: Local variable 'c' shadows outer argument [shadowArgument]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:993:72: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:999:21: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1594:38: style: Local variable 'r' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1203:26: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1594:38: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1950:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1937:19: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1950:21: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2013:21: style: Local variable 'out_sz' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1985:19: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2013:21: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:677:41: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:993:55: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1044:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1056:21: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1987:20: style: Variable 'TN' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2191:39: style: Parameter 'md5' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2844:47: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:2849:17: style: Variable 'aux_orig' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:3336:21: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_decode.c:1505:34: style: Variable 'dlen' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/errmod.c:88:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:147:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:163:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:172:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:179:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:195:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:209:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:224:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/faidx.c:78:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/faidx.c:337:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/faidx.c:380:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SCNu64 [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/faidx.c:492:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/faidx.c:582:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/faidx.c:777:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/pairToBed/pairToBedMain.cpp:43:10: style: The scope of the variable 'haveFraction' can be reduced. [variableScope]
bedtools2-2.31.1/src/pairToBed/pairToBedMain.cpp:26:36: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/pairToBed/pairToBedMain.cpp:43:29: style: Variable 'haveFraction' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/pairToBed/pairToBedMain.cpp:108:30: style: Variable 'haveFraction' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:3234:9: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:376:13: style: Condition 'val==-1' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:375:19: note: Assignment 'val=(unsigned char)hgetc(fd->fp)', assigned value is greater than -1
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:376:13: note: Condition 'val==-1' is always false
bedtools2-2.31.1/src/utils/htslib/hfile.c:145:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:175:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:216:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:226:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:272:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:305:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:345:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:356:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:366:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:389:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:404:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:425:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:469:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:481:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:521:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:532:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:567:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:582:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:604:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:622:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:639:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:699:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:769:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:794:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:827:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:865:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:911:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile.c:1073:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1515:11: warning: Either the condition '!r' is redundant or there is possible null pointer dereference: r. [nullPointerRedundantCheck]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1518:9: note: Assuming that condition '!r' is not redundant
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1515:11: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4031:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4030:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4031:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4032:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4031:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4032:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4033:55: style: Variable 'fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j]' is reassigned a value before the old one has been used. [redundantAssignment]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4032:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is assigned
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4033:55: note: fd->cram_sub_matrix["ACGTN"[i>>2]&0x1f][j] is overwritten
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2801:25: style: Local variable 'c' shadows outer argument [shadowArgument]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2752:42: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2801:25: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4317:13: style: Local variable 'i' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4259:9: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4317:13: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:123:16: style: Variable 'nbytes' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:131:16: style: Variable 'nbits' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:181:16: style: Variable 'nbytes' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:189:16: style: Variable 'nbits' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1857:22: style: Variable 'tag' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1914:41: style: Parameter 'dir' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:1915:16: style: Variable 'start' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2029:20: style: Variable 's' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2349:15: style: Variable 'cp_to' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2566:28: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2942:41: style: Parameter 'c' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4080:11: style: Variable 'cp' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:4378:23: style: Parameter 'fd' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/errmod.c:59:13: warning: If memory allocation fails, then there is a possible null pointer dereference: logbinom [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:55:39: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:55:24: note: Assignment 'logbinom=(double*)calloc(n_size*n_size,sizeof(double))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:59:13: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/errmod.c:71:5: warning: If memory allocation fails, then there is a possible null pointer dereference: em [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:10: note: Assignment 'em=(struct errmod_t*)calloc(1,sizeof(struct errmod_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:112:14: note: Calling function 'cal_coef', 1st argument 'em' value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:71:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/errmod.c:72:5: warning: If memory allocation fails, then there is a possible null pointer dereference: em [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:10: note: Assignment 'em=(struct errmod_t*)calloc(1,sizeof(struct errmod_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:112:14: note: Calling function 'cal_coef', 1st argument 'em' value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:72:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/errmod.c:74:9: warning: If memory allocation fails, then there is a possible null pointer dereference: em [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:10: note: Assignment 'em=(struct errmod_t*)calloc(1,sizeof(struct errmod_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:112:14: note: Calling function 'cal_coef', 1st argument 'em' value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:74:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/errmod.c:77:5: warning: If memory allocation fails, then there is a possible null pointer dereference: em [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:10: note: Assignment 'em=(struct errmod_t*)calloc(1,sizeof(struct errmod_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:112:14: note: Calling function 'cal_coef', 1st argument 'em' value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:77:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/errmod.c:86:28: warning: If memory allocation fails, then there is a possible null pointer dereference: em [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:10: note: Assignment 'em=(struct errmod_t*)calloc(1,sizeof(struct errmod_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:112:14: note: Calling function 'cal_coef', 1st argument 'em' value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:86:28: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/errmod.c:97:5: warning: If memory allocation fails, then there is a possible null pointer dereference: em [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:10: note: Assignment 'em=(struct errmod_t*)calloc(1,sizeof(struct errmod_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:112:14: note: Calling function 'cal_coef', 1st argument 'em' value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:97:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/errmod.c:111:5: warning: If memory allocation fails, then there is a possible null pointer dereference: em [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:110:10: note: Assignment 'em=(struct errmod_t*)calloc(1,sizeof(struct errmod_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:111:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/errmod.c:86:37: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/errmod.c:77:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/errmod.c:77:16: note: Assignment 'em->beta=(double*)calloc(256*256*64,sizeof(double))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/errmod.c:86:37: note: Null pointer addition
bedtools2-2.31.1/src/utils/htslib/errmod.c:33:1: style: Parameter 'array' can be declared as const array [constParameter]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:427:39: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:1208:61: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:1221:42: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:477:15: style: Local variable 'k' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:442:48: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:477:15: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:517:15: style: Local variable 'k' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:442:48: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:517:15: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:54:23: style: Variable 't1' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:54:28: style: Variable 't2' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:571:48: style: Parameter 'type' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:572:34: style: Parameter 'ID_key' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:573:24: style: Variable 't2' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:643:19: style: Variable 'ty' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:679:45: style: Parameter 'type' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:680:37: style: Parameter 'key' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:757:49: style: Parameter 'hdr' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:768:23: style: Variable 'ty' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:801:23: style: Variable 'ty' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:816:23: style: Variable 't1' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:816:28: style: Variable 't2' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/cram/sam_header.c:427:46: error: va_list 'args' was opened but not closed by va_end(). [va_end_missing]
bedtools2-2.31.1/src/utils/htslib/cram/cram_io.c:2567:25: style: Variable 'e' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/hfile_gcs.c:73:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_net.c:91:40: style: Condition 'net_init()<0' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/hfile_net.c:91:37: note: Calling function 'net_init' returns 0
bedtools2-2.31.1/src/utils/htslib/hfile_net.c:91:40: note: Condition 'net_init()<0' is always false
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:123:39: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:128:40: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/hfile_gcs.c:91:66: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
bedtools2-2.31.1/src/utils/htslib/hfile_s3.c:83:0: error: #error No HMAC() routine found by configure [preprocessorErrorDirective]
bedtools2-2.31.1/src/utils/htslib/hfile_s3.c:83:2: error: #error No HMAC() routine found by configure [preprocessorErrorDirective]
bedtools2-2.31.1/src/utils/htslib/cram/cram_structs.h:63:1: error: There is an unknown macro here somewhere. Configuration is required. If KHASH_MAP_INIT_INT is a macro then please configure it. [unknownMacro]
bedtools2-2.31.1/src/utils/htslib/hfile.c:567:17: style: Condition 'ret<0' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/hfile.c:556:15: note: Assignment 'ret=0', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/hfile.c:567:17: note: Condition 'ret<0' is always false
bedtools2-2.31.1/src/utils/htslib/hfile.c:568:18: style: Condition 'ret<0' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/hfile.c:556:15: note: Assignment 'ret=0', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/hfile.c:568:18: note: Condition 'ret<0' is always false
bedtools2-2.31.1/src/utils/htslib/hfile.c:679:2: warning: Either the condition 'ret' is redundant or there is possible null pointer dereference: ret. [nullPointerRedundantCheck]
bedtools2-2.31.1/src/utils/htslib/hfile.c:676:5: note: Assuming that condition 'ret' is not redundant
bedtools2-2.31.1/src/utils/htslib/hfile.c:679:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/hfile.c:1104:26: style:inconclusive: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/hfile.h:74:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'.
bedtools2-2.31.1/src/utils/htslib/hfile.c:1104:26: note: Function 'hopen' argument 1 names different: declaration 'filename' definition 'fname'.
bedtools2-2.31.1/src/utils/htslib/hfile.c:1129:27: style:inconclusive: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/hfile.h:98:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'.
bedtools2-2.31.1/src/utils/htslib/hfile.c:1129:27: note: Function 'hisremote' argument 1 names different: declaration 'filename' definition 'fname'.
bedtools2-2.31.1/src/utils/htslib/hfile.c:151:50: style: Parameter 'fp' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/hfile.c:221:11: style: Variable 'found' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/hfile.c:550:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/hfile.c:554:28: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'fd_flush' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/hfile.c:589:33: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/hfile.c:554:28: note: Parameter 'fpv' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/hfile.c:574:15: style: Variable 'fp' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/hfile.c:825:30: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'mem_seek' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/hfile.c:838:17: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/hfile.c:825:30: note: Parameter 'fpv' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/hfile.c:831:29: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'mem_close' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/hfile.c:838:33: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/hfile.c:831:29: note: Parameter 'fpv' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/hfile.c:909:35: style: Parameter 'file' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:120:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ENOSYS [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:149:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINVAL [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:227:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EBADF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:267:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLSHE_OK [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:300:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:314:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:355:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable next [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:498:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:553:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:686:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLM_OK [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:722:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_WRITEFUNC_PAUSE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:763:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:802:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_READFUNC_PAUSE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:821:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:846:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:926:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLOPT_HTTPHEADER [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1049:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURLPAUSE_CONT [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1098:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1268:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1351:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_GLOBAL_ALL [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:101:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AF_UNSPEC [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:450:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:477:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:544:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EINTR [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:573:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/vcf.h:754:112: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htslib/vcf.h:755:117: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htsfile.c:48:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htsfile.c:76:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htsfile.c:120:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htsfile.c:159:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/htsfile.c:213:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/kstring.c:56:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/kstring.c:258:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:313:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:313:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:314:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:314:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:317:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:317:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:318:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:318:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:320:10: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:320:10: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:321:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:321:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:322:10: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:322:10: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:323:5: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:323:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:324:13: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:324:13: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:325:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:312:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:325:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:389:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:388:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:388:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:389:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:390:10: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:388:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:388:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:390:10: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:391:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:388:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:388:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:391:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:392:11: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:388:24: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:388:7: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:392:11: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:506:3: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:505:25: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:505:8: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:506:3: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:507:3: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:505:25: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:505:8: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:507:3: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:508:3: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:505:25: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:505:8: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:508:3: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:520:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:519:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:519:17: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:520:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:521:2: warning: If memory allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:519:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:519:17: note: Assignment 'fp=(struct knetFile*)calloc(1,sizeof(struct knetFile))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:521:2: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/knetfile.c:423:19: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:420:21: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/knetfile.c:420:8: note: Assignment 'buf=(char*)calloc(0x10000,1)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/knetfile.c:423:19: note: Null pointer addition
bedtools2-2.31.1/src/utils/htslib/knetfile.c:442:10: style: Local variable 'l' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/knetfile.c:416:11: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/knetfile.c:442:10: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/faidx.c:213:31: style: Condition 'c!='\n'' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/faidx.c:211:27: note: Assuming that condition 'c=='+'' is not redundant
bedtools2-2.31.1/src/utils/htslib/faidx.c:213:31: note: Condition 'c!='\n'' is always true
bedtools2-2.31.1/src/utils/htslib/faidx.c:255:27: style: Condition 'c!='\n'' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/faidx.c:253:23: note: Assuming that condition 'c=='+'' is not redundant
bedtools2-2.31.1/src/utils/htslib/faidx.c:255:27: note: Condition 'c!='\n'' is always true
bedtools2-2.31.1/src/utils/htslib/htslib/khash.h:397:24: warning: If memory allocation fails, then there is a possible null pointer dereference: s [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/faidx.c:72:28: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/faidx.c:72:28: note: Assignment 'name_key=strdup(name)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/faidx.c:74:17: note: Calling function 'kh_put_s', 2nd argument 'name_key' value is 0
bedtools2-2.31.1/src/utils/htslib/faidx.c:51:1: note: Calling function '__ac_X31_hash_string', 1st argument 'key' value is 0
bedtools2-2.31.1/src/utils/htslib/htslib/khash.h:397:24: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/faidx.c:113:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/faidx.c:112:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/faidx.c:112:11: note: Assignment 'idx=(struct faidx_t*)calloc(1,sizeof(struct faidx_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/faidx.c:113:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/faidx.c:114:5: warning: If memory allocation fails, then there is a possible null pointer dereference: idx [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/faidx.c:112:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/faidx.c:112:11: note: Assignment 'idx=(struct faidx_t*)calloc(1,sizeof(struct faidx_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/faidx.c:114:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/faidx.c:783:17: style: Variable 'beg' is reassigned a value before the old one has been used. [redundantAssignment]
bedtools2-2.31.1/src/utils/htslib/faidx.c:734:9: note: beg is assigned
bedtools2-2.31.1/src/utils/htslib/faidx.c:783:17: note: beg is overwritten
bedtools2-2.31.1/src/utils/htslib/faidx.c:789:13: style: Variable 'end' is reassigned a value before the old one has been used. [redundantAssignment]
bedtools2-2.31.1/src/utils/htslib/faidx.c:734:15: note: end is assigned
bedtools2-2.31.1/src/utils/htslib/faidx.c:789:13: note: end is overwritten
bedtools2-2.31.1/src/utils/htslib/faidx.c:747:14: style: Variable 'name_end' is reassigned a value before the old one has been used. [redundantAssignment]
bedtools2-2.31.1/src/utils/htslib/faidx.c:736:14: note: name_end is assigned
bedtools2-2.31.1/src/utils/htslib/faidx.c:747:14: note: name_end is overwritten
bedtools2-2.31.1/src/utils/htslib/faidx.c:162:21: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
bedtools2-2.31.1/src/utils/htslib/faidx.c:813:49: style:inconclusive: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/faidx.h:167:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'.
bedtools2-2.31.1/src/utils/htslib/faidx.c:813:49: note: Function 'fai_fetch' argument 2 names different: declaration 'reg' definition 'str'.
bedtools2-2.31.1/src/utils/htslib/faidx.c:827:53: style:inconclusive: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/faidx.h:178:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'.
bedtools2-2.31.1/src/utils/htslib/faidx.c:827:53: note: Function 'fai_fetchqual' argument 2 names different: declaration 'reg' definition 'str'.
bedtools2-2.31.1/src/utils/htslib/htslib/vcf.h:755:73: style: Parameter 'rec' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/htslib/vcf.h:918:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/htslib/vcf.h:919:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/htslib/vcf.h:920:28: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/multipart.c:115:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/multipart.c:121:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/multipart.c:165:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/multipart.c:258:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/plugin.c:59:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/plugin.c:77:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUGIN_EXT [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/plugin.c:165:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/plugin.c:182:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/multipart.c:88:54: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
bedtools2-2.31.1/src/utils/htslib/multipart.c:89:68: portability: Passing NULL after the last typed argument to a variadic function leads to undefined behaviour. [varFuncNullUB]
bedtools2-2.31.1/src/utils/htslib/multipart.c:113:39: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'multipart_write' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/multipart.c:139:21: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/multipart.c:113:39: note: Parameter 'fpv' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/multipart.c:119:36: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'multipart_seek' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/multipart.c:139:38: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/multipart.c:119:36: note: Parameter 'fpv' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/kstring.c:293:3: warning: If memory allocation fails, then there is a possible null pointer dereference: suff [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/kstring.c:290:21: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/kstring.c:290:9: note: Assignment 'suff=(int*)calloc(m,sizeof(int))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/kstring.c:293:3: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/kstring.c:296:17: warning: If memory allocation fails, then there is a possible null pointer dereference: suff [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/kstring.c:290:21: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/kstring.c:290:9: note: Assignment 'suff=(int*)calloc(m,sizeof(int))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/kstring.c:296:17: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/kstring.c:285:27: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/kstring.c:284:21: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/kstring.c:284:9: note: Assignment 'prep=(int*)calloc(m+256,sizeof(int))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/kstring.c:285:27: note: Null pointer addition
bedtools2-2.31.1/src/utils/htslib/kstring.c:177:44: style:inconclusive: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/kstring.h:96:45: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'.
bedtools2-2.31.1/src/utils/htslib/kstring.c:177:44: note: Function 'kstrtok' argument 2 names different: declaration 'sep' definition 'sep_in'.
bedtools2-2.31.1/src/utils/htslib/kstring.c:323:31: style: Variable 'bmBc' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/plugin.c:107:24: style: Variable 'e' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/md5.c:270:35: style:inconclusive: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/hts.h:802:39: note: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'.
bedtools2-2.31.1/src/utils/htslib/md5.c:270:35: note: Function 'hts_md5_final' argument 1 names different: declaration 'digest' definition 'result'.
bedtools2-2.31.1/src/utils/htslib/probaln.c:83:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/realn.c:193:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/tbx.c:323:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/tabix.c:56:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/tabix.c:302:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/tabix.c:340:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/tabix.c:402:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:403:15: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:546:15: style: Variable 'header' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:717:35: style: Parameter 'ptr' can be declared as pointer to const. However it seems that 'recv_callback' is a callback function, if 'ptr' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1135:66: note: You might need to cast the function pointer here
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:717:35: note: Parameter 'ptr' can be declared as pointer to const
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:924:28: style: Variable 'list' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1080:64: style: Parameter 'headers' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1083:24: style: Variable 'list' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1152:15: style: Variable 'env_curl_ca_bundle' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1258:22: style: Variable 'args2' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/textutils.c:166:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/textutils.c:317:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/probaln.c:256:77: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
bedtools2-2.31.1/src/utils/htslib/probaln.c:146:36: style: Variable 'fi1' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/probaln.c:151:16: style: Variable 'E' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/probaln.c:207:36: style: Variable 'bi1' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/probaln.c:211:16: style: Variable 'E' can be declared as const array [constVariable]
bedtools2-2.31.1/src/utils/htslib/probaln.c:247:27: style: Variable 'fi' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/probaln.c:247:46: style: Variable 'bi' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/probaln.c:259:25: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/textutils.c:182:23: style: Variable 'lim' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/textutils.c:198:40: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/textutils.c:222:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/textutils.c:230:42: style: Parameter 'token' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/realn.c:56:51: style: Condition 'qual[z]>=13' is always true [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/realn.c:54:53: note: Assuming that condition 'qual[z]>=13' is not redundant
bedtools2-2.31.1/src/utils/htslib/realn.c:56:51: note: Condition 'qual[z]>=13' is always true
bedtools2-2.31.1/src/utils/htslib/realn.c:40:14: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/realn.c:41:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/realn.c:42:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/realn.c:107:15: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/realn.c:108:18: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/realn.c:182:18: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/realn.c:46:27: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/realn.c:71:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/realn.c:75:20: style: Variable 'clip_l' is assigned a value that is never used. [unreadVariable]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:679:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PTHREAD_MUTEX_RECURSIVE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:742:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/tbx.c:198:18: style: Condition 'ed_is_big()' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/htslib/hts.h:839:15: note: Assignment 'one=1', assigned value is 1
bedtools2-2.31.1/src/utils/htslib/tbx.c:198:18: note: Calling function 'ed_is_big' returns 0
bedtools2-2.31.1/src/utils/htslib/tbx.c:198:18: note: Condition 'ed_is_big()' is always false
bedtools2-2.31.1/src/utils/htslib/tbx.c:201:12: warning: If memory allocation fails, then there is a possible null pointer dereference: meta [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tbx.c:197:28: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tbx.c:197:12: note: Assignment 'meta=(uint8_t*)malloc(l_nm+28)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tbx.c:201:12: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tbx.c:222:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tbx [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tbx.c:221:25: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tbx.c:221:11: note: Assignment 'tbx=(struct tbx_t*)calloc(1,sizeof(struct tbx_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tbx.c:222:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tbx.c:227:23: warning: If memory allocation fails, then there is a possible null pointer dereference: tbx [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tbx.c:221:25: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tbx.c:221:11: note: Assignment 'tbx=(struct tbx_t*)calloc(1,sizeof(struct tbx_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tbx.c:227:23: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tbx.c:227:58: warning: If memory allocation fails, then there is a possible null pointer dereference: tbx [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tbx.c:221:25: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tbx.c:221:11: note: Assignment 'tbx=(struct tbx_t*)calloc(1,sizeof(struct tbx_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tbx.c:227:58: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tbx.c:299:5: warning: If memory allocation fails, then there is a possible null pointer dereference: tbx [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tbx.c:298:25: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tbx.c:298:11: note: Assignment 'tbx=(struct tbx_t*)calloc(1,sizeof(struct tbx_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tbx.c:299:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tbx.c:300:11: warning: If memory allocation fails, then there is a possible null pointer dereference: tbx [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tbx.c:298:25: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tbx.c:298:11: note: Assignment 'tbx=(struct tbx_t*)calloc(1,sizeof(struct tbx_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tbx.c:300:11: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tbx.c:204:21: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tbx.c:197:28: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tbx.c:197:12: note: Assignment 'meta=(uint8_t*)malloc(l_nm+28)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tbx.c:204:21: note: Null pointer addition
bedtools2-2.31.1/src/utils/htslib/tbx.c:203:13: style: Local variable 'x' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/tbx.c:183:14: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/tbx.c:203:13: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/tbx.c:296:11: style: Variable 'nm' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:79:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:101:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:167:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __func__ [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:110:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:110:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:111:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:111:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:111:30: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:111:30: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:112:9: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:112:9: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:113:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:113:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:113:29: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:113:29: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:114:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:114:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:115:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:115:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:115:33: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:115:33: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:116:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:116:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:117:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:117:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:55:45: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:61:11: style: Variable 't' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:182:39: style: Parameter 'sw' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/tabFile/tabFile.cpp:30:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cin [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/tabFile/tabFile.cpp:20:10: warning: Member variable 'TabFile::_tabStream' is not initialized in the constructor. [uninitMemberVar]
bedtools2-2.31.1/src/utils/tabFile/tabFile.h:63:26: performance:inconclusive: Technically the member function 'TabFile::parseTabLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
bedtools2-2.31.1/src/utils/tabFile/tabFile.h:42:5: style: Class 'TabFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
bedtools2-2.31.1/src/utils/tabFile/tabFile.cpp:59:51: style:inconclusive: Function 'GetNextTabLine' argument 1 names different: declaration 'tab' definition 'tabFields'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/tabFile/tabFile.h:54:47: note: Function 'GetNextTabLine' argument 1 names different: declaration 'tab' definition 'tabFields'.
bedtools2-2.31.1/src/utils/tabFile/tabFile.cpp:59:51: note: Function 'GetNextTabLine' argument 1 names different: declaration 'tab' definition 'tabFields'.
bedtools2-2.31.1/src/windowBed/windowBed.cpp:143:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowBed/windowBed.cpp:162:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:896:36: style: Condition 'hts_tpool_process_flush(q)!=0' is always false [knownConditionTrueFalse]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:896:32: note: Calling function 'hts_tpool_process_flush' returns 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:896:36: note: Condition 'hts_tpool_process_flush(q)!=0' is always false
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:351:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:351:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:352:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:352:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:353:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:353:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:354:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:354:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:355:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:355:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:356:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:356:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:357:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:357:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:358:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:358:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:359:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:359:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:360:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:360:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:361:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:361:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:362:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:362:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:363:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:363:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:364:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:364:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:365:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:365:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:367:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:367:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:368:5: warning: If memory allocation fails, then there is a possible null pointer dereference: q [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:344:34: note: Assignment 'q=malloc(sizeof(*q))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:368:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:667:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:667:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:668:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:668:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:669:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:669:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:670:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:670:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:671:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:671:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:672:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:672:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:673:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:673:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:674:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:674:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:675:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:675:5: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:683:11: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:666:26: note: Assignment 'p=malloc(sizeof(*p))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:683:11: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:329:47: style: Parameter 'r' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:437:43: style: Variable 'first' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:709:31: style: Parameter 'p' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/thread_pool.c:918:48: style: Parameter 'q' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:67:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BED_VALID [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:75:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FIXED_WINDOW_SIZE [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:95:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:109:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:67:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:200:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:283:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable info [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:103:19: style:inconclusive: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const. [functionConst]
bedtools2-2.31.1/src/windowMaker/windowMaker.h:60:10: note: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const.
bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:103:19: note: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const.
bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:81:23: style:inconclusive: Technically the member function 'WindowMaker::CalculateWindows' can be const. [functionConst]
bedtools2-2.31.1/src/windowMaker/windowMaker.h:61:14: note: Technically the member function 'WindowMaker::CalculateWindows' can be const.
bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:81:23: note: Technically the member function 'WindowMaker::CalculateWindows' can be const.
bedtools2-2.31.1/src/windowBed/windowMain.cpp:147:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowBed/windowMain.cpp:209:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowMaker/windowMakerMain.cpp:111:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowMaker/windowMakerMain.cpp:173:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
bedtools2-2.31.1/src/windowBed/windowBed.cpp:24:5: performance: Variable '_bedAFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/windowBed/windowBed.cpp:25:5: performance: Variable '_bedBFile' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
bedtools2-2.31.1/src/windowBed/windowBed.cpp:235:17: style:inconclusive: Technically the member function 'BedWindow::AddWindow' can be const. [functionConst]
bedtools2-2.31.1/src/windowBed/windowBed.h:68:10: note: Technically the member function 'BedWindow::AddWindow' can be const.
bedtools2-2.31.1/src/windowBed/windowBed.cpp:235:17: note: Technically the member function 'BedWindow::AddWindow' can be const.
bedtools2-2.31.1/src/windowBed/windowBed.cpp:41:5: warning: Class 'BedWindow' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
bedtools2-2.31.1/src/windowBed/windowBed.cpp:41:5: warning: Class 'BedWindow' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
bedtools2-2.31.1/src/windowBed/windowBed.cpp:88:13: style: The scope of the variable 'overlapBases' can be reduced. [variableScope]
bedtools2-2.31.1/src/windowBed/windowBed.cpp:89:13: style: The scope of the variable 'aLength' can be reduced. [variableScope]
bedtools2-2.31.1/src/utils/htslib/tabix.c:119:17: warning: If memory allocation fails, then there is a possible null pointer dereference: regs [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tabix.c:107:31: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tabix.c:107:16: note: Assignment 'regs=(char**)malloc(sizeof(char*)*(*nregs))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tabix.c:119:17: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tabix.c:134:13: warning: If memory allocation fails, then there is a possible null pointer dereference: regs [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tabix.c:133:35: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tabix.c:133:20: note: Assignment 'regs=(char**)malloc(sizeof(char*))', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tabix.c:134:13: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tabix.c:307:30: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tabix.c:304:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tabix.c:304:27: note: Assignment 'buf=malloc(page_size)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tabix.c:307:30: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tabix.c:309:39: warning: If memory allocation fails, then there is a possible null pointer dereference: buf [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tabix.c:304:27: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tabix.c:304:27: note: Assignment 'buf=malloc(page_size)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tabix.c:309:39: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tabix.c:506:19: warning: If memory allocation fails, then there is a possible null pointer dereference: idx_fname [nullPointerOutOfMemory]
bedtools2-2.31.1/src/utils/htslib/tabix.c:505:29: note: Assuming allocation function fails
bedtools2-2.31.1/src/utils/htslib/tabix.c:505:29: note: Assignment 'idx_fname=calloc(strlen(fname)+5,1)', assigned value is 0
bedtools2-2.31.1/src/utils/htslib/tabix.c:506:19: note: Null pointer dereference
bedtools2-2.31.1/src/utils/htslib/tabix.c:264:81: style: Parameter 'conf' can be declared as pointer to const [constParameterPointer]
bedtools2-2.31.1/src/utils/htslib/tabix.c:271:15: style: Variable 'buffer' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/tabix.c:371:11: style: Variable 'reheader' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/tabix.c:500:11: style: Variable 'suffix' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:393:36: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:443:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:477:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:694:36: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:748:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:802:35: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:120:55: style:inconclusive: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/vcfutils.h:112:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'.
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:120:55: note: Function 'bcf_gt_type' argument 3 names different: declaration 'ial' definition '_ial'.
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:120:66: style:inconclusive: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/vcfutils.h:112:65: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'.
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:120:66: note: Function 'bcf_gt_type' argument 4 names different: declaration 'jal' definition '_jal'.
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:225:68: style:inconclusive: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'. [funcArgNamesDifferent]
bedtools2-2.31.1/src/utils/htslib/htslib/vcfutils.h:58:68: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'.
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:225:68: note: Function 'bcf_remove_alleles' argument 3 names different: declaration 'mask' definition 'rm_mask'.
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:41:13: style: Local variable 'i' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:32:9: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:41:13: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:83:13: style: Local variable 'i' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:32:9: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:83:13: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:557:17: style: Local variable 'size' shadows outer variable [shadowVariable]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:541:13: note: Shadowed declaration
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:557:17: note: Shadow variable
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:64:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:65:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:66:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:109:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:110:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:111:32: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:152:28: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:153:28: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:154:28: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:200:28: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:201:28: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:202:28: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:390:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:391:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:392:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:393:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:442:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:443:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:476:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:477:35: style: Variable 'ptr' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:602:56: style: Variable 'se' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:691:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:692:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:693:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:694:36: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:747:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:748:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:801:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/utils/htslib/vcfutils.c:802:35: style: Variable 'ptr_src' can be declared as pointer to const [constVariablePointer]
bedtools2-2.31.1/src/windowMaker/windowMakerMain.cpp:150:14: style: Checking if unsigned expression 'step' is less than zero. [unsignedLessThanZero]
bedtools2-2.31.1/src/windowMaker/windowMakerMain.cpp:27:38: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/windowBed/windowMain.cpp:27:33: style: Parameter 'argv' can be declared as const array [constParameter]
bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageMain.cpp:42:10: style: The scope of the variable 'startSites' can be reduced. [variableScope]
diff:
head bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:293:12: style: Variable 'header' is assigned a value that is never used. [unreadVariable]
head bedtools2-2.31.1/src/bamToBed/bamToBed.cpp:329:12: style: Variable 'header' is assigned a value that is never used. [unreadVariable]
head bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:175:17: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/bamToFastq/bamToFastq.cpp:207:17: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/expand/expand.cpp:50:12: style: Variable 'groupColumnsString' is assigned a value that is never used. [unreadVariable]
head bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:68:25: style:inconclusive: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const. [functionConst]
     bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.h:109:10: note: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const.
     bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:68:25: note: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const.
2.17.0 bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.h:109:10: style:inconclusive: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const. [functionConst]
     bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.cpp:68:25: note: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const.
     bedtools2-2.31.1/src/genomeCoverageBed/genomeCoverageBed.h:109:10: note: Technically the member function 'BedGenomeCoverage::PrintTrackDefinitionLine' can be const.
head bedtools2-2.31.1/src/linksBed/linksBed.cpp:36:16: style:inconclusive: Technically the member function 'BedLinks::WriteURL' can be const. [functionConst]
     bedtools2-2.31.1/src/linksBed/linksBed.h:42:10: note: Technically the member function 'BedLinks::WriteURL' can be const.
     bedtools2-2.31.1/src/linksBed/linksBed.cpp:36:16: note: Technically the member function 'BedLinks::WriteURL' can be const.
2.17.0 bedtools2-2.31.1/src/linksBed/linksBed.h:42:10: style:inconclusive: Technically the member function 'BedLinks::WriteURL' can be const. [functionConst]
     bedtools2-2.31.1/src/linksBed/linksBed.cpp:36:16: note: Technically the member function 'BedLinks::WriteURL' can be const.
     bedtools2-2.31.1/src/linksBed/linksBed.h:42:10: note: Technically the member function 'BedLinks::WriteURL' can be const.
head bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:149:24: performance:inconclusive: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.h:55:10: note: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:149:24: note: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace).
2.17.0 bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.h:55:10: performance:inconclusive: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.cpp:149:24: note: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/maskFastaFromBed/maskFastaFromBed.h:55:10: note: Technically the member function 'MaskFastaFromBed::PrettyPrintChrom' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:228:19: performance:inconclusive: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:71:10: note: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:228:19: note: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:52:19: style:inconclusive: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const. [functionConst]
     bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:68:10: note: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const.
     bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:52:19: note: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const.
2.17.0 bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:68:10: style:inconclusive: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const. [functionConst]
     bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:52:19: note: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const.
     bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:68:10: note: Technically the member function 'MultiCovBam::FindBlockedOverlaps' can be const.
2.17.0 bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:71:10: performance:inconclusive: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/multiBamCov/multiBamCov.cpp:228:19: note: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/multiBamCov/multiBamCov.h:71:10: note: Technically the member function 'MultiCovBam::ReportCounts' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/nucBed/nucBed.cpp:68:14: style:inconclusive: Technically the member function 'NucBed::PrintHeader' can be const. [functionConst]
     bedtools2-2.31.1/src/nucBed/nucBed.h:53:10: note: Technically the member function 'NucBed::PrintHeader' can be const.
     bedtools2-2.31.1/src/nucBed/nucBed.cpp:68:14: note: Technically the member function 'NucBed::PrintHeader' can be const.
2.17.0 bedtools2-2.31.1/src/nucBed/nucBed.h:53:10: style:inconclusive: Technically the member function 'NucBed::PrintHeader' can be const. [functionConst]
     bedtools2-2.31.1/src/nucBed/nucBed.cpp:68:14: note: Technically the member function 'NucBed::PrintHeader' can be const.
     bedtools2-2.31.1/src/nucBed/nucBed.h:53:10: note: Technically the member function 'NucBed::PrintHeader' can be const.
head bedtools2-2.31.1/src/randomBed/randomBedMain.cpp:33:12: style: Variable 'bedFile' is assigned a value that is never used. [unreadVariable]
head bedtools2-2.31.1/src/regressTest/RegressTest.cpp:149:19: performance:inconclusive: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/regressTest/RegressTest.h:77:7: note: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/regressTest/RegressTest.cpp:149:19: note: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/regressTest/RegressTest.cpp:573:21: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     bedtools2-2.31.1/src/regressTest/RegressTest.cpp:570:18: note: Assuming allocation function fails
     bedtools2-2.31.1/src/regressTest/RegressTest.cpp:570:18: note: Assignment 'fp=std::fopen(pidFilename.c_str(),"r")', assigned value is 0
     bedtools2-2.31.1/src/regressTest/RegressTest.cpp:573:21: note: Null pointer dereference
head bedtools2-2.31.1/src/regressTest/RegressTest.cpp:574:9: warning: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
     bedtools2-2.31.1/src/regressTest/RegressTest.cpp:570:18: note: Assuming allocation function fails
     bedtools2-2.31.1/src/regressTest/RegressTest.cpp:570:18: note: Assignment 'fp=std::fopen(pidFilename.c_str(),"r")', assigned value is 0
     bedtools2-2.31.1/src/regressTest/RegressTest.cpp:574:9: note: Null pointer dereference
2.17.0 bedtools2-2.31.1/src/regressTest/RegressTest.h:77:7: performance:inconclusive: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/regressTest/RegressTest.cpp:149:19: note: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/regressTest/RegressTest.h:77:7: note: Technically the member function 'RegressTest::usage' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/split/splitBed.cpp:339:16: performance:inconclusive: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/split/splitBed.h:35:10: note: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/split/splitBed.cpp:339:16: note: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace).
2.17.0 bedtools2-2.31.1/src/split/splitBed.h:35:10: performance:inconclusive: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/split/splitBed.cpp:339:16: note: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/split/splitBed.h:35:10: note: Technically the member function 'BedSplit::usage' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: style: Virtual function 'upCast' is called from constructor 'SubtractFile(ContextSubtract*context)' at line 10. Dynamic binding is not used. [virtualCallInConstructor]
     bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:10:72: note: Calling upCast
     bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: note: upCast is a virtual function
head bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: style: Virtual function 'upCast' is called from constructor 'SubtractFile(ContextSubtract*context)' at line 16. Dynamic binding is not used. [virtualCallInConstructor]
     bedtools2-2.31.1/src/subtractFile/subtractFile.cpp:16:41: note: Calling upCast
     bedtools2-2.31.1/src/subtractFile/subtractFile.h:30:27: note: upCast is a virtual function
head bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:124:30: performance:inconclusive: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/BinTree/BinTree.h:66:13: note: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:124:30: note: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace).
2.17.0 bedtools2-2.31.1/src/utils/BinTree/BinTree.h:66:13: performance:inconclusive: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/BinTree/BinTree.cpp:124:30: note: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/BinTree/BinTree.h:66:13: note: Technically the member function 'BinTree::getBin' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:763:19: performance:inconclusive: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:312:10: note: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:763:19: note: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace).
2.17.0 bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:312:10: performance:inconclusive: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/Contexts/ContextBase.cpp:763:19: note: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/Contexts/ContextBase.h:312:10: note: Technically the member function 'ContextBase::setErrorMsg' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:84:20: performance:inconclusive: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static. [functionStatic]
     bedtools2-2.31.1/src/utils/Fasta/Fasta.h:54:16: note: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static.
     bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:84:20: note: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static.
2.17.0 bedtools2-2.31.1/src/utils/Fasta/Fasta.h:54:16: performance:inconclusive: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static. [functionStatic]
     bedtools2-2.31.1/src/utils/Fasta/Fasta.cpp:84:20: note: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static.
     bedtools2-2.31.1/src/utils/Fasta/Fasta.h:54:16: note: Either there is a missing 'override', or the member function 'FastaIndex::indexFileExtension' can be static.
head bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:111:25: style: C-style pointer casting [cstyleCast]
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:111:26: style: C-style pointer casting [cstyleCast]
head bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:111:45: style: C-style pointer casting [cstyleCast]
head bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:113:26: style: C-style pointer casting [cstyleCast]
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/BufferedStreamMgr.cpp:113:27: style: C-style pointer casting [cstyleCast]
head bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:148:39: style:inconclusive: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:55:9: note: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const.
     bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:148:39: note: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const.
head bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:60:28: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:55:9: style:inconclusive: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.cpp:148:39: note: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const.
     bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTextFileReader.h:55:9: note: Technically the member function 'SingleLineDelimTextFileReader::getVcfSVlen' can be const.
head bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:36:26: style: C-style pointer casting [cstyleCast]
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:36:27: style: C-style pointer casting [cstyleCast]
head bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:37:26: style: C-style pointer casting [cstyleCast]
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/FileReaders/SingleLineDelimTransferBuffer.cpp:37:27: style: C-style pointer casting [cstyleCast]
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/Records/BamRecord.cpp:50:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _bamAlignment [valueFlowBailoutIncompleteVar]
head bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.cpp:38:51: style:inconclusive: Technically the member function 'RecordKeyList::end' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.h:27:25: note: Technically the member function 'RecordKeyList::end' can be const.
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.cpp:38:51: note: Technically the member function 'RecordKeyList::end' can be const.
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.h:27:25: style:inconclusive: Technically the member function 'RecordKeyList::end' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.cpp:38:51: note: Technically the member function 'RecordKeyList::end' can be const.
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordKeyList.h:27:25: note: Technically the member function 'RecordKeyList::end' can be const.
head bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:150:29: performance:inconclusive: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:106:18: note: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:150:29: note: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:173:18: performance:inconclusive: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:112:7: note: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:173:18: note: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace).
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:106:18: performance:inconclusive: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:150:29: note: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:106:18: note: Technically the member function 'RecordList::sortedMerge' can be static (but you may consider moving to unnamed namespace).
2.17.0 bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:112:7: performance:inconclusive: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.cpp:173:18: note: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/FileRecordTools/Records/RecordList.h:112:7: note: Technically the member function 'RecordList::frontBackSplit' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/utils/FileRecordTools/Records/StrandQueue.cpp:101:11: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/utils/FileRecordTools/Records/StrandQueue.cpp:108:29: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:107:22: style:inconclusive: Technically the member function 'GenomeFile::getGenomeSize' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:54:14: note: Technically the member function 'GenomeFile::getGenomeSize' can be const.
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:107:22: note: Technically the member function 'GenomeFile::getGenomeSize' can be const.
head bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:111:28: style:inconclusive: Technically the member function 'GenomeFile::getChromList' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:55:20: note: Technically the member function 'GenomeFile::getChromList' can be const.
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:111:28: note: Technically the member function 'GenomeFile::getChromList' can be const.
head bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:115:17: style:inconclusive: Technically the member function 'GenomeFile::getNumberOfChroms' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:56:9: note: Technically the member function 'GenomeFile::getNumberOfChroms' can be const.
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:115:17: note: Technically the member function 'GenomeFile::getNumberOfChroms' can be const.
head bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:119:20: style:inconclusive: Technically the member function 'GenomeFile::getGenomeFileName' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:57:12: note: Technically the member function 'GenomeFile::getGenomeFileName' can be const.
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:119:20: note: Technically the member function 'GenomeFile::getGenomeFileName' can be const.
2.17.0 bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:54:14: style:inconclusive: Technically the member function 'GenomeFile::getGenomeSize' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:107:22: note: Technically the member function 'GenomeFile::getGenomeSize' can be const.
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:54:14: note: Technically the member function 'GenomeFile::getGenomeSize' can be const.
2.17.0 bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:55:20: style:inconclusive: Technically the member function 'GenomeFile::getChromList' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:111:28: note: Technically the member function 'GenomeFile::getChromList' can be const.
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:55:20: note: Technically the member function 'GenomeFile::getChromList' can be const.
2.17.0 bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:56:9: style:inconclusive: Technically the member function 'GenomeFile::getNumberOfChroms' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:115:17: note: Technically the member function 'GenomeFile::getNumberOfChroms' can be const.
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:56:9: note: Technically the member function 'GenomeFile::getNumberOfChroms' can be const.
2.17.0 bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:57:12: style:inconclusive: Technically the member function 'GenomeFile::getGenomeFileName' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.cpp:119:20: note: Technically the member function 'GenomeFile::getGenomeFileName' can be const.
     bedtools2-2.31.1/src/utils/GenomeFile/GenomeFile.h:57:12: note: Technically the member function 'GenomeFile::getGenomeFileName' can be const.
head bedtools2-2.31.1/src/utils/KeyListOps/KeyListOps.cpp:152:31: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:634:18: style:inconclusive: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:149:10: note: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:634:18: note: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const.
head bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:723:18: style:inconclusive: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:122:7: note: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:723:18: note: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const.
head bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:731:44: style:inconclusive: Technically the member function 'CloseSweep::purgePointException' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:154:24: note: Technically the member function 'CloseSweep::purgePointException' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:731:44: note: Technically the member function 'CloseSweep::purgePointException' can be const.
2.17.0 bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:122:7: style:inconclusive: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:723:18: note: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:122:7: note: Technically the member function 'CloseSweep::allHitsRightOfQueryIgnored' can be const.
2.17.0 bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:149:10: style:inconclusive: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:634:18: note: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:149:10: note: Technically the member function 'CloseSweep::beforeLeftClosestEndPos' can be const.
2.17.0 bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:154:24: style:inconclusive: Technically the member function 'CloseSweep::purgePointException' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.cpp:731:44: note: Technically the member function 'CloseSweep::purgePointException' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/CloseSweep.h:154:24: note: Technically the member function 'CloseSweep::purgePointException' can be const.
head bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:320:34: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:327:21: style:inconclusive: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:108:10: note: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:327:21: note: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const.
head bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:329:37: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:431:21: style:inconclusive: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:128:10: note: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:431:21: note: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const.
2.17.0 bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:108:10: style:inconclusive: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:327:21: note: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:108:10: note: Technically the member function 'NewChromSweep::allCurrDBrecsNull' can be const.
2.17.0 bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:128:10: style:inconclusive: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.cpp:431:21: note: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const.
     bedtools2-2.31.1/src/utils/NewChromsweep/NewChromsweep.h:128:10: note: Technically the member function 'NewChromSweep::verifyChromOrderMismatch' can be const.
head bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:224:21: style:inconclusive: Technically the member function 'VectorOps::GetCount' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:69:14: note: Technically the member function 'VectorOps::GetCount' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:224:21: note: Technically the member function 'VectorOps::GetCount' can be const.
head bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:236:19: style:inconclusive: Technically the member function 'VectorOps::GetCollapse' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:73:12: note: Technically the member function 'VectorOps::GetCollapse' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:236:19: note: Technically the member function 'VectorOps::GetCollapse' can be const.
head bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:247:19: style:inconclusive: Technically the member function 'VectorOps::GetConcat' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:75:12: note: Technically the member function 'VectorOps::GetConcat' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:247:19: note: Technically the member function 'VectorOps::GetConcat' can be const.
head bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:295:19: style:inconclusive: Technically the member function 'VectorOps::GetFreqDesc' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:81:12: note: Technically the member function 'VectorOps::GetFreqDesc' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:295:19: note: Technically the member function 'VectorOps::GetFreqDesc' can be const.
head bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:331:19: style:inconclusive: Technically the member function 'VectorOps::GetFreqAsc' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:83:12: note: Technically the member function 'VectorOps::GetFreqAsc' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:331:19: note: Technically the member function 'VectorOps::GetFreqAsc' can be const.
head bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:367:19: style:inconclusive: Technically the member function 'VectorOps::GetFirst' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:85:12: note: Technically the member function 'VectorOps::GetFirst' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:367:19: note: Technically the member function 'VectorOps::GetFirst' can be const.
head bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:373:19: style:inconclusive: Technically the member function 'VectorOps::GetLast' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:87:12: note: Technically the member function 'VectorOps::GetLast' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:373:19: note: Technically the member function 'VectorOps::GetLast' can be const.
2.17.0 bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:69:14: style:inconclusive: Technically the member function 'VectorOps::GetCount' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:224:21: note: Technically the member function 'VectorOps::GetCount' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:69:14: note: Technically the member function 'VectorOps::GetCount' can be const.
2.17.0 bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:73:12: style:inconclusive: Technically the member function 'VectorOps::GetCollapse' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:236:19: note: Technically the member function 'VectorOps::GetCollapse' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:73:12: note: Technically the member function 'VectorOps::GetCollapse' can be const.
2.17.0 bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:75:12: style:inconclusive: Technically the member function 'VectorOps::GetConcat' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:247:19: note: Technically the member function 'VectorOps::GetConcat' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:75:12: note: Technically the member function 'VectorOps::GetConcat' can be const.
2.17.0 bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:81:12: style:inconclusive: Technically the member function 'VectorOps::GetFreqDesc' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:295:19: note: Technically the member function 'VectorOps::GetFreqDesc' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:81:12: note: Technically the member function 'VectorOps::GetFreqDesc' can be const.
2.17.0 bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:83:12: style:inconclusive: Technically the member function 'VectorOps::GetFreqAsc' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:331:19: note: Technically the member function 'VectorOps::GetFreqAsc' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:83:12: note: Technically the member function 'VectorOps::GetFreqAsc' can be const.
2.17.0 bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:85:12: style:inconclusive: Technically the member function 'VectorOps::GetFirst' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:367:19: note: Technically the member function 'VectorOps::GetFirst' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:85:12: note: Technically the member function 'VectorOps::GetFirst' can be const.
2.17.0 bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:87:12: style:inconclusive: Technically the member function 'VectorOps::GetLast' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.cpp:373:19: note: Technically the member function 'VectorOps::GetLast' can be const.
     bedtools2-2.31.1/src/utils/VectorOps/VectorOps.h:87:12: note: Technically the member function 'VectorOps::GetLast' can be const.
head bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:158:15: style:inconclusive: Technically the member function 'BedFile::Empty' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFile/bedFile.h:395:10: note: Technically the member function 'BedFile::Empty' can be const.
     bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:158:15: note: Technically the member function 'BedFile::Empty' can be const.
head bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:201:15: style:inconclusive: Technically the member function 'BedFile::PrintHeader' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFile/bedFile.h:404:10: note: Technically the member function 'BedFile::PrintHeader' can be const.
     bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:201:15: note: Technically the member function 'BedFile::PrintHeader' can be const.
head bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:329:24: style:inconclusive: Technically the member function 'BedFile::getTotalLength' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFile/bedFile.h:477:19: note: Technically the member function 'BedFile::getTotalLength' can be const.
     bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:329:24: note: Technically the member function 'BedFile::getTotalLength' can be const.
head bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:333:24: style:inconclusive: Technically the member function 'BedFile::getTotalFlattenedLength' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFile/bedFile.h:481:19: note: Technically the member function 'BedFile::getTotalFlattenedLength' can be const.
     bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:333:24: note: Technically the member function 'BedFile::getTotalFlattenedLength' can be const.
head bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:789:19: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/utils/bedFile/bedFile.h:338:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
2.17.0 bedtools2-2.31.1/src/utils/bedFile/bedFile.h:395:10: style:inconclusive: Technically the member function 'BedFile::Empty' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:158:15: note: Technically the member function 'BedFile::Empty' can be const.
     bedtools2-2.31.1/src/utils/bedFile/bedFile.h:395:10: note: Technically the member function 'BedFile::Empty' can be const.
2.17.0 bedtools2-2.31.1/src/utils/bedFile/bedFile.h:404:10: style:inconclusive: Technically the member function 'BedFile::PrintHeader' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:201:15: note: Technically the member function 'BedFile::PrintHeader' can be const.
     bedtools2-2.31.1/src/utils/bedFile/bedFile.h:404:10: note: Technically the member function 'BedFile::PrintHeader' can be const.
2.17.0 bedtools2-2.31.1/src/utils/bedFile/bedFile.h:477:19: style:inconclusive: Technically the member function 'BedFile::getTotalLength' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:329:24: note: Technically the member function 'BedFile::getTotalLength' can be const.
     bedtools2-2.31.1/src/utils/bedFile/bedFile.h:477:19: note: Technically the member function 'BedFile::getTotalLength' can be const.
2.17.0 bedtools2-2.31.1/src/utils/bedFile/bedFile.h:481:19: style:inconclusive: Technically the member function 'BedFile::getTotalFlattenedLength' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFile/bedFile.cpp:333:24: note: Technically the member function 'BedFile::getTotalFlattenedLength' can be const.
     bedtools2-2.31.1/src/utils/bedFile/bedFile.h:481:19: note: Technically the member function 'BedFile::getTotalFlattenedLength' can be const.
head bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:138:17: style:inconclusive: Technically the member function 'BedFilePE::reportBedPENewLine' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:73:10: note: Technically the member function 'BedFilePE::reportBedPENewLine' can be const.
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:138:17: note: Technically the member function 'BedFilePE::reportBedPENewLine' can be const.
head bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:504:17: performance:inconclusive: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:75:10: note: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:504:17: note: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:91:17: style:inconclusive: Technically the member function 'BedFilePE::reportBedPETab' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:72:10: note: Technically the member function 'BedFilePE::reportBedPETab' can be const.
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:91:17: note: Technically the member function 'BedFilePE::reportBedPETab' can be const.
2.17.0 bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:72:10: style:inconclusive: Technically the member function 'BedFilePE::reportBedPETab' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:91:17: note: Technically the member function 'BedFilePE::reportBedPETab' can be const.
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:72:10: note: Technically the member function 'BedFilePE::reportBedPETab' can be const.
2.17.0 bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:73:10: style:inconclusive: Technically the member function 'BedFilePE::reportBedPENewLine' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:138:17: note: Technically the member function 'BedFilePE::reportBedPENewLine' can be const.
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:73:10: note: Technically the member function 'BedFilePE::reportBedPENewLine' can be const.
2.17.0 bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:75:10: performance:inconclusive: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.cpp:504:17: note: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/bedFilePE/bedFilePE.h:75:10: note: Technically the member function 'BedFilePE::splitBedPEIntoBeds' can be static (but you may consider moving to unnamed namespace).
head bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:140:18: style:inconclusive: Technically the member function 'ChromSweep::IsValidHit' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/chromsweep/chromsweep.h:101:10: note: Technically the member function 'ChromSweep::IsValidHit' can be const.
     bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:140:18: note: Technically the member function 'ChromSweep::IsValidHit' can be const.
2.17.0 bedtools2-2.31.1/src/utils/chromsweep/chromsweep.h:101:10: style:inconclusive: Technically the member function 'ChromSweep::IsValidHit' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/chromsweep/chromsweep.cpp:140:18: note: Technically the member function 'ChromSweep::IsValidHit' can be const.
     bedtools2-2.31.1/src/utils/chromsweep/chromsweep.h:101:10: note: Technically the member function 'ChromSweep::IsValidHit' can be const.
head bedtools2-2.31.1/src/utils/fileType/FileRecordTypeChecker.cpp:367:25: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
head bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:111:19: style:inconclusive: Technically the member function 'Tokenizer::fetchElem' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/general/Tokenizer.h:48:9: note: Technically the member function 'Tokenizer::fetchElem' can be const.
     bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:111:19: note: Technically the member function 'Tokenizer::fetchElem' can be const.
head bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:24:16: performance:inconclusive: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/general/Tokenizer.h:38:6: note: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:24:16: note: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace).
2.17.0 bedtools2-2.31.1/src/utils/general/Tokenizer.h:38:6: performance:inconclusive: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:24:16: note: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace).
     bedtools2-2.31.1/src/utils/general/Tokenizer.h:38:6: note: Technically the member function 'Tokenizer::getNumFields' can be static (but you may consider moving to unnamed namespace).
2.17.0 bedtools2-2.31.1/src/utils/general/Tokenizer.h:48:9: style:inconclusive: Technically the member function 'Tokenizer::fetchElem' can be const. [functionConst]
     bedtools2-2.31.1/src/utils/general/Tokenizer.cpp:111:19: note: Technically the member function 'Tokenizer::fetchElem' can be const.
     bedtools2-2.31.1/src/utils/general/Tokenizer.h:48:9: note: Technically the member function 'Tokenizer::fetchElem' can be const.
head bedtools2-2.31.1/src/utils/htslib/bgzip.c:316:29: warning: If memory allocation fails, then there is a possible null pointer dereference: name [nullPointerOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/bgzip.c:315:30: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/bgzip.c:315:30: note: Assignment 'name=strdup(argv[optind])', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/bgzip.c:316:29: note: Null pointer dereference
2.17.0 bedtools2-2.31.1/src/utils/htslib/errmod.c:86:37: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/errmod.c:77:31: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/errmod.c:77:16: note: Assignment 'em->beta=(double*)calloc(256*256*64,sizeof(double))', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/errmod.c:86:37: note: Null pointer addition
head bedtools2-2.31.1/src/utils/htslib/errmod.c:86:37: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/errmod.c:77:31: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/errmod.c:77:16: note: Assignment 'em->beta=(double*)calloc(256*256*64,sizeof(double))', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/errmod.c:86:37: note: Null pointer addition
2.17.0 bedtools2-2.31.1/src/utils/htslib/hfile.c:831:29: style: Parameter 'fpv' can be declared as pointer to const [constParameterPointer]
head bedtools2-2.31.1/src/utils/htslib/hfile.c:831:29: style: Parameter 'fpv' can be declared as pointer to const. However it seems that 'mem_close' is a callback function, if 'fpv' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     bedtools2-2.31.1/src/utils/htslib/hfile.c:838:33: note: You might need to cast the function pointer here
     bedtools2-2.31.1/src/utils/htslib/hfile.c:831:29: note: Parameter 'fpv' can be declared as pointer to const
2.17.0 bedtools2-2.31.1/src/utils/htslib/hfile.c:932:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hopenv_mem [valueFlowBailoutIncompleteVar]
2.17.0 bedtools2-2.31.1/src/utils/htslib/hfile_gcs.c:122:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gcs_vopen [valueFlowBailoutIncompleteVar]
2.17.0 bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1336:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vhopen_libcurl [valueFlowBailoutIncompleteVar]
head bedtools2-2.31.1/src/utils/htslib/hfile_libcurl.c:1351:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CURL_GLOBAL_ALL [valueFlowBailoutIncompleteVar]
head bedtools2-2.31.1/src/utils/htslib/hfile_s3.c:83:2: error: #error No HMAC() routine found by configure [preprocessorErrorDirective]
2.17.0 bedtools2-2.31.1/src/utils/htslib/knetfile.c:423:19: error:inconclusive: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/knetfile.c:420:21: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/knetfile.c:420:8: note: Assignment 'buf=(char*)calloc(0x10000,1)', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/knetfile.c:423:19: note: Null pointer addition
head bedtools2-2.31.1/src/utils/htslib/knetfile.c:423:19: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/knetfile.c:420:21: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/knetfile.c:420:8: note: Assignment 'buf=(char*)calloc(0x10000,1)', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/knetfile.c:423:19: note: Null pointer addition
2.17.0 bedtools2-2.31.1/src/utils/htslib/kstring.c:285:27: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/kstring.c:284:21: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/kstring.c:284:9: note: Assignment 'prep=(int*)calloc(m+256,sizeof(int))', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/kstring.c:285:27: note: Null pointer addition
head bedtools2-2.31.1/src/utils/htslib/kstring.c:285:27: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/kstring.c:284:21: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/kstring.c:284:9: note: Assignment 'prep=(int*)calloc(m+256,sizeof(int))', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/kstring.c:285:27: note: Null pointer addition
2.17.0 bedtools2-2.31.1/src/utils/htslib/plugin.c:108:21: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
2.17.0 bedtools2-2.31.1/src/utils/htslib/tbx.c:204:21: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/tbx.c:197:28: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/tbx.c:197:12: note: Assignment 'meta=(uint8_t*)malloc(l_nm+28)', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/tbx.c:204:21: note: Null pointer addition
head bedtools2-2.31.1/src/utils/htslib/tbx.c:204:21: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/tbx.c:197:28: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/tbx.c:197:12: note: Assignment 'meta=(uint8_t*)malloc(l_nm+28)', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/tbx.c:204:21: note: Null pointer addition
head bedtools2-2.31.1/src/utils/htslib/tbx.c:227:58: warning: If memory allocation fails, then there is a possible null pointer dereference: tbx [nullPointerOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/tbx.c:221:25: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/tbx.c:221:11: note: Assignment 'tbx=(struct tbx_t*)calloc(1,sizeof(struct tbx_t))', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/tbx.c:227:58: note: Null pointer dereference
2.17.0 bedtools2-2.31.1/src/utils/htslib/thread_pool.c:684:9: error: Memory leak: p [memleak]
head bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:111:30: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:111:30: note: Null pointer dereference
head bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:113:29: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:113:29: note: Null pointer dereference
head bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:115:33: warning: If memory allocation fails, then there is a possible null pointer dereference: sw [nullPointerOutOfMemory]
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:44: note: Assuming allocation function fails
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:109:23: note: Assignment 'sw=(struct bcf_sweep_t*)calloc(1,sizeof(struct bcf_sweep_t))', assigned value is 0
     bedtools2-2.31.1/src/utils/htslib/vcf_sweep.c:115:33: note: Null pointer dereference
head bedtools2-2.31.1/src/windowBed/windowBed.cpp:235:17: style:inconclusive: Technically the member function 'BedWindow::AddWindow' can be const. [functionConst]
     bedtools2-2.31.1/src/windowBed/windowBed.h:68:10: note: Technically the member function 'BedWindow::AddWindow' can be const.
     bedtools2-2.31.1/src/windowBed/windowBed.cpp:235:17: note: Technically the member function 'BedWindow::AddWindow' can be const.
2.17.0 bedtools2-2.31.1/src/windowBed/windowBed.h:68:10: style:inconclusive: Technically the member function 'BedWindow::AddWindow' can be const. [functionConst]
     bedtools2-2.31.1/src/windowBed/windowBed.cpp:235:17: note: Technically the member function 'BedWindow::AddWindow' can be const.
     bedtools2-2.31.1/src/windowBed/windowBed.h:68:10: note: Technically the member function 'BedWindow::AddWindow' can be const.
head bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:103:19: style:inconclusive: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const. [functionConst]
     bedtools2-2.31.1/src/windowMaker/windowMaker.h:60:10: note: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const.
     bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:103:19: note: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const.
head bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:81:23: style:inconclusive: Technically the member function 'WindowMaker::CalculateWindows' can be const. [functionConst]
     bedtools2-2.31.1/src/windowMaker/windowMaker.h:61:14: note: Technically the member function 'WindowMaker::CalculateWindows' can be const.
     bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:81:23: note: Technically the member function 'WindowMaker::CalculateWindows' can be const.
2.17.0 bedtools2-2.31.1/src/windowMaker/windowMaker.h:60:10: style:inconclusive: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const. [functionConst]
     bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:103:19: note: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const.
     bedtools2-2.31.1/src/windowMaker/windowMaker.h:60:10: note: Technically the member function 'WindowMaker::MakeFixedCountWindow' can be const.
2.17.0 bedtools2-2.31.1/src/windowMaker/windowMaker.h:61:14: style:inconclusive: Technically the member function 'WindowMaker::CalculateWindows' can be const. [functionConst]
     bedtools2-2.31.1/src/windowMaker/windowMaker.cpp:81:23: note: Technically the member function 'WindowMaker::CalculateWindows' can be const.
     bedtools2-2.31.1/src/windowMaker/windowMaker.h:61:14: note: Technically the member function 'WindowMaker::CalculateWindows' can be const.


DONE