2026-05-26 11:18
ftp://ftp.de.debian.org/debian/pool/main/c/canu/canu_2.2+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=boost --library=openmp  --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 -j2
platform: Linux-6.12.90+deb13-amd64-x86_64-with-glibc2.41
python: 3.13.5
client-version: 1.3.70
compiler: g++ (20250906) 15.2.0
cppcheck: head 2.20.0
head-info: bc33aee (2026-05-26 08:48:42 +0200)
count: 1855 1779
elapsed-time: 322.5 396.5
head-timing-info:

old-timing-info:

head results:
canu-2.2/src/bogart/AS_BAT_ReadInfo.H:121:59: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/bogart/AS_BAT_Logging.C:94:39: error: There is an unknown macro here somewhere. Configuration is required. If F_U64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:36:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable evalue [valueFlowBailoutIncompleteVar]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:95:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable evalue [valueFlowBailoutIncompleteVar]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:105:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable evalue [valueFlowBailoutIncompleteVar]
canu-2.2/src/bogart/AS_BAT_Unitig.H:336:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/bogart/AS_BAT_Unitig.H:351:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/bogart/AS_BAT_TigVector.C:172:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:37:5: performance: Variable 'a_hang' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:38:5: performance: Variable 'b_hang' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:39:5: performance: Variable 'flipped' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:41:5: performance: Variable 'filtered' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:42:5: performance: Variable 'symmetric' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:44:5: performance: Variable 'a_iid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:45:5: performance: Variable 'b_iid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:156:5: performance: Variable '_osAllocLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:168:5: performance: Variable '_osAllocLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:169:5: performance: Variable '_osLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:170:5: performance: Variable '_osPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:171:5: performance: Variable '_osMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:41:5: performance: Variable 'bgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:42:5: performance: Variable 'end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:126:5: performance: Variable 'ident' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:127:5: performance: Variable 'contained' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:128:5: performance: Variable 'parent' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:130:5: performance: Variable 'ahang' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:131:5: performance: Variable 'bhang' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:133:5: performance: Variable 'position' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:136:5: performance: Variable 'ident' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:137:5: performance: Variable 'contained' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:138:5: performance: Variable 'parent' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:140:5: performance: Variable 'ahang' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:141:5: performance: Variable 'bhang' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:212:5: performance: Variable '_length' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:213:5: performance: Variable '_id' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:220:5: performance: Variable '_circularLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:285:7: performance: Variable 'bgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:286:7: performance: Variable 'end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:292:7: performance: Variable 'bgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_Unitig.H:293:7: performance: Variable 'end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/bogart/AS_BAT_TigVector.H:33:13: style:inconclusive: Technically the member function 'TigVector::size' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_TigVector.H:50:13: style:inconclusive: Technically the member function 'TigVector::inUnitig' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_TigVector.H:51:13: style:inconclusive: Technically the member function 'TigVector::ufpathIdx' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:94:3: style: The member function 'BAToverlap::erate' can be static. [functionStatic]
canu-2.2/src/bogart/AS_BAT_Unitig.H:165:10: style:inconclusive: Technically the member function 'ufNode::hangToMinCoord' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_Unitig.H:172:10: style:inconclusive: Technically the member function 'ufNode::hangToMaxCoord' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_Unitig.H:266:10: style:inconclusive: Technically the member function 'Unitig::id' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_Unitig.H:268:10: style:inconclusive: Technically the member function 'Unitig::getLength' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_Unitig.H:269:10: style:inconclusive: Technically the member function 'Unitig::getNumReads' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_Unitig.H:298:15: style:inconclusive: Technically the member function 'Unitig::epValue::max' can be const. [functionConst]
canu-2.2/src/bogart/AS_BAT_TigVector.C:31:3: warning: Class 'TigVector' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/bogart/AS_BAT_TigVector.C:31:3: warning: Class 'TigVector' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:160:5: warning: Class 'OverlapStorage' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:160:5: warning: Class 'OverlapStorage' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/bogart/AS_BAT_TigVector.H:27:3: style: Class 'TigVector' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:155:3: style: Class 'OverlapStorage' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:167:3: style: Class 'OverlapStorage' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/bogart/AS_BAT_Unitig.H:135:3: style: Class 'ufNode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/bogart/AS_BAT_Unitig.H:210:3: style: Class 'Unitig' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/bogart/AS_BAT_Unitig.H:165:31: style: Argument 'ahang' shadows outer member [shadowMember]
canu-2.2/src/bogart/AS_BAT_Unitig.H:200:20: note: Shadowed member
canu-2.2/src/bogart/AS_BAT_Unitig.H:165:31: note: Shadow argument
canu-2.2/src/bogart/AS_BAT_Unitig.H:165:44: style: Argument 'bhang' shadows outer member [shadowMember]
canu-2.2/src/bogart/AS_BAT_Unitig.H:201:20: note: Shadowed member
canu-2.2/src/bogart/AS_BAT_Unitig.H:165:44: note: Shadow argument
canu-2.2/src/bogart/AS_BAT_Unitig.H:172:31: style: Argument 'ahang' shadows outer member [shadowMember]
canu-2.2/src/bogart/AS_BAT_Unitig.H:200:20: note: Shadowed member
canu-2.2/src/bogart/AS_BAT_Unitig.H:172:31: note: Shadow argument
canu-2.2/src/bogart/AS_BAT_Unitig.H:172:44: style: Argument 'bhang' shadows outer member [shadowMember]
canu-2.2/src/bogart/AS_BAT_Unitig.H:201:20: note: Shadowed member
canu-2.2/src/bogart/AS_BAT_Unitig.H:172:44: note: Shadow argument
canu-2.2/src/bogart/AS_BAT_Unitig.H:89:26: style: Parameter 'A' can be declared as reference to const [constParameterReference]
canu-2.2/src/bogart/AS_BAT_Unitig.H:89:42: style: Parameter 'B' can be declared as reference to const [constParameterReference]
canu-2.2/src/bogart/AS_BAT_Unitig.H:109:28: style: Parameter 'A' can be declared as reference to const [constParameterReference]
canu-2.2/src/bogart/AS_BAT_Unitig.H:109:44: style: Parameter 'B' can be declared as reference to const [constParameterReference]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:167:34: style: Parameter 'original' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/bogart/AS_BAT_OverlapCache.H:220:41: style: Parameter 'that' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/correction/computeGlobalScore.C:36:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/errorEstimate.C:52:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/computeGlobalScore.H:27:5: performance: Variable 'totalOverlaps' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:28:5: performance: Variable 'lowErate' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:29:5: performance: Variable 'highErate' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:30:5: performance: Variable 'tooShort' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:31:5: performance: Variable 'tooLong' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:32:5: performance: Variable 'belowCutoff' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:33:5: performance: Variable 'retained' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:35:5: performance: Variable 'reads00OlapsFiltered' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:36:5: performance: Variable 'reads50OlapsFiltered' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:37:5: performance: Variable 'reads80OlapsFiltered' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:38:5: performance: Variable 'reads95OlapsFiltered' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:39:5: performance: Variable 'reads99OlapsFiltered' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:68:5: performance: Variable 'histLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:69:5: performance: Variable 'histMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:73:5: performance: Variable 'minOvlLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:74:5: performance: Variable 'maxOvlLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:75:5: performance: Variable 'minEvalue' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/computeGlobalScore.H:96:15: style:inconclusive: Technically the member function 'globalScore::totalOverlaps' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:97:15: style:inconclusive: Technically the member function 'globalScore::lowErate' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:98:15: style:inconclusive: Technically the member function 'globalScore::highErate' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:99:15: style:inconclusive: Technically the member function 'globalScore::tooShort' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:100:15: style:inconclusive: Technically the member function 'globalScore::tooLong' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:101:15: style:inconclusive: Technically the member function 'globalScore::belowCutoff' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:102:15: style:inconclusive: Technically the member function 'globalScore::retained' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:104:15: style:inconclusive: Technically the member function 'globalScore::reads00OlapsFiltered' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:105:15: style:inconclusive: Technically the member function 'globalScore::reads50OlapsFiltered' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:106:15: style:inconclusive: Technically the member function 'globalScore::reads80OlapsFiltered' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:107:15: style:inconclusive: Technically the member function 'globalScore::reads95OlapsFiltered' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:108:15: style:inconclusive: Technically the member function 'globalScore::reads99OlapsFiltered' can be const. [functionConst]
canu-2.2/src/correction/computeGlobalScore.H:84:15: warning: Class 'globalScore' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/correction/computeGlobalScore.H:84:15: warning: Class 'globalScore' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/correction/computeGlobalScore.C:127:7: warning: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/correction/computeGlobalScore.C:74:13: style: Variable 'isC' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/correction/computeGlobalScore.C:75:13: style: Variable 'isD' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/correction/falconConsensus-msa.H:84:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MIN [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/falconConsensus-alignTag.C:69:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/falconConsensus-alignTag.C:247:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint16max [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/falconConsensus-alignTag.H:68:5: performance: Variable 't_pos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-alignTag.H:69:5: performance: Variable 'p_t_pos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-alignTag.H:70:5: performance: Variable 'delta' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-alignTag.H:71:5: performance: Variable 'p_delta' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-alignTag.H:72:5: performance: Variable 'q_base' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-alignTag.H:73:5: performance: Variable 'p_q_base' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-alignTag.H:100:5: performance: Variable 'tagsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-msa.H:63:5: performance: Variable 'size' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-msa.H:156:5: performance: Variable 'coverage' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-msa.H:158:5: performance: Variable 'deltaAlloc' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-msa.H:159:5: performance: Variable 'deltaLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-msa.H:162:5: performance: Variable 'deltaPtrsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-msa.H:263:5: performance: Variable 'dgLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-msa.H:264:5: performance: Variable 'dgMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:84:5: performance: Variable 'readLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:86:5: performance: Variable 'ident' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:88:5: performance: Variable 'placedBgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:89:5: performance: Variable 'placedEnd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:91:5: performance: Variable 'alignedBgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:92:5: performance: Variable 'alignedEnd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:139:5: performance: Variable 'len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:146:5: performance: Variable 'len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:169:5: performance: Variable 'minOutputCoverage' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:171:5: performance: Variable 'minOlapLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:173:5: performance: Variable 'minRSS' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus.H:174:5: performance: Variable 'maxRSS' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/correction/falconConsensus-alignTag.H:109:18: style:inconclusive: Technically the member function 'alignTagList::numberOfTags' can be const. [functionConst]
canu-2.2/src/correction/falconConsensus-msa.H:119:10: style:inconclusive: Technically the member function 'align_tag_col_t::getCount' can be const. [functionConst]
canu-2.2/src/correction/falconConsensus-msa.H:244:10: style:inconclusive: Technically the member function 'msa_delta_group_t::getCoverage' can be const. [functionConst]
canu-2.2/src/correction/falconConsensus.H:210:15: style:inconclusive: Technically the member function 'falconConsensus::getRSS' can be const. [functionConst]
canu-2.2/src/correction/falconConsensus-msa.H:64:5: warning: Class 'align_tag_col_t' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/correction/falconConsensus-msa.H:64:5: warning: Class 'align_tag_col_t' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/correction/falconConsensus-msa.H:160:5: warning: Class 'msa_delta_group_t' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/correction/falconConsensus-msa.H:160:5: warning: Class 'msa_delta_group_t' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/correction/falconConsensus.H:143:5: warning: Class 'falconData' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/correction/falconConsensus.H:143:5: warning: Class 'falconData' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/correction/falconConsensus-alignTag.H:99:3: style: Class 'alignTagList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/correction/falconConsensus.H:142:3: style: Class 'falconData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/correction/falconConsensus-alignTag.C:114:23: style: Parameter 'evidence' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/correction/falconConsensus-alignTag.C:146:24: style: Parameter 'tAln' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/correction/falconConsensus-alignTag.C:181:25: style: Parameter 'tAln' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/correction/falconConsensus-alignTag.C:217:26: style: Parameter 'Qalign' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/correction/falconConsensus-alignTag.C:218:26: style: Parameter 'Talign' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/correction/falconConsensus.H:96:25: style: Parameter 'read_' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/correction/falconConsensus-msa.H:87:28: style: Parameter 'tag' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/correction/falconConsensus.C:103:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint16max [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/falconConsensus.C:360:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable int32 [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/falconsense.C:54:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/falconsense.C:117:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/falconsense.C:363:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/correction/falconConsensus.C:376:50: style:inconclusive: Function 'analyzeLength' argument 3 names different: declaration 'memoryNeeded' definition 'memoryRequired'. [funcArgNamesDifferent]
canu-2.2/src/correction/falconConsensus.H:226:43: note: Function 'analyzeLength' argument 3 names different: declaration 'memoryNeeded' definition 'memoryRequired'.
canu-2.2/src/correction/falconConsensus.C:376:50: note: Function 'analyzeLength' argument 3 names different: declaration 'memoryNeeded' definition 'memoryRequired'.
canu-2.2/src/correction/filterCorrectionLayouts.C:193:38: error: There is an unknown macro here somewhere. Configuration is required. If F_U32P is a macro then please configure it. [unknownMacro]
canu-2.2/src/correction/filterCorrectionOverlaps.C:265:27: error: There is an unknown macro here somewhere. Configuration is required. If F_U32P is a macro then please configure it. [unknownMacro]
canu-2.2/src/correction/falconsense.C:208:5: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/correction/falconsense.C:208:5: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/correction/generateCorrectionLayouts.C:81:50: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/correction/falconsense.C:631:21: style: Local variable 'ii' shadows outer variable [shadowVariable]
canu-2.2/src/correction/falconsense.C:590:17: note: Shadowed variable
canu-2.2/src/correction/falconsense.C:631:21: note: Shadow local variable
canu-2.2/src/correction/falconsense.C:86:21: performance: Searching before insertion is not necessary. Instead of 'reads[readID]=new sqRead' consider using 'reads.try_emplace(readID, new sqRead);'. [stlFindInsert]
canu-2.2/src/gfa/alignGFA.C:600:34: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/gfa/bed.C:136:35: error: There is an unknown macro here somewhere. Configuration is required. If F_SIZE_T is a macro then please configure it. [unknownMacro]
canu-2.2/src/gfa/gfa.C:349:35: error: There is an unknown macro here somewhere. Configuration is required. If F_SIZE_T is a macro then please configure it. [unknownMacro]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:192:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:278:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:356:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/haplotyping/splitHaplotype.C:196:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/haplotyping/splitHaplotype.C:255:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/haplotyping/splitHaplotype.C:401:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/haplotyping/splitHaplotype.C:472:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/haplotyping/splitHaplotype.C:533:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/haplotyping/splitHaplotype.C:634:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MIN [valueFlowBailoutIncompleteVar]
canu-2.2/src/haplotyping/splitHaplotype.C:755:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:35:5: performance: Variable '_minValue' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:36:5: performance: Variable '_maxValue' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:41:5: performance: Variable '_histoLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:42:5: performance: Variable '_histoMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:49:14: style:inconclusive: Technically the member function 'denseHistogram::minValue' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:50:14: style:inconclusive: Technically the member function 'denseHistogram::maxValue' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:62:14: style:inconclusive: Technically the member function 'denseHistogram::report' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:104:14: style:inconclusive: Technically the member function 'sparseHistogram < uint64 , uint32 >::minValue' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:105:14: style:inconclusive: Technically the member function 'sparseHistogram < uint64 , uint32 >::maxValue' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:43:5: warning: Class 'denseHistogram' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:43:5: warning: Class 'denseHistogram' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:154:25: style: Parameter 'outPrefix' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/meryl/src/meryl-analyze/meryl-analyze.C:215:25: style: Parameter 'outPrefix' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/haplotyping/splitHaplotype.C:73:5: performance: Variable '_idMin' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:74:5: performance: Variable '_idCur' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:75:5: performance: Variable '_idMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:77:5: performance: Variable '_numReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:82:5: performance: Variable '_minOutputLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:87:5: performance: Variable '_ambiguousReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:88:5: performance: Variable '_ambiguousBases' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:90:5: performance: Variable '_filteredReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:91:5: performance: Variable '_filteredBases' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:93:5: performance: Variable '_numThreads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:175:5: performance: Variable '_strLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:176:5: performance: Variable '_strMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:223:5: performance: Variable '_numReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:224:5: performance: Variable '_maxReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/haplotyping/splitHaplotype.C:205:11: style:inconclusive: Technically the member function 'simpleString::length' can be const. [functionConst]
canu-2.2/src/haplotyping/splitHaplotype.C:273:10: warning: Class 'hapData' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/haplotyping/splitHaplotype.C:273:10: warning: Class 'hapData' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/haplotyping/splitHaplotype.C:100:14: warning: Class 'allData' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/haplotyping/splitHaplotype.C:100:14: warning: Class 'allData' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/haplotyping/splitHaplotype.C:226:5: warning: Class 'readBatch' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/haplotyping/splitHaplotype.C:226:5: warning: Class 'readBatch' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/haplotyping/splitHaplotype.C:222:3: style: Class 'readBatch' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/haplotyping/splitHaplotype.C:821:3: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/haplotyping/splitHaplotype.C:491:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/haplotyping/splitHaplotype.C:584:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/haplotyping/splitHaplotype.C:585:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/haplotyping/splitHaplotype.C:586:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/haplotyping/splitHaplotype.C:666:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/haplotyping/splitHaplotype.C:667:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/haplotyping/splitHaplotype.C:254:24: style: Parameter 'merylname' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/haplotyping/splitHaplotype.C:254:41: style: Parameter 'histoname' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/haplotyping/splitHaplotype.C:254:58: style: Parameter 'fastaname' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/haplotyping/splitHaplotype.C:585:16: style: Variable 't' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/haplotyping/splitHaplotype.C:585:18: style: Variable 't' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/meryl/src/meryl-import/meryl-import.C:91:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:262:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:313:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:377:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.H:65:12: warning: Class 'lookupGlobal' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.H:65:12: warning: Class 'lookupGlobal' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:29:14: warning: Class 'dumpInput' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:29:14: warning: Class 'dumpInput' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:71:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:89:27: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:90:27: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:416:30: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:417:30: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/dump.C:437:29: style:inconclusive: Function 'dumpExistence' argument 1 names different: declaration 'G' definition 'g'. [funcArgNamesDifferent]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.H:132:34: note: Function 'dumpExistence' argument 1 names different: declaration 'G' definition 'g'.
canu-2.2/src/meryl/src/meryl-lookup/dump.C:437:29: note: Function 'dumpExistence' argument 1 names different: declaration 'G' definition 'g'.
canu-2.2/src/meryl/src/meryl-lookup/existence.C:102:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/existence.C:43:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/existence.C:59:23: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/existence.C:60:23: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/existence.C:96:23: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/existence.C:97:23: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/existence.C:134:31: style:inconclusive: Function 'reportExistence' argument 1 names different: declaration 'G' definition 'g'. [funcArgNamesDifferent]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.H:133:36: note: Function 'reportExistence' argument 1 names different: declaration 'G' definition 'g'.
canu-2.2/src/meryl/src/meryl-lookup/existence.C:134:31: note: Function 'reportExistence' argument 1 names different: declaration 'G' definition 'g'.
canu-2.2/src/meryl/src/meryl-lookup/include-exclude.C:140:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/include-exclude.C:44:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/include-exclude.C:83:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/include-exclude.C:84:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/include-exclude.C:114:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/include-exclude.C:115:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl-lookup/include-exclude.C:137:22: style:inconclusive: Function 'filter' argument 1 names different: declaration 'G' definition 'g'. [funcArgNamesDifferent]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.H:134:27: note: Function 'filter' argument 1 names different: declaration 'G' definition 'g'.
canu-2.2/src/meryl/src/meryl-lookup/include-exclude.C:137:22: note: Function 'filter' argument 1 names different: declaration 'G' definition 'g'.
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup-help.C:26:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup-help.C:80:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup-help.C:115:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup-help.C:147:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup-help.C:183:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup-help.C:222:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.C:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.C:113:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.C:130:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-lookup/meryl-lookup.C:250:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-simple/meryl-simple.C:77:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl-simple/meryl-simple.C:175:18: style: Array index 'jj' is used before limits check. [arrayIndexThenCheck]
canu-2.2/src/meryl/src/meryl-simple/meryl-simple.C:31:11: style: Variable 'mOutput' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/meryl/src/meryl/meryl.C:98:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylInput.H:44:15: style:inconclusive: Technically the member function 'merylInput::inputType' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylInput.H:68:10: style:inconclusive: Technically the member function 'merylInput::isFromOperation' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylInput.H:69:10: style:inconclusive: Technically the member function 'merylInput::isFromDatabase' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylInput.H:70:10: style:inconclusive: Technically the member function 'merylInput::isFromSequence' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylInput.H:71:10: style:inconclusive: Technically the member function 'merylInput::isFromStore' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylInput.H:73:10: style:inconclusive: Technically the member function 'merylInput::isMultiSet' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:128:11: style:inconclusive: Technically the member function 'merylOperation::getOperation' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:150:11: style:inconclusive: Technically the member function 'merylOperation::getMemoryLimit' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:151:11: style:inconclusive: Technically the member function 'merylOperation::getThreadLimit' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:153:11: style:inconclusive: Technically the member function 'merylOperation::isCounting' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:163:11: style:inconclusive: Technically the member function 'merylOperation::needsThreshold' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:172:11: style:inconclusive: Technically the member function 'merylOperation::needsConstant' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:185:11: style:inconclusive: Technically the member function 'merylOperation::isMultiSet' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:188:11: style:inconclusive: Technically the member function 'merylOperation::theValue' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:205:11: style:inconclusive: Technically the member function 'merylOperation::validMer' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylCountArray.H:101:20: style:inconclusive: Technically the member function 'merylCountArray::numBits' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylCountArray.H:102:20: style:inconclusive: Technically the member function 'merylCountArray::numKmers' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylCountArray.H:127:20: style:inconclusive: Technically the member function 'merylCountArray::usedSize' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/meryl.H:57:20: style:inconclusive: Technically the member function 'merylCommandBuilder::numOperations' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/meryl.H:60:20: style:inconclusive: Technically the member function 'merylCommandBuilder::numRoots' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylInput.H:38:3: style: Class 'merylInput' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/meryl/src/meryl/merylOp.H:229:10: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
canu-2.2/src/meryl/src/meryl/merylOp.H:230:5: note: Found duplicate branches for 'if' and 'else'.
canu-2.2/src/meryl/src/meryl/merylOp.H:229:10: note: Found duplicate branches for 'if' and 'else'.
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:91:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:113:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:258:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:399:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:522:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:562:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:582:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:664:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:173:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint64 [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:181:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:202:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:258:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable copyData [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:60:3: performance: Variable '_allowedThreads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:580:22: style: The member function 'merylCommandBuilder::printTree' can be static. [functionStatic]
canu-2.2/src/meryl/src/meryl/meryl.H:54:11: note: The member function 'merylCommandBuilder::printTree' can be static.
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:580:22: note: The member function 'merylCommandBuilder::printTree' can be static.
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:39:16: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:110:39: style: Parameter 'opt' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/meryl/src/meryl/merylCommandBuilder.C:191:17: style: Variable 'key' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:74:3: performance: Variable '_sWidth' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:75:3: performance: Variable '_vWidth' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:77:3: performance: Variable '_prefix' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:81:3: performance: Variable '_nKmers' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:83:3: performance: Variable '_bitsPerPage' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:84:3: performance: Variable '_nReAlloc' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:86:3: performance: Variable '_segSize' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:87:3: performance: Variable '_segAlloc' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:92:3: performance: Variable '_nBits' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:93:3: performance: Variable '_nBitsTrigger' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylCountArray.C:94:3: performance: Variable '_nBitsOldSize' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:44:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylInput.C:74:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylInput.C:101:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp-count.C:267:26: error: There is an unknown macro here somewhere. Configuration is required. If F_U32P is a macro then please configure it. [unknownMacro]
canu-2.2/src/meryl/src/meryl/merylInput.C:109:13: warning: Member variable 'merylInput::_name' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/meryl/src/meryl/merylInput.C:109:13: warning: Member variable 'merylInput::_read' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/meryl/src/meryl/merylInput.C:31:3: performance: Variable '_value' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:34:3: performance: Variable '_sqBgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:35:3: performance: Variable '_sqEnd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:38:3: performance: Variable '_readID' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:39:3: performance: Variable '_readPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:88:3: performance: Variable '_value' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:91:3: performance: Variable '_sqBgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:92:3: performance: Variable '_sqEnd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:95:3: performance: Variable '_readID' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:96:3: performance: Variable '_readPos' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:117:3: performance: Variable '_value' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:120:3: performance: Variable '_sqBgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:121:3: performance: Variable '_sqEnd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylInput.C:243:13: style: The member function 'merylInput::loadBasesFromCanu' can be static. [functionStatic]
canu-2.2/src/meryl/src/meryl/merylInput.H:57:10: note: The member function 'merylInput::loadBasesFromCanu' can be static.
canu-2.2/src/meryl/src/meryl/merylInput.C:243:13: note: The member function 'merylInput::loadBasesFromCanu' can be static.
canu-2.2/src/meryl/src/meryl/merylInput.C:190:10: warning: Class 'merylInput' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/meryl/src/meryl/merylInput.C:190:10: warning: Class 'merylInput' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/meryl/src/meryl/merylInput.C:321:49: style: Assigned value 'loadBasesFromCanu(seq,maxLength,seqLength,endOfSequence)' is always false [knownConditionTrueFalse]
canu-2.2/src/meryl/src/meryl/merylInput.C:321:49: note: Calling function 'loadBasesFromCanu' returns 0
canu-2.2/src/meryl/src/meryl/merylInput.C:321:49: note: Assigned value 'loadBasesFromCanu(seq,maxLength,seqLength,endOfSequence)' is always false
canu-2.2/src/meryl/src/meryl/merylInput.C:50:66: style:inconclusive: Function 'merylInput' argument 3 names different: declaration 'fileNum' definition 'threadFile'. [funcArgNamesDifferent]
canu-2.2/src/meryl/src/meryl/merylInput.H:39:56: note: Function 'merylInput' argument 3 names different: declaration 'fileNum' definition 'threadFile'.
canu-2.2/src/meryl/src/meryl/merylInput.C:50:66: note: Function 'merylInput' argument 3 names different: declaration 'fileNum' definition 'threadFile'.
canu-2.2/src/meryl/src/meryl/merylInput.C:245:40: style: Parameter 'seqLength' can be declared as reference to const [constParameterReference]
canu-2.2/src/meryl/src/meryl/merylInput.C:246:40: style: Parameter 'endOfSequence' can be declared as reference to const [constParameterReference]
canu-2.2/src/meryl/src/meryl/merylInput.C:109:48: style: Parameter 's' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/meryl/src/meryl/merylInput.C:243:40: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/meryl/src/meryl/merylInput.C:214:8: style: Unused variable: kmerString [unusedVariable]
canu-2.2/src/meryl/src/meryl/merylOp-countSimple.C:185:53: error: There is an unknown macro here somewhere. Configuration is required. If F_S32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/meryl/src/meryl/merylOp-histogram.C:40:32: error: There is an unknown macro here somewhere. Configuration is required. If F_U64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:271:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:307:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kmdata [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:446:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp-nextMer.C:448:78: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:39:5: performance: Variable '_nPrefix' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:40:5: performance: Variable '_wData' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:41:5: performance: Variable '_wDataMask' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:116:5: performance: Variable '_bufferMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:45:5: warning: Class 'mcGlobalData' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:45:5: warning: Class 'mcGlobalData' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:117:5: warning: Class 'mcComputation' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:117:5: warning: Class 'mcComputation' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:115:3: style: Class 'mcComputation' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:266:7: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:140:26: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:237:25: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:238:25: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:287:25: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl/merylOp-countThreads.C:288:25: style: C-style pointer casting [cstyleCast]
canu-2.2/src/meryl/src/meryl/merylOp.C:37:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp.C:112:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp.C:145:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp.C:157:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp.C:179:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp.C:197:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp.C:240:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp.C:258:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/tests/merylCountArrayTest.C:31:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/tests/merylCountArrayTest.C:121:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/meryl/merylOp.C:75:3: performance: Variable '_mathConstant' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp.C:76:3: performance: Variable '_threshold' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp.C:81:3: performance: Variable '_maxThreads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp.C:82:3: performance: Variable '_maxMemory' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp.C:85:3: performance: Variable '_fileNumber' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/meryl/src/meryl/merylOp.C:138:17: style:inconclusive: Technically the member function 'merylOperation::checkInputs' can be const. [functionConst]
canu-2.2/src/meryl/src/meryl/merylOp.H:100:11: note: Technically the member function 'merylOperation::checkInputs' can be const.
canu-2.2/src/meryl/src/meryl/merylOp.C:138:17: note: Technically the member function 'merylOperation::checkInputs' can be const.
canu-2.2/src/meryl/src/meryl/merylOp.C:214:17: style: The member function 'merylOperation::addInputFromCanu' can be static. [functionStatic]
canu-2.2/src/meryl/src/meryl/merylOp.H:117:11: note: The member function 'merylOperation::addInputFromCanu' can be static.
canu-2.2/src/meryl/src/meryl/merylOp.C:214:17: note: The member function 'merylOperation::addInputFromCanu' can be static.
canu-2.2/src/meryl/src/meryl/merylOp.C:88:3: warning: Class 'merylOperation' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/meryl/src/meryl/merylOp.C:88:3: warning: Class 'merylOperation' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/meryl/src/meryl/merylOp.C:214:40: style:inconclusive: Function 'addInputFromCanu' argument 1 names different: declaration 'stName' definition 'sqName'. [funcArgNamesDifferent]
canu-2.2/src/meryl/src/meryl/merylOp.H:117:34: note: Function 'addInputFromCanu' argument 1 names different: declaration 'stName' definition 'sqName'.
canu-2.2/src/meryl/src/meryl/merylOp.C:214:40: note: Function 'addInputFromCanu' argument 1 names different: declaration 'stName' definition 'sqName'.
canu-2.2/src/meryl/src/meryl/merylOp.C:36:41: style: Parameter 'prName' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/meryl/src/meryl/merylOp.C:214:40: style: Parameter 'sqName' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/meryl/src/tests/merylCountArrayTest.C:114:41: style: Expression is always false because 'else if' condition matches previous condition at line 111. [multiCondition]
canu-2.2/src/meryl/src/tests/merylCountArrayTest.C:117:41: style: Expression is always false because 'else if' condition matches previous condition at line 111. [multiCondition]
canu-2.2/src/meryl/src/tests/merylCountArrayTest.C:92:10: style: Variable 'err' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/meryl/src/tests/merylExactLookupTest.C:33:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/tests/merylExactLookupTest.C:53:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/meryl/src/tests/merylExactLookupTest.C:91:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint64max [valueFlowBailoutIncompleteVar]
canu-2.2/src/mhap/mhapConvert.C:139:53: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/minimap/mmapConvert.C:127:44: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapAlign/clearRangeFile.C:25:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/clearRangeFile.C:76:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/clearRangeFile.C:100:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/clearRangeFile.C:126:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/clearRangeFile.C:148:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable copyData [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/clearRangeFile.H:44:13: style:inconclusive: Technically the member function 'clearRangeFile::bgn' can be const. [functionConst]
canu-2.2/src/overlapAlign/clearRangeFile.H:45:13: style:inconclusive: Technically the member function 'clearRangeFile::end' can be const. [functionConst]
canu-2.2/src/overlapAlign/clearRangeFile.H:46:13: style:inconclusive: Technically the member function 'clearRangeFile::valid' can be const. [functionConst]
canu-2.2/src/overlapAlign/clearRangeFile.H:47:13: style:inconclusive: Technically the member function 'clearRangeFile::deleted' can be const. [functionConst]
canu-2.2/src/overlapAlign/clearRangeFile.H:30:3: style: Class 'clearRangeFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/overlapAlign/clearRangeFile.H:49:45: style: Argument 'bgn' shadows outer function [shadowFunction]
canu-2.2/src/overlapAlign/clearRangeFile.H:44:13: note: Shadowed function
canu-2.2/src/overlapAlign/clearRangeFile.H:49:45: note: Shadow argument
canu-2.2/src/overlapAlign/clearRangeFile.H:49:57: style: Argument 'end' shadows outer function [shadowFunction]
canu-2.2/src/overlapAlign/clearRangeFile.H:45:13: note: Shadowed function
canu-2.2/src/overlapAlign/clearRangeFile.H:49:57: note: Shadow argument
canu-2.2/src/overlapAlign/clearRangeFile.H:49:67: style: Argument 'deleted' shadows outer function [shadowFunction]
canu-2.2/src/overlapAlign/clearRangeFile.H:47:13: note: Shadowed function
canu-2.2/src/overlapAlign/clearRangeFile.H:49:67: note: Shadow argument
canu-2.2/src/meryl/src/tests/merylExactLookupTest.C:77:3: portability: %lu in format string (no. 3) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
canu-2.2/src/meryl/src/tests/merylExactLookupTest.C:195:17: style: The comparison 'fail == false' is always true because 'fail' and 'false' represent the same value. [knownConditionTrueFalse]
canu-2.2/src/meryl/src/tests/merylExactLookupTest.C:185:24: note: 'fail' is assigned value 'false' here.
canu-2.2/src/meryl/src/tests/merylExactLookupTest.C:195:17: note: The comparison 'fail == false' is always true because 'fail' and 'false' represent the same value.
canu-2.2/src/meryl/src/tests/merylExactLookupTest.C:89:11: style: Variable 'inputDBname' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:420:77: debug: Function::addArguments found argument 'alen' with varid 0. [varid0]
canu-2.2/src/overlapAlign/overlapAlign-globalData.H:85:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:67:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable b_iid [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeAlignments.C:122:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeAlignments.C:228:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeAlignments.C:347:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeAlignments.C:379:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeAlignments.C:405:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_EVALUE [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeAlignments.C:469:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:199:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EDLIB_EDOP_DELETE [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:350:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EDLIB_EDOP_DELETE [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:432:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:546:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapAlign/overlapAlign-globalData.H:21:5: performance: Variable 'clrBgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-globalData.H:22:5: performance: Variable 'clrEnd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-globalData.H:24:5: performance: Variable 'rawLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-globalData.H:25:5: performance: Variable 'trimmedLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-globalData.H:49:5: performance: Variable 'numThreads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-threadData.H:21:5: performance: Variable 'threadID' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-threadData.H:23:5: performance: Variable 'bSeqsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-threadData.H:24:5: performance: Variable 'bSeqsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:32:5: performance: Variable '_verboseTrim' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:33:5: performance: Variable '_verboseAlign' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:38:5: performance: Variable '_minLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:39:5: performance: Variable '_maxEdge' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:41:5: performance: Variable '_overlapSlop' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:42:5: performance: Variable '_maxRepeatLength' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:44:5: performance: Variable '_wellContainedThreshold' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:52:5: performance: Variable '_overlapsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapAlign/overlapAlign-globalData.H:152:12: warning: Class 'trGlobalData' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/overlapAlign/overlapAlign-globalData.H:152:12: warning: Class 'trGlobalData' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:59:5: warning: Class 'maComputation' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/overlapAlign/overlapAlign-computation.H:59:5: warning: Class 'maComputation' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/overlapAlign/overlapAlign-threadData.H:20:30: style: Parameter 'g' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:564:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:564:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:565:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:565:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:567:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:567:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:568:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:568:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:609:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:609:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:610:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:610:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:612:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:612:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:613:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:613:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:657:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:657:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:658:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:658:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:660:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:660:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:661:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:661:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:702:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:702:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:703:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:703:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:705:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:705:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:706:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:706:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:739:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:739:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:740:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:740:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:742:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:742:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:743:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:743:13: note: Shadow local variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:748:22: style: Local variable 'result' shadows outer variable [shadowVariable]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:543:21: note: Shadowed variable
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:748:22: note: Shadow local variable
canu-2.2/src/overlapAlign/alignStats.H:81:33: error: There is an unknown macro here somewhere. Configuration is required. If F_U64P is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapAlign/computeOverlapAlignment.C:57:54: style: Parameter 'aend' can be declared as reference to const [constParameterReference]
canu-2.2/src/overlapBasedTrimming/clearRangeFile.H:44:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapBasedTrimming/clearRangeFile.H:129:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32 [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapBasedTrimming/clearRangeFile.H:48:5: warning: Class 'clearRangeFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/overlapBasedTrimming/clearRangeFile.H:48:5: warning: Class 'clearRangeFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/overlapBasedTrimming/clearRangeFile.H:123:34: style: Parameter 'source' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapBasedTrimming/mergeRanges.C:66:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapBasedTrimming/splitReads-subReads.C:286:52: error: There is an unknown macro here somewhere. Configuration is required. If F_S32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapBasedTrimming/splitReads-trimBad.C:109:40: debug: Function::addArguments found argument 'seq' with varid 0. [varid0]
canu-2.2/src/overlapBasedTrimming/splitReads-trimBad.C:123:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapBasedTrimming/splitReads-workUnit.C:92:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapBasedTrimming/splitReads.H:90:5: performance: Variable 'id' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapBasedTrimming/splitReads.H:91:5: performance: Variable 'type' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapBasedTrimming/splitReads.H:92:5: performance: Variable 'bgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapBasedTrimming/splitReads.H:93:5: performance: Variable 'end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapBasedTrimming/splitReads.H:97:5: performance: Variable 'id' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapBasedTrimming/splitReads.H:98:5: performance: Variable 'type' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapBasedTrimming/splitReads.H:99:5: performance: Variable 'bgn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapBasedTrimming/splitReads.H:100:5: performance: Variable 'end' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapBasedTrimming/splitReads.H:124:3: style: Class 'workUnit' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/overlapBasedTrimming/splitReads.C:205:41: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapBasedTrimming/trimReads-bestEdge.C:48:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable a_iid [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapBasedTrimming/trimReads-largestCovered.C:28:30: debug: Function::addArguments found argument 'ibgn' with varid 0. [varid0]
canu-2.2/src/overlapBasedTrimming/trimReads-largestCovered.C:42:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable a_iid [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapBasedTrimming/trimReads-bestEdge.C:39:23: style:inconclusive: Function 'bestEdge' argument 10 names different: declaration 'errorRate' definition 'errorValue'. [funcArgNamesDifferent]
canu-2.2/src/overlapBasedTrimming/trimReads.H:68:23: note: Function 'bestEdge' argument 10 names different: declaration 'errorRate' definition 'errorValue'.
canu-2.2/src/overlapBasedTrimming/trimReads-bestEdge.C:39:23: note: Function 'bestEdge' argument 10 names different: declaration 'errorRate' definition 'errorValue'.
canu-2.2/src/overlapBasedTrimming/trimReads.C:246:41: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapErrorAdjustment/computeDiff.H:41:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable int32 [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/computeDiff.C:65:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable int32 [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapCheck/overlapCheck.C:148:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapCheck/overlapCheck.C:246:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapCheck/overlapCheck.C:330:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapCheck/overlapCheck.C:478:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/computeDiff.C:50:25: style: Condition 'i<-prefix_len' is always false [knownConditionTrueFalse]
canu-2.2/src/overlapErrorAdjustment/computeDiff.C:153:29: style: Parameter 'deltas' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/correctOverlaps.H:213:36: error: There is an unknown macro here somewhere. Configuration is required. If F_SIZE_T is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapCheck/overlapCheck.C:299:5: portability: %lu in format string (no. 3) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapCheck/overlapCheck.C:299:5: portability: %lu in format string (no. 4) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapCheck/overlapCheck.C:300:5: portability: %lu in format string (no. 3) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapCheck/overlapCheck.C:300:5: portability: %lu in format string (no. 4) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapCheck/overlapCheck.C:238:27: error:inconclusive: Pointer addition with NULL pointer. [nullPointerArithmetic]
canu-2.2/src/overlapCheck/overlapCheck.C:215:60: note: Assignment 'Abases=nullptr', assigned value is 0
canu-2.2/src/overlapCheck/overlapCheck.C:238:27: note: Null pointer addition
canu-2.2/src/overlapCheck/overlapCheck.C:239:27: error:inconclusive: Pointer addition with NULL pointer. [nullPointerArithmetic]
canu-2.2/src/overlapCheck/overlapCheck.C:216:60: note: Assignment 'Bbases=nullptr', assigned value is 0
canu-2.2/src/overlapCheck/overlapCheck.C:239:27: note: Null pointer addition
canu-2.2/src/overlapCheck/overlapCheck.C:253:33: error:inconclusive: Pointer addition with NULL pointer. [nullPointerArithmetic]
canu-2.2/src/overlapCheck/overlapCheck.C:215:60: note: Assignment 'Abases=nullptr', assigned value is 0
canu-2.2/src/overlapCheck/overlapCheck.C:253:33: note: Null pointer addition
canu-2.2/src/overlapCheck/overlapCheck.C:254:33: error:inconclusive: Pointer addition with NULL pointer. [nullPointerArithmetic]
canu-2.2/src/overlapCheck/overlapCheck.C:216:60: note: Assignment 'Bbases=nullptr', assigned value is 0
canu-2.2/src/overlapCheck/overlapCheck.C:254:33: note: Null pointer addition
canu-2.2/src/overlapCheck/overlapCheck.C:160:85: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary]
canu-2.2/src/overlapCheck/overlapCheck.C:212:19: style: The scope of the variable 'Ain' can be reduced. [variableScope]
canu-2.2/src/overlapCheck/overlapCheck.C:212:24: style: The scope of the variable 'Aall' can be reduced. [variableScope]
canu-2.2/src/overlapCheck/overlapCheck.C:213:19: style: The scope of the variable 'Bin' can be reduced. [variableScope]
canu-2.2/src/overlapCheck/overlapCheck.C:213:24: style: The scope of the variable 'Ball' can be reduced. [variableScope]
canu-2.2/src/overlapCheck/overlapCheck.C:428:24: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapCheck/overlapCheck.C:429:24: style: Parameter 'ovfA' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapCheck/overlapCheck.C:429:39: style: Parameter 'ovfB' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapCheck/overlapCheck.C:430:33: style: Parameter 'lookup' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/correctionOutput.H:70:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/correctionOutput.H:88:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:132:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:264:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable int32 [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:284:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors-Dump.C:37:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:64:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:83:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/correctionOutput.H:96:9: warning: Member variable 'Correction_Output_t::keep_left' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapErrorAdjustment/correctionOutput.H:97:9: warning: Member variable 'Correction_Output_t::keep_right' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapErrorAdjustment/correctionOutput.H:98:17: warning: Member variable 'Correction_Output_t::type' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:169:17: warning: Member variable 'Vote_t::vote_val' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:312:17: warning: Member variable 'Thread_Work_Area_t::rev_seq' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:315:17: warning: Member variable 'Thread_Work_Area_t::globalvote' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:333:3: warning: Member variable 'feParameters::Edit_Match_Limit' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:333:3: warning: Member variable 'feParameters::Error_Bound' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:100:6: performance: Variable 'confirmed' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:101:6: performance: Variable 'conf_no_insert' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:102:6: performance: Variable 'deletes' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:103:6: performance: Variable 'a_subst' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:104:6: performance: Variable 'c_subst' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:105:6: performance: Variable 'g_subst' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:106:6: performance: Variable 't_subst' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:107:6: performance: Variable 'no_insert' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:109:6: performance: Variable 'insertion_cnt' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:178:5: performance: Variable 'clear_len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:179:5: performance: Variable 'left_degree' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:180:5: performance: Variable 'right_degree' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:181:5: performance: Variable 'shredded' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:182:5: performance: Variable 'unused' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:196:5: performance: Variable 'a_iid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:197:5: performance: Variable 'b_iid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:198:5: performance: Variable 'a_hang' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:199:5: performance: Variable 'b_hang' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:200:5: performance: Variable 'innie' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:201:5: performance: Variable 'normal' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:230:5: performance: Variable 'readsMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:231:5: performance: Variable 'readsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:234:5: performance: Variable 'basesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:235:5: performance: Variable 'basesLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:337:5: performance: Variable 'bgnID' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:338:5: performance: Variable 'endID' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:343:5: performance: Variable 'readsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:346:5: performance: Variable 'olapsLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors.H:350:5: performance: Variable 'numThreads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/overlapErrorAdjustment/findErrors-Dump.C:73:36: style: C-style pointer casting [cstyleCast]
canu-2.2/src/overlapErrorAdjustment/findErrors-Dump.C:73:25: style: Variable 'C' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/overlapErrorAdjustment/findErrors-Output.C:303:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors-Output.C:108:27: style: Variable 'is_change' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:248:18: style: Local variable 'p' shadows outer variable [shadowVariable]
canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:124:10: note: Shadowed variable
canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:248:18: note: Shadow local variable
canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:103:27: style: Parameter 'a_part' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:104:27: style: Parameter 'b_part' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C:139:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors-Process_Olap.C:90:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors-Process_Olap.C:226:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C:163:26: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/findErrors-Prefix_Edit_Distance.C:164:26: style: Parameter 'T' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/findErrors-Process_Olap.C:31:28: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/findErrors-Process_Olap.C:32:28: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/findErrors-Process_Olap.C:33:28: style: Parameter 'delta' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapErrorAdjustment/findErrors-Read_Frags.C:61:58: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapErrorAdjustment/findErrors-Read_Olaps.C:32:45: error: There is an unknown macro here somewhere. Configuration is required. If F_U64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapErrorAdjustment/findErrors.C:103:53: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapInCore/edalign.C:66:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EDLIB_CIGAR_EXTENDED [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/edalign.C:130:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EDLIB_CIGAR_EXTENDED [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/edalign.C:206:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:45:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:176:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sl [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/edalign.C:157:7: warning: %u in format string (no. 5) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapInCore/edalign.C:157:7: warning: %u in format string (no. 6) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapInCore/edalign.C:157:7: warning: %u in format string (no. 7) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapInCore/edalign.C:157:7: warning: %u in format string (no. 8) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapInCore/edalign.C:157:7: warning: %u in format string (no. 9) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapInCore/edalign.C:157:7: warning: %u in format string (no. 10) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:37:11: style: The scope of the variable 'Normal_Z' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:37:21: style: The scope of the variable 'Mu_Power' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:37:31: style: The scope of the variable 'Factorial' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:37:42: style: The scope of the variable 'Poisson_Coeff' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:38:19: style: The scope of the variable 'P_Power' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:38:28: style: The scope of the variable 'Q_Power' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:38:37: style: The scope of the variable 'X' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:39:14: style: The scope of the variable 'Bin_Coeff' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:39:25: style: The scope of the variable 'Ct' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:104:58: style:inconclusive: Function 'Initialize_Match_Limit' argument 3 names different: declaration 'MAX_ERRORS' definition 'maxErrors'. [funcArgNamesDifferent]
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.H:27:58: note: Function 'Initialize_Match_Limit' argument 3 names different: declaration 'MAX_ERRORS' definition 'maxErrors'.
canu-2.2/src/overlapInCore/liboverlap/Binomial_Bound.C:104:58: note: Function 'Initialize_Match_Limit' argument 3 names different: declaration 'MAX_ERRORS' definition 'maxErrors'.
canu-2.2/src/overlapInCore/liboverlap/Display_Alignment.C:32:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C:82:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:186:11: style: The member function 'prefixEditDistance::pruneAlign_pos' can be static. [functionStatic]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:234:3: style:inconclusive: Technically the member function 'prefixEditDistance::pruneAlign_ml' can be const. [functionConst]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:241:3: style:inconclusive: Technically the member function 'prefixEditDistance::pruneAlign_ML' can be const. [functionConst]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:249:3: style:inconclusive: Technically the member function 'prefixEditDistance::pruneAlign' can be const. [functionConst]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:200:24: style: Redundant initialization for 'allowedErrorRate'. The initialized value is overwritten before it is read. [redundantInitialization]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:192:29: note: allowedErrorRate is initialized
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:200:24: note: allowedErrorRate is overwritten
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:223:7: style: Variable 'allowedErrorRate' is assigned an expression that holds the same value. [redundantAssignment]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:192:29: note: allowedErrorRate is assigned 'maxErate' here.
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.H:223:7: note: Variable 'allowedErrorRate' is assigned an expression that holds the same value.
canu-2.2/src/overlapInCore/liboverlap/Display_Alignment.C:27:26: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/liboverlap/Display_Alignment.C:28:26: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/liboverlap/Display_Alignment.C:29:26: style: Parameter 'delta' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:33:8: style: The scope of the variable 'from' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:33:20: style: The scope of the variable 'max' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:34:11: style: The scope of the variable 'j' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:103:17: style: The scope of the variable 'j' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:94:38: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:95:38: style: Parameter 'T' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:102:24: style: Unused variable: From [unusedVariable]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:102:30: style: Unused variable: Last [unusedVariable]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:102:45: style: Unused variable: Max [unusedVariable]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:103:14: style: Unused variable: i [unusedVariable]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-forward.C:103:20: style: Unused variable: k [unusedVariable]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-extend.C:36:52: style: Parameter 'Match' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:59:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:115:50: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:108:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:108:22: note: Assignment 'F=fopen(N,"r")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:109:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:115:50: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:144:55: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:140:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:140:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:141:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:144:55: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:161:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:157:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:157:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:158:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:161:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:183:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:183:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:184:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:184:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:185:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:185:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:186:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:186:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:187:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:187:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:188:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:188:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:189:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:189:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:190:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:190:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:191:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:191:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:192:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:192:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:193:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:193:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:194:15: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assuming allocation function fails
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:179:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:180:11: note: Assuming condition is false
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:194:15: note: Null pointer dereference
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.C:27:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.C:32:3: warning: Class 'prefixEditDistance' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance.C:32:3: warning: Class 'prefixEditDistance' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:38:8: style: The scope of the variable 'from' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:38:20: style: The scope of the variable 'max' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:39:8: style: The scope of the variable 'j' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:125:14: style: The scope of the variable 'j' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:114:38: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:115:38: style: Parameter 'T' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/overlapConvert.C:30:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ovOverlapAsCoords [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:124:24: style: Unused variable: From [unusedVariable]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:124:30: style: Unused variable: Last [unusedVariable]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:124:45: style: Unused variable: Max [unusedVariable]
canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-reverse.C:125:17: style: Unused variable: k [unusedVariable]
canu-2.2/src/overlapInCore/overlapImport.C:65:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sqRead_raw [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/overlapInCore-Build_Hash_Index.C:303:41: error: There is an unknown macro here somewhere. Configuration is required. If F_S64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapInCore/overlapInCore-Find_Overlaps.C:37:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Next [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/overlapInCore-Find_Overlaps.C:145:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/overlapInCore-Find_Overlaps.C:245:3: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
canu-2.2/src/overlapInCore/overlapInCore.H:198:11: warning: Member variable 'String_Olap_Node::diag_sum' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:200:11: warning: Member variable 'String_Olap_Node::diag_bgn' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:201:11: warning: Member variable 'String_Olap_Node::diag_end' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:202:15: warning: Member variable 'String_Olap_Node::Next' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:203:13: warning: Member variable 'String_Olap_Node::Full' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:204:13: warning: Member variable 'String_Olap_Node::consistent' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:227:20: warning: Member variable 'Work_Area::String_Olap_Space' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:231:19: warning: Member variable 'Work_Area::Match_Node_Space' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:240:13: warning: Member variable 'Work_Area::readStore' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:241:13: warning: Member variable 'Work_Area::readCache' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:243:10: warning: Member variable 'Work_Area::left_end_screened' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:244:10: warning: Member variable 'Work_Area::right_end_screened' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:246:10: warning: Member variable 'Work_Area::status' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:247:10: warning: Member variable 'Work_Area::thread_id' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:256:18: warning: Member variable 'Work_Area::overlaps' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:270:24: warning: Member variable 'Work_Area::editDist' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:273:11: warning: Member variable 'Work_Area::q_diff' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:274:18: warning: Member variable 'Work_Area::distinct_olap' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:319:18: warning: Member variable 'Hash_Bucket::Check' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore.H:320:18: warning: Member variable 'Hash_Bucket::Hits' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/overlapInCore/overlapInCore-Find_Overlaps.C:179:11: style: The scope of the variable 'T' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/overlapInCore-Find_Overlaps.C:177:41: style: Parameter 'S' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/overlapInCore-Find_Overlaps.C:179:11: style: Variable 'T' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/overlapInCore/overlapInCore-Find_Overlaps.C:237:11: style: Variable 'P' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/overlapInCore/overlapImport.C:207:9: style: Variable 'bID' is assigned an expression that holds the same value. [redundantAssignment]
canu-2.2/src/overlapInCore/overlapImport.C:206:13: note: aID is assigned 'bID' here.
canu-2.2/src/overlapInCore/overlapImport.C:207:9: note: Variable 'bID' is assigned an expression that holds the same value.
canu-2.2/src/overlapInCore/overlapInCore-Process_Overlaps.C:45:52: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapInCore/overlapInCore-Output.C:199:43: style:inconclusive: Function 'Output_Partial_Overlap' argument 4 names different: declaration 'p' definition 'olap'. [funcArgNamesDifferent]
canu-2.2/src/overlapInCore/overlapInCore.H:497:44: note: Function 'Output_Partial_Overlap' argument 4 names different: declaration 'p' definition 'olap'.
canu-2.2/src/overlapInCore/overlapInCore-Output.C:199:43: note: Function 'Output_Partial_Overlap' argument 4 names different: declaration 'p' definition 'olap'.
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:210:97: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable int32 [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:368:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:601:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/overlapInCore/overlapInCore.C:228:31: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapInCore/overlapInCorePartition.C:116:29: error: There is an unknown macro here somewhere. Configuration is required. If F_U64P is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapInCore/overlapPair.C:114:33: error: There is an unknown macro here somewhere. Configuration is required. If F_U64P is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapInCore/overlapReadCache.C:174:45: error: There is an unknown macro here somewhere. Configuration is required. If F_U64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/seqrequester/src/seqrequester/generate.H:72:41: error: There is an unknown macro here somewhere. Configuration is required. If F_U64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:563:7: style: C-style pointer casting [cstyleCast]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:564:7: style: C-style pointer casting [cstyleCast]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:369:11: style: The scope of the variable 'Quality' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:370:8: style: The scope of the variable 'Olap_Len' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:373:8: style: The scope of the variable 'Max_Len' can be reduced. [variableScope]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:137:26: style: Variable 'discard' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:262:76: style: Parameter 'WA' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:320:22: style: Parameter 'a' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:561:20: style: Variable 'x' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:561:25: style: Variable 'y' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:378:15: style: Variable 'Done_S_Left' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/overlapInCore/overlapInCore-Process_String_Overlaps.C:378:30: style: Variable 'Done_S_Right' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/seqrequester/src/seqrequester/outAT.C:6:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/seqrequester/src/seqrequester/outGA.C:7:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/seqrequester/src/seqrequester/outAT.C:10:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/seqrequester/src/seqrequester/outGC.C:6:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/seqrequester/src/seqrequester/outGC.C:10:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/seqrequester/src/seqrequester/outGA.C:16:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/seqrequester/src/seqrequester/outGA.C:18:3: warning: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/stores/dumpBlob.C:85:41: error: There is an unknown macro here somewhere. Configuration is required. If F_U64P is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/loadCorrectedReads.C:162:26: error: There is an unknown macro here somewhere. Configuration is required. If F_U64P is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/ovStore.H:71:109: error: There is an unknown macro here somewhere. Configuration is required. If F_U64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/sqRead.H:437:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqRead.H:488:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqStore.H:106:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqStore.H:274:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/loadTrimmedReads.C:75:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/loadTrimmedReads.C:158:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/objectStore.C:38:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable splitPaths [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/objectStore.C:76:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable splitPaths [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/objectStore.C:229:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/objectStore.C:222:12: style: Condition 'path==NULL' is always true [knownConditionTrueFalse]
canu-2.2/src/stores/objectStore.C:220:18: note: Assignment 'path=NULL', assigned value is 0
canu-2.2/src/stores/objectStore.C:222:12: note: Condition 'path==NULL' is always true
canu-2.2/src/stores/objectStore.C:265:15: style: Obsolescent function 'vfork' called. It is recommended to use 'fork' instead. [prohibitedvforkCalled]
canu-2.2/src/stores/objectStore.C:159:15: style: Redundant initialization for 'storename'. The initialized value is overwritten before it is read. [redundantInitialization]
canu-2.2/src/stores/objectStore.C:82:20: note: storename is initialized
canu-2.2/src/stores/objectStore.C:159:15: note: storename is overwritten
canu-2.2/src/stores/objectStore.C:193:28: style:inconclusive: Function 'fetchFromObjectStore' argument 1 names different: declaration 'filename' definition 'requested'. [funcArgNamesDifferent]
canu-2.2/src/stores/objectStore.H:35:35: note: Function 'fetchFromObjectStore' argument 1 names different: declaration 'filename' definition 'requested'.
canu-2.2/src/stores/objectStore.C:193:28: note: Function 'fetchFromObjectStore' argument 1 names different: declaration 'filename' definition 'requested'.
canu-2.2/src/stores/objectStore.C:44:10: style: Variable 'storename' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/objectStore.C:81:10: style: Variable 'basename' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/objectStore.C:82:10: style: Variable 'storename' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/objectStore.C:202:10: style: Variable 'ns' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/objectStore.C:203:10: style: Variable 'pr' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/sqLibrary.H:53:1: style: The class 'sqLibrary' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
canu-2.2/src/stores/sqLibrary.H:116:19: warning: Member variable 'sqLibrary::_libraryName' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/stores/sqLibrary.H:119:19: warning: Member variable 'sqLibrary::_techType' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/stores/sqLibrary.H:127:19: warning: Member variable 'sqLibrary::_U_keys' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/stores/sqLibrary.H:128:19: warning: Member variable 'sqLibrary::_U_values' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/stores/sqLibrary.H:132:19: warning: Member variable 'sqLibrary::_U_kvData' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/stores/sqLibrary.H:107:20: style:inconclusive: Technically the member function 'sqLibrary::sqLibrary_libraryName' can be const. [functionConst]
canu-2.2/src/stores/sqLibrary.H:108:20: style:inconclusive: Technically the member function 'sqLibrary::sqLibrary_libraryID' can be const. [functionConst]
canu-2.2/src/stores/sqLibrary.H:110:20: style:inconclusive: Technically the member function 'sqLibrary::sqLibrary_techType' can be const. [functionConst]
canu-2.2/src/stores/sqLibrary.H:111:20: style:inconclusive: Technically the member function 'sqLibrary::sqLibrary_techTypeString' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:183:15: style:inconclusive: Technically the member function 'sqReadSeq::sqReadSeq_length' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:189:15: style:inconclusive: Technically the member function 'sqReadSeq::sqReadSeq_valid' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:190:15: style:inconclusive: Technically the member function 'sqReadSeq::sqReadSeq_trimmed' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:192:15: style:inconclusive: Technically the member function 'sqReadSeq::sqReadSeq_ignoreU' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:193:15: style:inconclusive: Technically the member function 'sqReadSeq::sqReadSeq_ignoreT' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:298:15: style:inconclusive: Technically the member function 'sqReadMeta::sqRead_readID' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:299:15: style:inconclusive: Technically the member function 'sqReadMeta::sqRead_libraryID' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:301:15: style:inconclusive: Technically the member function 'sqReadMeta::sqRead_assignment' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:302:15: style:inconclusive: Technically the member function 'sqReadMeta::sqRead_assignmentScore' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:304:15: style:inconclusive: Technically the member function 'sqReadMeta::sqRead_mSegm' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:305:15: style:inconclusive: Technically the member function 'sqReadMeta::sqRead_mByte' can be const. [functionConst]
canu-2.2/src/stores/sqStore.H:123:13: style:inconclusive: Technically the member function 'sqStoreInfo::sqInfo_lastLibraryID' can be const. [functionConst]
canu-2.2/src/stores/sqStore.H:124:13: style:inconclusive: Technically the member function 'sqStoreInfo::sqInfo_lastReadID' can be const. [functionConst]
canu-2.2/src/stores/sqStore.H:133:13: style:inconclusive: Technically the member function 'sqStoreInfo::sqInfo_numReads' can be const. [functionConst]
canu-2.2/src/stores/sqStore.H:134:13: style:inconclusive: Technically the member function 'sqStoreInfo::sqInfo_numBases' can be const. [functionConst]
canu-2.2/src/stores/sqStore.H:229:16: style:inconclusive: Technically the member function 'sqStore::sqStore_path' can be const. [functionConst]
canu-2.2/src/stores/sqRead.H:536:3: style: Class 'sqReadDataWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/stores/sqStore.H:203:3: style: Class 'sqStoreBlobReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/stores/sqStore.H:223:3: style: Class 'sqStore' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/stores/sqRead.H:479:17: style: Variable 'isTrm' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/stores/sqStore.H:265:17: style: Variable 'isTrm' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/stores/ovStoreHistogram.C:337:65: error: There is an unknown macro here somewhere. Configuration is required. If F_U64P is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/sqReadData.C:39:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqReadData.C:52:26: style: C-style pointer casting [cstyleCast]
canu-2.2/src/stores/sqReadData.C:53:26: style: C-style pointer casting [cstyleCast]
canu-2.2/src/stores/sqReadData.C:52:13: style: Variable 'chunkName' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/sqReadDataWriter.C:70:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqReadDataWriter.C:90:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqStore.C:38:44: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/sqStoreBlob.C:30:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqStoreBlob.C:81:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqStoreBlob.C:110:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable copyData [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/sqStoreBlob.C:40:3: warning: Class 'sqStoreBlobWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/stores/sqStoreBlob.C:40:3: warning: Class 'sqStoreBlobWriter' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/stores/sqStoreBlob.C:96:12: warning: Class 'sqStoreBlobReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/stores/sqStoreBlob.C:96:12: warning: Class 'sqStoreBlobReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/stores/sqStoreBlob.C:56:48: style:inconclusive: Function 'writeData' argument 1 names different: declaration 'readData' definition 'rdw'. [funcArgNamesDifferent]
canu-2.2/src/stores/sqStore.H:187:46: note: Function 'writeData' argument 1 names different: declaration 'readData' definition 'rdw'.
canu-2.2/src/stores/sqStoreBlob.C:56:48: note: Function 'writeData' argument 1 names different: declaration 'readData' definition 'rdw'.
canu-2.2/src/stores/sqReadDataWriter.C:115:12: style: Variable 'null' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/sqReadDataWriter.C:115:12: style: Variable 'null' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/stores/sqStoreConstructor.C:338:49: error: There is an unknown macro here somewhere. Configuration is required. If F_U32P is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/sqStoreCreate.C:88:29: error: There is an unknown macro here somewhere. Configuration is required. If F_U32P is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/sqStoreDumpFASTQ.C:330:77: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/sqStoreDumpMetaData.C:53:27: error: There is an unknown macro here somewhere. Configuration is required. If F_U32P is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/sqStoreInfo.C:57:67: error: There is an unknown macro here somewhere. Configuration is required. If F_X64P is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/tgStore.C:383:81: error: There is an unknown macro here somewhere. Configuration is required. If F_S32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/tgStoreCompress.C:42:66: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/tgStoreDump.C:207:26: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/tgTig.H:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgTig.H:267:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable copyData [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgStoreLoad.C:30:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgStoreLoad.C:65:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgStoreLoad.C:84:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgStoreLoad.C:108:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgStoreLoad.C:186:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgTig.C:449:21: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/stores/tgTigDisplay.C:52:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgTig.H:81:24: style:inconclusive: Technically the member function 'tgPosition::anchor' can be const. [functionConst]
canu-2.2/src/stores/tgTig.H:82:24: style:inconclusive: Technically the member function 'tgPosition::aHang' can be const. [functionConst]
canu-2.2/src/stores/tgTig.H:83:24: style:inconclusive: Technically the member function 'tgPosition::bHang' can be const. [functionConst]
canu-2.2/src/stores/tgTig.H:103:24: style:inconclusive: Technically the member function 'tgPosition::deltaOffset' can be const. [functionConst]
canu-2.2/src/stores/tgTig.H:104:24: style:inconclusive: Technically the member function 'tgPosition::deltaLength' can be const. [functionConst]
canu-2.2/src/stores/tgTig.H:246:18: style:inconclusive: Technically the member function 'tgTig::tigID' can be const. [functionConst]
canu-2.2/src/stores/tgTig.H:248:18: style:inconclusive: Technically the member function 'tgTig::consensusExists' can be const. [functionConst]
canu-2.2/src/stores/tgTig.H:253:18: style:inconclusive: Technically the member function 'tgTig::length' can be const. [functionConst]
canu-2.2/src/stores/tgTig.H:258:18: style:inconclusive: Technically the member function 'tgTig::numberOfChildren' can be const. [functionConst]
canu-2.2/src/stores/tgStore.H:82:18: style:inconclusive: Technically the member function 'tgStore::numTigs' can be const. [functionConst]
canu-2.2/src/stores/tgStore.H:45:3: style: Class 'tgStore' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/stores/tgStoreLoad.C:139:30: style: The scope of the variable 'tigInputsFile' can be reduced. [variableScope]
canu-2.2/src/stores/tgTig.H:107:41: style: Argument 'anchor' shadows outer function [shadowFunction]
canu-2.2/src/stores/tgTig.H:81:24: note: Shadowed function
canu-2.2/src/stores/tgTig.H:107:41: note: Shadow argument
canu-2.2/src/stores/tgTig.H:114:46: style: Argument 'anchor' shadows outer function [shadowFunction]
canu-2.2/src/stores/tgTig.H:81:24: note: Shadowed function
canu-2.2/src/stores/tgTig.H:114:46: note: Shadow argument
canu-2.2/src/stores/tgTig.H:114:87: style: Argument 'bgn' shadows outer function [shadowFunction]
canu-2.2/src/stores/tgTig.H:90:24: note: Shadowed function
canu-2.2/src/stores/tgTig.H:114:87: note: Shadow argument
canu-2.2/src/stores/tgTig.H:114:99: style: Argument 'end' shadows outer function [shadowFunction]
canu-2.2/src/stores/tgTig.H:91:24: note: Shadowed function
canu-2.2/src/stores/tgTig.H:114:99: note: Shadow argument
canu-2.2/src/stores/tgTig.H:144:40: style: Argument 'min' shadows outer function [shadowFunction]
canu-2.2/src/stores/tgTig.H:93:24: note: Shadowed function
canu-2.2/src/stores/tgTig.H:144:40: note: Shadow argument
canu-2.2/src/stores/tgTig.H:144:51: style: Argument 'max' shadows outer function [shadowFunction]
canu-2.2/src/stores/tgTig.H:94:24: note: Shadowed function
canu-2.2/src/stores/tgTig.H:144:51: note: Shadow argument
canu-2.2/src/stores/tgTigDisplay.C:27:10: style: Variable 'seqName' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/tgTigMultiAlignDisplay.C:184:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/stores/tgTigSizeAnalysis.C:94:31: error: There is an unknown macro here somewhere. Configuration is required. If F_U64P is a macro then please configure it. [unknownMacro]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:45:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:37:11: style: The scope of the variable 'Normal_Z' can be reduced. [variableScope]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:37:21: style: The scope of the variable 'Mu_Power' can be reduced. [variableScope]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:37:31: style: The scope of the variable 'Factorial' can be reduced. [variableScope]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:37:42: style: The scope of the variable 'Poisson_Coeff' can be reduced. [variableScope]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:38:19: style: The scope of the variable 'P_Power' can be reduced. [variableScope]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:38:28: style: The scope of the variable 'Q_Power' can be reduced. [variableScope]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:38:37: style: The scope of the variable 'X' can be reduced. [variableScope]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:39:14: style: The scope of the variable 'Bin_Coeff' can be reduced. [variableScope]
canu-2.2/src/utgcns/libNDalign/Binomial_Bound.C:39:25: style: The scope of the variable 'Ct' can be reduced. [variableScope]
canu-2.2/src/stores/tgTigMultiAlignDisplay.C:114:5: performance: Variable 'lastColumn' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/stores/tgTigMultiAlignDisplay.C:67:3: warning: Class 'alignRowEntry' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/stores/tgTigMultiAlignDisplay.C:67:3: warning: Class 'alignRowEntry' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:89:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:143:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C:82:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:131:10: style: The member function 'NDalgorithm::isMatch' can be static. [functionStatic]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:159:10: style:inconclusive: Technically the member function 'NDalgorithm::mismatchScore' can be const. [functionConst]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:170:10: style:inconclusive: Technically the member function 'NDalgorithm::isFreeGap' can be const. [functionConst]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:184:19: style:inconclusive: Technically the member function 'NDalgorithm::score' can be const. [functionConst]
canu-2.2/src/stores/tgTigMultiAlignDisplay.C:76:10: style: Variable 'b' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/tgTigMultiAlignDisplay.C:191:14: style: Variable 'row' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/stores/tgTigMultiAlignDisplay.C:191:14: style: Variable 'row' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-extend.C:36:45: style: Parameter 'Match' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-extend.C:70:28: style: Variable 'invertLeftDeltas' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-extend.C:71:28: style: Variable 'invertRightDeltas' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:219:88: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:220:88: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:99:42: style:inconclusive: Function 'forward' argument 2 names different: declaration 'm' definition 'Alen'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:110:38: note: Function 'forward' argument 2 names different: declaration 'm' definition 'Alen'.
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:99:42: note: Function 'forward' argument 2 names different: declaration 'm' definition 'Alen'.
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:100:42: style:inconclusive: Function 'forward' argument 4 names different: declaration 'n' definition 'Tlen'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:111:38: note: Function 'forward' argument 4 names different: declaration 'n' definition 'Tlen'.
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:100:42: note: Function 'forward' argument 4 names different: declaration 'n' definition 'Tlen'.
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:219:84: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:220:84: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:244:84: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:245:84: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:99:31: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-forward.C:100:31: style: Parameter 'T' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:76:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:62:3: performance: Variable 'ERRORS_FOR_FREE' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:63:3: performance: Variable 'MIN_BRANCH_END_DIST' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:66:3: performance: Variable 'Left_Score' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:67:3: performance: Variable 'Left_Delta_Len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:70:3: performance: Variable 'Right_Score' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:71:3: performance: Variable 'Right_Delta_Len' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:76:3: performance: Variable 'allocated' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:68:3: warning: Class 'NDalgorithm' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.C:68:3: warning: Class 'NDalgorithm' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:220:88: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:221:88: style: Same expression in both branches of ternary operator. [duplicateExpressionTernary]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:96:42: style:inconclusive: Function 'reverse' argument 2 names different: declaration 'm' definition 'Alen'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:120:38: note: Function 'reverse' argument 2 names different: declaration 'm' definition 'Alen'.
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:96:42: note: Function 'reverse' argument 2 names different: declaration 'm' definition 'Alen'.
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:97:42: style:inconclusive: Function 'reverse' argument 4 names different: declaration 'n' definition 'Tlen'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/libNDalign/NDalgorithm.H:121:38: note: Function 'reverse' argument 4 names different: declaration 'n' definition 'Tlen'.
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:97:42: note: Function 'reverse' argument 4 names different: declaration 'n' definition 'Tlen'.
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:220:84: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:221:84: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:244:84: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:245:84: style: Clarify calculation precedence for '+' and '?'. [clarifyCalculation]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:96:31: style: Parameter 'A' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utgcns/libNDalign/NDalgorithm-reverse.C:97:31: style: Parameter 'T' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utgcns/libNDalign/NDalign.C:464:53: error: There is an unknown macro here somewhere. Configuration is required. If F_X64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/utgcns/libNNalign/NNalign.C:46:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNNalign/NNalign.C:27:16: warning: Member variable 'Optimal_Overlap_Data::h_alignA' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/utgcns/libNNalign/NNalign.C:28:16: warning: Member variable 'Optimal_Overlap_Data::h_alignB' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/utgcns/libNNalign/NNalign.C:29:16: warning: Member variable 'Optimal_Overlap_Data::h_trace' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:60:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:65:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:80:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:143:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alignLinker_s [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:59:3: warning: Member variable 'dpActions::actionLength' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:60:5: warning: Class 'dpActions' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:60:5: warning: Class 'dpActions' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:78:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable base [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:101:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable base [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:117:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vertex_index [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:178:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:205:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable visited [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:229:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable base [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:283:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable base [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:330:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable deleted [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:340:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable backbone [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:358:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable base [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:402:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable base [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:438:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable visited [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:521:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable deleted [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:132:29: style: Parameter 'stringA' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:133:29: style: Parameter 'stringB' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:74:13: style: class member 'dpActions::actionLength' is never used. [unusedStructMember]
canu-2.2/src/utgcns/stashContains.C:206:75: error: There is an unknown macro here somewhere. Configuration is required. If F_SIZE_T is a macro then please configure it. [unknownMacro]
canu-2.2/src/utgcns/unitigConsensus.C:135:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:158:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:227:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:283:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:320:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AS_MAX_READLEN [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:665:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:822:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:847:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:961:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:1002:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable doNothing [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:1049:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EDLIB_EDOP_MATCH [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:1105:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/unitigConsensus.C:1336:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.H:120:9: warning: Member variable 'CnsResult::range' has no initializer. [uninitMemberVarNoCtor]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:94:5: performance: Variable '_g' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.H:135:5: style: Class 'AlnGraphBoost' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.H:140:5: style: Class 'AlnGraphBoost' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:132:75: style: Condition 'MAX_OFFSET==0' is always false [knownConditionTrueFalse]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:139:51: style: Condition 'targetBase!='-'' is always true [knownConditionTrueFalse]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:156:75: style: Condition 'MAX_OFFSET==0' is always false [knownConditionTrueFalse]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:163:61: style: Condition 'MAX_OFFSET==0' is always false [knownConditionTrueFalse]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:387:83: style:inconclusive: Function 'consensus' argument 3 names different: declaration 'minLength' definition 'minLen'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.H:180:74: note: Function 'consensus' argument 3 names different: declaration 'minLength' definition 'minLen'.
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:387:83: note: Function 'consensus' argument 3 names different: declaration 'minLength' definition 'minLen'.
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:24: style: Local variable 'ii' shadows outer variable [shadowVariable]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:224:16: note: Shadowed variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:24: note: Shadow local variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:28: style: Local variable 'ie' shadows outer variable [shadowVariable]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:224:20: note: Shadowed variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:28: note: Shadow local variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:257:21: style: Local variable 'n' shadows outer argument [shadowArgument]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:222:42: note: Shadowed argument
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:257:21: note: Shadow local variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:25: style: Local variable 'oi' shadows outer variable [shadowVariable]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:279:17: note: Shadowed variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:25: note: Shadow local variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:29: style: Local variable 'oe' shadows outer variable [shadowVariable]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:279:21: note: Shadowed variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:29: note: Shadow local variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:310:21: style: Local variable 'n' shadows outer argument [shadowArgument]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:277:43: note: Shadowed argument
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:310:21: note: Shadow local variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:25: style: Local variable 'oi' shadows outer variable [shadowVariable]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:458:21: note: Shadowed variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:25: note: Shadow local variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:29: style: Local variable 'oe' shadows outer variable [shadowVariable]
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:458:25: note: Shadowed variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:29: note: Shadow local variable
canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:116:42: style: Parameter 'aln' can be declared as reference to const [constParameterReference]
canu-2.2/src/utgcns/utgcns.C:363:51: error: There is an unknown macro here somewhere. Configuration is required. If F_U32 is a macro then please configure it. [unknownMacro]
canu-2.2/src/utgcns/unitigConsensus.H:39:5: performance: Variable '_iid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/unitigConsensus.H:43:5: performance: Variable '_length' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/unitigConsensus.C:38:3: performance: Variable '_iid' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/unitigConsensus.C:39:3: performance: Variable '_length' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/unitigConsensus.C:85:3: performance: Variable '_numReads' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/unitigConsensus.C:87:3: performance: Variable '_sequencesMax' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/unitigConsensus.C:88:3: performance: Variable '_sequencesLen' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/unitigConsensus.C:94:3: performance: Variable '_minOverlap' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
canu-2.2/src/utgcns/unitigConsensus.H:57:15: style:inconclusive: Technically the member function 'abSequence::seqIdent' can be const. [functionConst]
canu-2.2/src/utgcns/unitigConsensus.H:59:15: style:inconclusive: Technically the member function 'abSequence::isForward' can be const. [functionConst]
canu-2.2/src/utgcns/unitigConsensus.H:61:15: style:inconclusive: Technically the member function 'abSequence::length' can be const. [functionConst]
canu-2.2/src/utgcns/unitigConsensus.H:62:15: style:inconclusive: Technically the member function 'abSequence::getBase' can be const. [functionConst]
canu-2.2/src/utgcns/unitigConsensus.C:1310:18: style: The member function 'unitigConsensus::findRawAlignments' can be static. [functionStatic]
canu-2.2/src/utgcns/unitigConsensus.H:120:10: note: The member function 'unitigConsensus::findRawAlignments' can be static.
canu-2.2/src/utgcns/unitigConsensus.C:1310:18: note: The member function 'unitigConsensus::findRawAlignments' can be static.
canu-2.2/src/utgcns/unitigConsensus.H:124:10: style:inconclusive: Technically the member function 'unitigConsensus::showProgress' can be const. [functionConst]
canu-2.2/src/utgcns/unitigConsensus.H:125:10: style:inconclusive: Technically the member function 'unitigConsensus::showAlgorithm' can be const. [functionConst]
canu-2.2/src/utgcns/unitigConsensus.H:126:10: style:inconclusive: Technically the member function 'unitigConsensus::showPlacement' can be const. [functionConst]
canu-2.2/src/utgcns/unitigConsensus.H:127:10: style:inconclusive: Technically the member function 'unitigConsensus::showAlignments' can be const. [functionConst]
canu-2.2/src/utgcns/unitigConsensus.C:42:3: warning: Class 'abSequence' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utgcns/unitigConsensus.C:42:3: warning: Class 'abSequence' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utgcns/unitigConsensus.C:103:12: warning: Class 'unitigConsensus' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utgcns/unitigConsensus.C:103:12: warning: Class 'unitigConsensus' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utgcns/unitigConsensus.C:1451:96: style: Condition 'headTest' is always false [knownConditionTrueFalse]
canu-2.2/src/utgcns/unitigConsensus.C:1449:19: note: Assuming that condition 'headTest==false' is not redundant
canu-2.2/src/utgcns/unitigConsensus.C:1451:96: note: Condition 'headTest' is always false
canu-2.2/src/utgcns/unitigConsensus.C:1358:7: warning: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint]
canu-2.2/src/utgcns/unitigConsensus.C:333:5: warning:inconclusive: Possible null pointer dereference: tigseq [nullPointer]
canu-2.2/src/utgcns/unitigConsensus.C:322:25: note: Assignment 'tigseq=NULL', assigned value is 0
canu-2.2/src/utgcns/unitigConsensus.C:333:5: note: Null pointer dereference
canu-2.2/src/utgcns/unitigConsensus.C:335:3: warning:inconclusive: Possible null pointer dereference: tigseq [nullPointer]
canu-2.2/src/utgcns/unitigConsensus.C:322:25: note: Assignment 'tigseq=NULL', assigned value is 0
canu-2.2/src/utgcns/unitigConsensus.C:335:3: note: Null pointer dereference
canu-2.2/src/utgcns/unitigConsensus.C:815:66: style:inconclusive: Function 'initializeGenerate' argument 1 names different: declaration 'tig' definition 'tig_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:105:58: note: Function 'initializeGenerate' argument 1 names different: declaration 'tig' definition 'tig_'.
canu-2.2/src/utgcns/unitigConsensus.C:815:66: note: Function 'initializeGenerate' argument 1 names different: declaration 'tig' definition 'tig_'.
canu-2.2/src/utgcns/unitigConsensus.C:816:66: style:inconclusive: Function 'initializeGenerate' argument 2 names different: declaration 'reads' definition 'reads_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:106:58: note: Function 'initializeGenerate' argument 2 names different: declaration 'reads' definition 'reads_'.
canu-2.2/src/utgcns/unitigConsensus.C:816:66: note: Function 'initializeGenerate' argument 2 names different: declaration 'reads' definition 'reads_'.
canu-2.2/src/utgcns/unitigConsensus.C:834:61: style:inconclusive: Function 'generatePBDAG' argument 1 names different: declaration 'tig' definition 'tig_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:109:53: note: Function 'generatePBDAG' argument 1 names different: declaration 'tig' definition 'tig_'.
canu-2.2/src/utgcns/unitigConsensus.C:834:61: note: Function 'generatePBDAG' argument 1 names different: declaration 'tig' definition 'tig_'.
canu-2.2/src/utgcns/unitigConsensus.C:835:61: style:inconclusive: Function 'generatePBDAG' argument 2 names different: declaration 'aligner' definition 'aligner_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:110:53: note: Function 'generatePBDAG' argument 2 names different: declaration 'aligner' definition 'aligner_'.
canu-2.2/src/utgcns/unitigConsensus.C:835:61: note: Function 'generatePBDAG' argument 2 names different: declaration 'aligner' definition 'aligner_'.
canu-2.2/src/utgcns/unitigConsensus.C:836:61: style:inconclusive: Function 'generatePBDAG' argument 3 names different: declaration 'reads' definition 'reads_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:111:53: note: Function 'generatePBDAG' argument 3 names different: declaration 'reads' definition 'reads_'.
canu-2.2/src/utgcns/unitigConsensus.C:836:61: note: Function 'generatePBDAG' argument 3 names different: declaration 'reads' definition 'reads_'.
canu-2.2/src/utgcns/unitigConsensus.C:948:61: style:inconclusive: Function 'generateQuick' argument 1 names different: declaration 'tig' definition 'tig_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:113:53: note: Function 'generateQuick' argument 1 names different: declaration 'tig' definition 'tig_'.
canu-2.2/src/utgcns/unitigConsensus.C:948:61: note: Function 'generateQuick' argument 1 names different: declaration 'tig' definition 'tig_'.
canu-2.2/src/utgcns/unitigConsensus.C:949:61: style:inconclusive: Function 'generateQuick' argument 2 names different: declaration 'reads' definition 'reads_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:114:53: note: Function 'generateQuick' argument 2 names different: declaration 'reads' definition 'reads_'.
canu-2.2/src/utgcns/unitigConsensus.C:949:61: note: Function 'generateQuick' argument 2 names different: declaration 'reads' definition 'reads_'.
canu-2.2/src/utgcns/unitigConsensus.C:988:65: style:inconclusive: Function 'generateSingleton' argument 1 names different: declaration 'tig' definition 'tig_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:116:57: note: Function 'generateSingleton' argument 1 names different: declaration 'tig' definition 'tig_'.
canu-2.2/src/utgcns/unitigConsensus.C:988:65: note: Function 'generateSingleton' argument 1 names different: declaration 'tig' definition 'tig_'.
canu-2.2/src/utgcns/unitigConsensus.C:989:65: style:inconclusive: Function 'generateSingleton' argument 2 names different: declaration 'reads' definition 'reads_'. [funcArgNamesDifferent]
canu-2.2/src/utgcns/unitigConsensus.H:117:57: note: Function 'generateSingleton' argument 2 names different: declaration 'reads' definition 'reads_'.
canu-2.2/src/utgcns/unitigConsensus.C:989:65: note: Function 'generateSingleton' argument 2 names different: declaration 'reads' definition 'reads_'.
canu-2.2/src/utgcns/unitigConsensus.C:36:32: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utgcns/unitigConsensus.C:999:16: style: Variable 'fragment' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utgcns/unitigConsensus.C:423:22: style: Variable 'aligned' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utgcns/unitigConsensus.C:657:26: style: Variable 'alignedErrRate' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/cigar_template.c:58:33: error: There is an unknown macro here somewhere. Configuration is required. If CONCAT is a macro then please configure it. [unknownMacro]
canu-2.2/src/utility/src/parasail/memory.c:467:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/memory.c:491:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/memory.c:578:5: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/memory.c:577:22: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/memory.c:577:9: note: Assignment 'r=(char*)malloc(sizeof(char)*(length+1))', assigned value is 0
canu-2.2/src/utility/src/parasail/memory.c:578:5: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/memory.c:580:9: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/memory.c:577:22: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/memory.c:577:9: note: Assignment 'r=(char*)malloc(sizeof(char)*(length+1))', assigned value is 0
canu-2.2/src/utility/src/parasail/memory.c:580:9: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/memory.c:594:9: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/memory.c:592:26: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/memory.c:592:9: note: Assignment 'r=(uint32_t*)malloc(sizeof(uint32_t)*(length))', assigned value is 0
canu-2.2/src/utility/src/parasail/memory.c:594:9: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/memory_avx2.c:17:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m256i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/memory_avx2.c:32:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:33:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:35:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:66:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:67:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:69:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:100:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:101:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:103:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:134:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:135:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:137:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:183:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:184:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:186:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:227:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:228:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:230:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:271:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:272:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:274:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:315:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:316:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_avx2.c:318:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:17:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/memory_sse.c:32:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:33:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:35:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:66:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:67:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:69:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:100:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:101:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:103:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:134:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:135:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:137:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:183:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:184:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:186:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:227:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:228:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:230:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:271:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:272:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:274:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:315:15: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:316:15: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/memory_sse.c:318:20: style: Variable 'segNum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/cigar.c:86:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/cigar.c:132:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/cigar_template.c:171:26: style: Condition 'NULL!=alphabet_aliases' is always true [knownConditionTrueFalse]
canu-2.2/src/utility/src/parasail/cigar.c:139:13: error: Common realloc mistake: 'ret' nulled but not freed upon failure [memleakOnRealloc]
canu-2.2/src/utility/src/parasail/cigar.c:79:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar.c:78:17: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar.c:78:17: note: Assignment 'ret=malloc(sizeof(struct parasail_cigar_t))', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar.c:79:5: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar.c:80:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar.c:78:17: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar.c:78:17: note: Assignment 'ret=malloc(sizeof(struct parasail_cigar_t))', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar.c:80:5: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar.c:91:9: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar.c:78:17: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar.c:78:17: note: Assignment 'ret=malloc(sizeof(struct parasail_cigar_t))', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar.c:85:15: note: Assuming condition is false
canu-2.2/src/utility/src/parasail/cigar.c:91:9: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar.c:92:21: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar.c:78:17: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar.c:78:17: note: Assignment 'ret=malloc(sizeof(struct parasail_cigar_t))', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar.c:85:15: note: Assuming condition is false
canu-2.2/src/utility/src/parasail/cigar.c:92:21: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar.c:124:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar.c:123:17: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar.c:123:17: note: Assignment 'ret=malloc(size+1)', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar.c:124:5: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar_template.c:116:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar_template.c:71:37: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar_template.c:71:37: note: Assignment 'cigar=malloc(sizeof(struct parasail_cigar_t))', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar_template.c:116:5: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar_template.c:117:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar_template.c:71:37: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar_template.c:71:37: note: Assignment 'cigar=malloc(sizeof(struct parasail_cigar_t))', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar_template.c:117:5: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar_template.c:118:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar_template.c:71:37: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar_template.c:71:37: note: Assignment 'cigar=malloc(sizeof(struct parasail_cigar_t))', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar_template.c:118:5: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar_template.c:119:5: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
canu-2.2/src/utility/src/parasail/cigar_template.c:71:37: note: Assuming allocation function fails
canu-2.2/src/utility/src/parasail/cigar_template.c:71:37: note: Assignment 'cigar=malloc(sizeof(struct parasail_cigar_t))', assigned value is 0
canu-2.2/src/utility/src/parasail/cigar_template.c:119:5: note: Null pointer dereference
canu-2.2/src/utility/src/parasail/cigar_template.c:108:16: style: Local variable 'i' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/parasail/cigar_template.c:77:13: note: Shadowed variable
canu-2.2/src/utility/src/parasail/cigar_template.c:108:16: note: Shadow local variable
canu-2.2/src/utility/src/parasail/cigar_template.c:172:28: style: Local variable 'i' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/parasail/cigar_template.c:77:13: note: Shadowed variable
canu-2.2/src/utility/src/parasail/cigar_template.c:172:28: note: Shadow local variable
canu-2.2/src/utility/src/parasail/cigar.c:113:47: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/parasail/cigar_template.c:80:8: style: Variable 'HT' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/parasail/cigar.c:66:24: style: Variable 'sscanf_retcode' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/sg.c:185:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARASAIL_FLAG_BITS_INT [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg.c:32:37: style:inconclusive: Function 'parasail_sg_flags' argument 1 names different: declaration 's1' definition '_s1'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/parasail/parasail.h:970:37: note: Function 'parasail_sg_flags' argument 1 names different: declaration 's1' definition '_s1'.
canu-2.2/src/utility/src/parasail/sg.c:32:37: note: Function 'parasail_sg_flags' argument 1 names different: declaration 's1' definition '_s1'.
canu-2.2/src/utility/src/parasail/sg.c:33:37: style:inconclusive: Function 'parasail_sg_flags' argument 3 names different: declaration 's2' definition '_s2'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/parasail/parasail.h:971:37: note: Function 'parasail_sg_flags' argument 3 names different: declaration 's2' definition '_s2'.
canu-2.2/src/utility/src/parasail/sg.c:33:37: note: Function 'parasail_sg_flags' argument 3 names different: declaration 's2' definition '_s2'.
canu-2.2/src/utility/src/parasail/sg_trace_striped_avx2_256_16.c:119:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m256i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg_trace.c:170:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARASAIL_FLAG_BITS_INT [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_avx2_256_16.c:253:19: warning: Uninitialized variable: vF_ext [uninitvar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_avx2_256_16.c:195:20: note: Assuming condition is false
canu-2.2/src/utility/src/parasail/sg_trace_striped_avx2_256_16.c:253:19: note: Uninitialized variable: vF_ext
canu-2.2/src/utility/src/parasail/sg_trace.c:25:37: style:inconclusive: Function 'parasail_sg_flags_trace' argument 1 names different: declaration 's1' definition '_s1'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/parasail/parasail.h:991:37: note: Function 'parasail_sg_flags_trace' argument 1 names different: declaration 's1' definition '_s1'.
canu-2.2/src/utility/src/parasail/sg_trace.c:25:37: note: Function 'parasail_sg_flags_trace' argument 1 names different: declaration 's1' definition '_s1'.
canu-2.2/src/utility/src/parasail/sg_trace.c:26:37: style:inconclusive: Function 'parasail_sg_flags_trace' argument 3 names different: declaration 's2' definition '_s2'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/parasail/parasail.h:992:37: note: Function 'parasail_sg_flags_trace' argument 3 names different: declaration 's2' definition '_s2'.
canu-2.2/src/utility/src/parasail/sg_trace.c:26:37: note: Function 'parasail_sg_flags_trace' argument 3 names different: declaration 's2' definition '_s2'.
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_16.c:106:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_16.c:240:19: warning: Uninitialized variable: vF_ext [uninitvar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_16.c:182:20: note: Assuming condition is false
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_16.c:240:19: note: Uninitialized variable: vF_ext
canu-2.2/src/utility/src/parasail/sg_trace_striped_avx2_256_32.c:119:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m256i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_avx2_256_32.c:253:19: warning: Uninitialized variable: vF_ext [uninitvar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_avx2_256_32.c:195:20: note: Assuming condition is false
canu-2.2/src/utility/src/parasail/sg_trace_striped_avx2_256_32.c:253:19: note: Uninitialized variable: vF_ext
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_32.c:126:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_32.c:260:19: warning: Uninitialized variable: vF_ext [uninitvar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_32.c:202:20: note: Assuming condition is false
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_32.c:260:19: note: Uninitialized variable: vF_ext
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse2_128_32.c:54:9: style: Variable 'A.m' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse41_128_16.c:101:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse41_128_16.c:235:19: warning: Uninitialized variable: vF_ext [uninitvar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse41_128_16.c:177:20: note: Assuming condition is false
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse41_128_16.c:235:19: note: Uninitialized variable: vF_ext
canu-2.2/src/utility/src/tests/alignTest-ksw2.C:105:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/alignTest-ksw2.C:50:16: style: The scope of the variable 'fileA' can be reduced. [variableScope]
canu-2.2/src/utility/src/tests/alignTest-ksw2.C:50:24: style: The scope of the variable 'fileB' can be reduced. [variableScope]
canu-2.2/src/utility/src/tests/alignTest-ssw.C:99:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/alignTest-ssw.C:165:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/alignTest-ssw.C:82:14: style: The scope of the variable 'profile' can be reduced. [variableScope]
canu-2.2/src/utility/src/tests/bitsTest.C:165:30: error: There is an unknown macro here somewhere. Configuration is required. If F_U64 is a macro then please configure it. [unknownMacro]
canu-2.2/src/utility/src/tests/fasta-fastq.C:65:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/fasta-fastq.C:153:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/fasta-fastq.C:109:11: style: Local variable 'F' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/tests/fasta-fastq.C:90:11: note: Shadowed variable
canu-2.2/src/utility/src/tests/fasta-fastq.C:109:11: note: Shadow local variable
canu-2.2/src/utility/src/tests/fasta-fastq.C:138:11: style: Local variable 'F' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/tests/fasta-fastq.C:90:11: note: Shadowed variable
canu-2.2/src/utility/src/tests/fasta-fastq.C:138:11: note: Shadow local variable
canu-2.2/src/utility/src/tests/fasta-fastq.C:55:47: style: Parameter 'linelength' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/tests/fasta-fastq.C:90:11: style: Variable 'F' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/tests/fasta-fastq.C:90:11: style: Variable 'F' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/tests/filesTest.C:40:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/intervalListTest.C:40:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/intervalsTest.C:40:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/intervalsTest.C:83:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/intervalsTest.C:113:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint32 [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/intervalsTest.C:217:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/intervalsTest.C:56:7: style: The if condition is the same as the previous if condition [duplicateCondition]
canu-2.2/src/utility/src/tests/intervalsTest.C:50:7: note: First condition
canu-2.2/src/utility/src/tests/intervalsTest.C:56:7: note: Second condition
canu-2.2/src/utility/src/tests/intervalsTest.C:92:7: style: The if condition is the same as the previous if condition [duplicateCondition]
canu-2.2/src/utility/src/tests/intervalsTest.C:82:7: note: First condition
canu-2.2/src/utility/src/tests/intervalsTest.C:92:7: note: Second condition
canu-2.2/src/utility/src/tests/loggingTest.C:66:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/magicNumber.C:26:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/magicNumber.C:42:41: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/utility/src/tests/magicNumber.C:41:12: note: Assuming allocation function fails
canu-2.2/src/utility/src/tests/magicNumber.C:41:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
canu-2.2/src/utility/src/tests/magicNumber.C:42:41: note: Null pointer dereference
canu-2.2/src/utility/src/tests/magicNumber.C:63:10: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/utility/src/tests/magicNumber.C:45:12: note: Assuming allocation function fails
canu-2.2/src/utility/src/tests/magicNumber.C:45:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
canu-2.2/src/utility/src/tests/magicNumber.C:46:29: note: Assuming condition is false
canu-2.2/src/utility/src/tests/magicNumber.C:63:10: note: Null pointer dereference
canu-2.2/src/utility/src/tests/magicNumber.C:79:10: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
canu-2.2/src/utility/src/tests/magicNumber.C:65:12: note: Assuming allocation function fails
canu-2.2/src/utility/src/tests/magicNumber.C:65:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
canu-2.2/src/utility/src/tests/magicNumber.C:66:29: note: Assuming condition is false
canu-2.2/src/utility/src/tests/magicNumber.C:79:10: note: Null pointer dereference
canu-2.2/src/utility/src/tests/magicNumber.C:50:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/tests/magicNumber.C:70:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/tests/mt19937arTest.C:27:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/parasailTest.C:38:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/parasailTest.C:54:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/parasailTest.C:91:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/parasailTest.C:215:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/parasailTest.C:80:23: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/tests/parasailTest.C:80:23: style: Variable 'cigar' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/tests/randTest.C:51:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/randTest.C:73:3: style: Variable 'num' is assigned an expression that holds the same value. [redundantAssignment]
canu-2.2/src/utility/src/tests/randTest.C:49:7: note: num is assigned '(double)1000000' here.
canu-2.2/src/utility/src/tests/randTest.C:73:3: note: Variable 'num' is assigned an expression that holds the same value.
canu-2.2/src/utility/src/tests/readLines.C:30:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/sequenceTest.C:62:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stddevTest.C:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stddevTest.C:82:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stddevTest.C:109:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stddevTest.C:137:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stddevTest.C:177:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stddevTest.C:222:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stddevTest.C:173:14: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/tests/stringsTest.C:28:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stringsTest.C:41:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stringsTest.C:54:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stringsTest.C:67:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stringsTest.C:83:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/stringsTest.C:202:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable splitPaths [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/systemTest.C:32:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/toHexTest.C:113:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/toHexTest.C:85:34: style: The scope of the variable 's1' can be reduced. [variableScope]
canu-2.2/src/utility/src/tests/toHexTest.C:86:34: style: The scope of the variable 's2' can be reduced. [variableScope]
canu-2.2/src/utility/src/tests/toHexTest.C:87:34: style: The scope of the variable 's3' can be reduced. [variableScope]
canu-2.2/src/utility/src/tests/toHexTest.C:88:34: style: The scope of the variable 's4' can be reduced. [variableScope]
canu-2.2/src/utility/src/tests/typesTest.C:60:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/typesTest.C:162:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/tests/typesTest.C:96:22: style: The scope of the variable 'outp' can be reduced. [variableScope]
canu-2.2/src/utility/src/tests/typesTest.C:96:22: style: Variable 'outp' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/arrays.H:86:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TT [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/arrays.H:102:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TT [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/arrays.H:117:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TT [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/arrays.H:141:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TT [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.H:91:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.H:159:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.H:165:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.H:171:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.H:187:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.H:193:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.H:199:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.H:58:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.H:63:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.H:68:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.H:152:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.H:157:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.H:162:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-memoryMapped.H:61:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sequence.H:73:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uint8 [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:55:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:86:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:129:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered-implementation.H:149:20: style: Array index '_bufferPos' is used before limits check. [arrayIndexThenCheck]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:45:12: style:inconclusive: Technically the member function 'ksw2Lib::percentIdentity' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:46:12: style:inconclusive: Technically the member function 'ksw2Lib::errorRate' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:47:12: style:inconclusive: Technically the member function 'ksw2Lib::score' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:49:12: style:inconclusive: Technically the member function 'ksw2Lib::numMatches' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:50:12: style:inconclusive: Technically the member function 'ksw2Lib::numMisMatches' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:51:12: style:inconclusive: Technically the member function 'ksw2Lib::numGaps' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:52:12: style:inconclusive: Technically the member function 'ksw2Lib::alignmentLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:54:12: style:inconclusive: Technically the member function 'ksw2Lib::bgnA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:55:12: style:inconclusive: Technically the member function 'ksw2Lib::endA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:57:12: style:inconclusive: Technically the member function 'ksw2Lib::bgnB' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:58:12: style:inconclusive: Technically the member function 'ksw2Lib::endB' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:60:12: style:inconclusive: Technically the member function 'ksw2Lib::cigarLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:61:12: style:inconclusive: Technically the member function 'ksw2Lib::cigarCode' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:62:12: style:inconclusive: Technically the member function 'ksw2Lib::cigarValu' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-compressed.H:49:9: style:inconclusive: Technically the member function 'compressedFileReader::isCompressed' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-compressed.H:50:9: style:inconclusive: Technically the member function 'compressedFileReader::isNormal' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-compressed.H:75:9: style:inconclusive: Technically the member function 'compressedFileWriter::isCompressed' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-buffered.H:43:24: style:inconclusive: Technically the member function 'readBuffer::eof' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-buffered.H:85:24: style:inconclusive: Technically the member function 'readBuffer::tell' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-buffered.H:87:24: style:inconclusive: Technically the member function 'readBuffer::filename' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-buffered.H:130:24: style:inconclusive: Technically the member function 'writeBuffer::filename' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-buffered.H:131:24: style:inconclusive: Technically the member function 'writeBuffer::tell' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-memoryMapped.H:70:26: style:inconclusive: Technically the member function 'memoryMappedFile::length' can be const. [functionConst]
canu-2.2/src/utility/src/utility/files-memoryMapped.H:71:26: style:inconclusive: Technically the member function 'memoryMappedFile::type' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:109:21: style:inconclusive: Technically the member function 'dnaSeq::ident' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:110:21: style:inconclusive: Technically the member function 'dnaSeq::flags' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:111:21: style:inconclusive: Technically the member function 'dnaSeq::bases' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:112:21: style:inconclusive: Technically the member function 'dnaSeq::quals' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:114:21: style:inconclusive: Technically the member function 'dnaSeq::length' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:126:21: style:inconclusive: Technically the member function 'dnaSeq::wasError' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:127:21: style:inconclusive: Technically the member function 'dnaSeq::wasReSync' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:202:15: style:inconclusive: Technically the member function 'dnaSeqFile::filename' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:203:15: style:inconclusive: Technically the member function 'dnaSeqFile::numberOfSequences' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:210:10: style:inconclusive: Technically the member function 'dnaSeqFile::isFASTA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:211:10: style:inconclusive: Technically the member function 'dnaSeqFile::isFASTQ' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:214:10: style:inconclusive: Technically the member function 'dnaSeqFile::seqIdx' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:27:3: style: Class 'ksw2Lib' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/files-compressed.H:39:3: style: Class 'compressedFileReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/files-compressed.H:67:3: style: Class 'compressedFileWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/files-buffered.H:29:3: style: Class 'readBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/files-buffered.H:31:3: style: Class 'readBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/files-memoryMapped.H:46:3: style: Class 'memoryMappedFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/sequence.H:194:3: style: Class 'dnaSeqFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/types.H:114:74: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:129:5: portability: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:129:5: portability: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:129:5: portability: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:129:5: portability: %u in format string (no. 6) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:129:5: portability: %u in format string (no. 7) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:129:5: portability: %u in format string (no. 8) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:224:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:224:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:225:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:225:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-ksw2.H:108:12: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/files-memoryMapped.H:66:12: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ksw2.H:122:56: style: The scope of the variable 'r' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:97:28: style:inconclusive: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:42:30: note: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:97:28: note: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:97:42: style:inconclusive: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:42:43: note: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:97:42: note: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:97:58: style:inconclusive: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:42:55: note: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:97:58: note: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:97:71: style:inconclusive: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:42:67: note: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:97:71: note: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:28: style:inconclusive: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:43:30: note: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:28: note: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:42: style:inconclusive: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:43:43: note: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:42: note: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:58: style:inconclusive: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:43:55: note: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:58: note: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:71: style:inconclusive: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:43:67: note: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:71: note: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:83: style:inconclusive: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2-driver.H:43:78: note: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'.
canu-2.2/src/utility/src/utility/align-ksw2-driver.C:98:83: note: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'.
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:28:30: warning: If memory allocation fails, then there is a possible null pointer dereference: qp [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:18:16: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:18:7: note: Assignment 'qp=(int8_t*)malloc(qlen*m)', assigned value is 0
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:28:30: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:32:2: warning: If memory allocation fails, then there is a possible null pointer dereference: eh [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:14: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:7: note: Assignment 'eh=(struct eh_t*)calloc(qlen+1,8)', assigned value is 0
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:32:2: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:32:15: warning: If memory allocation fails, then there is a possible null pointer dereference: eh [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:14: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:7: note: Assignment 'eh=(struct eh_t*)calloc(qlen+1,8)', assigned value is 0
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:32:15: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:34:3: warning: If memory allocation fails, then there is a possible null pointer dereference: eh [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:14: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:7: note: Assignment 'eh=(struct eh_t*)calloc(qlen+1,8)', assigned value is 0
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:34:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:34:40: warning: If memory allocation fails, then there is a possible null pointer dereference: eh [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:14: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:7: note: Assignment 'eh=(struct eh_t*)calloc(qlen+1,8)', assigned value is 0
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:34:40: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:18:7: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:19:7: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:21:7: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:22:9: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:6:126: style:inconclusive: Function 'ksw_extz' argument 8 names different: declaration 'q' definition 'gapo'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2.H:52:13: note: Function 'ksw_extz' argument 8 names different: declaration 'q' definition 'gapo'.
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:6:126: note: Function 'ksw_extz' argument 8 names different: declaration 'q' definition 'gapo'.
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:6:139: style:inconclusive: Function 'ksw_extz' argument 9 names different: declaration 'e' definition 'gape'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ksw2.H:52:23: note: Function 'ksw_extz' argument 9 names different: declaration 'e' definition 'gape'.
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:6:139: note: Function 'ksw_extz' argument 9 names different: declaration 'e' definition 'gape'.
canu-2.2/src/utility/src/utility/align-ksw2-extz.C:40:11: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:52:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parasail_sg_qb_de_trace [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:58:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parasail_sg_qb_de_trace [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:67:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parasail_sg_qx_trace [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:73:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parasail_sg_qx_trace [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:108:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:307:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:83:12: style:inconclusive: Technically the member function 'parasailLib::percentIdentity' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:84:12: style:inconclusive: Technically the member function 'parasailLib::errorRate' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:85:12: style:inconclusive: Technically the member function 'parasailLib::score' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:87:12: style:inconclusive: Technically the member function 'parasailLib::numMatches' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:88:12: style:inconclusive: Technically the member function 'parasailLib::numMisMatches' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:89:12: style:inconclusive: Technically the member function 'parasailLib::numGaps' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:90:12: style:inconclusive: Technically the member function 'parasailLib::alignmentLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:92:12: style:inconclusive: Technically the member function 'parasailLib::bgnA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:93:12: style:inconclusive: Technically the member function 'parasailLib::endA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:95:12: style:inconclusive: Technically the member function 'parasailLib::bgnB' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:96:12: style:inconclusive: Technically the member function 'parasailLib::endB' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:98:12: style:inconclusive: Technically the member function 'parasailLib::cigarLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:99:12: style:inconclusive: Technically the member function 'parasailLib::cigarCode' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:100:12: style:inconclusive: Technically the member function 'parasailLib::cigarValu' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:110:12: style:inconclusive: Technically the member function 'parasailLib::cigarToMapBgn' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:111:12: style:inconclusive: Technically the member function 'parasailLib::cigarToMapEnd' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:115:12: style:inconclusive: Technically the member function 'parasailLib::alignMapA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:116:12: style:inconclusive: Technically the member function 'parasailLib::alignMapB' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:117:12: style:inconclusive: Technically the member function 'parasailLib::alignMapC' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:37:3: style: Class 'parasailLib' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:108:5: portability: %u in format string (no. 2) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:108:5: portability: %u in format string (no. 3) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:108:5: portability: %u in format string (no. 4) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:108:5: portability: %u in format string (no. 6) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:108:5: portability: %u in format string (no. 7) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:108:5: portability: %u in format string (no. 8) requires 'unsigned int' but the argument type is 'int32 {aka signed int}'. [invalidPrintfArgType_uint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:201:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:201:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:202:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:202:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-parasail-driver.C:26:32: style:inconclusive: Function 'parasailLib' argument 1 names different: declaration 'match' definition 'matchScore'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:37:21: note: Function 'parasailLib' argument 1 names different: declaration 'match' definition 'matchScore'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:26:32: note: Function 'parasailLib' argument 1 names different: declaration 'match' definition 'matchScore'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:27:32: style:inconclusive: Function 'parasailLib' argument 2 names different: declaration 'mismatch' definition 'mismatchScore'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:38:21: note: Function 'parasailLib' argument 2 names different: declaration 'mismatch' definition 'mismatchScore'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:27:32: note: Function 'parasailLib' argument 2 names different: declaration 'mismatch' definition 'mismatchScore'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:28:32: style:inconclusive: Function 'parasailLib' argument 3 names different: declaration 'gapopen' definition 'gapopenPenalty'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:39:21: note: Function 'parasailLib' argument 3 names different: declaration 'gapopen' definition 'gapopenPenalty'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:28:32: note: Function 'parasailLib' argument 3 names different: declaration 'gapopen' definition 'gapopenPenalty'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:29:32: style:inconclusive: Function 'parasailLib' argument 4 names different: declaration 'gapextend' definition 'gapextendPenalty'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:40:21: note: Function 'parasailLib' argument 4 names different: declaration 'gapextend' definition 'gapextendPenalty'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:29:32: note: Function 'parasailLib' argument 4 names different: declaration 'gapextend' definition 'gapextendPenalty'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:74:32: style:inconclusive: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:77:30: note: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:74:32: note: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:74:46: style:inconclusive: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:77:43: note: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:74:46: note: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:74:62: style:inconclusive: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:77:55: note: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:74:62: note: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:74:75: style:inconclusive: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:77:67: note: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:74:75: note: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:75:32: style:inconclusive: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:78:30: note: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:75:32: note: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:75:46: style:inconclusive: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:78:43: note: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:75:46: note: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:75:62: style:inconclusive: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:78:55: note: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:75:62: note: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:75:75: style:inconclusive: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:78:67: note: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:75:75: note: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:76:25: style:inconclusive: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-parasail-driver.H:79:23: note: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'.
canu-2.2/src/utility/src/utility/align-parasail-driver.C:76:25: note: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:219:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ssw-driver.C:324:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:51:12: style:inconclusive: Technically the member function 'sswLib::percentIdentity' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:52:12: style:inconclusive: Technically the member function 'sswLib::errorRate' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:53:12: style:inconclusive: Technically the member function 'sswLib::score' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:55:12: style:inconclusive: Technically the member function 'sswLib::numMatches' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:56:12: style:inconclusive: Technically the member function 'sswLib::numMisMatches' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:57:12: style:inconclusive: Technically the member function 'sswLib::numGaps' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:58:12: style:inconclusive: Technically the member function 'sswLib::alignmentLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:60:12: style:inconclusive: Technically the member function 'sswLib::bgnA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:61:12: style:inconclusive: Technically the member function 'sswLib::endA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:63:12: style:inconclusive: Technically the member function 'sswLib::bgnB' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:64:12: style:inconclusive: Technically the member function 'sswLib::endB' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:66:12: style:inconclusive: Technically the member function 'sswLib::cigarLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:67:12: style:inconclusive: Technically the member function 'sswLib::cigarCode' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:68:12: style:inconclusive: Technically the member function 'sswLib::cigarValu' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:78:12: style:inconclusive: Technically the member function 'sswLib::cigarToMapBgn' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:79:12: style:inconclusive: Technically the member function 'sswLib::cigarToMapEnd' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:83:12: style:inconclusive: Technically the member function 'sswLib::alignMapA' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:84:12: style:inconclusive: Technically the member function 'sswLib::alignMapB' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:85:12: style:inconclusive: Technically the member function 'sswLib::alignMapC' can be const. [functionConst]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:32:3: style: Class 'sswLib' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/align-ssw-driver.C:220:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-ssw-driver.C:220:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-ssw-driver.C:221:5: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-ssw-driver.C:221:5: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/align-ssw-driver.C:99:27: style:inconclusive: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:47:30: note: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:99:27: note: Function 'align' argument 1 names different: declaration 'seqA' definition 'seqA_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:99:41: style:inconclusive: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:47:43: note: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:99:41: note: Function 'align' argument 2 names different: declaration 'lenA' definition 'seqlenA_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:99:57: style:inconclusive: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:47:55: note: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:99:57: note: Function 'align' argument 3 names different: declaration 'bgnA' definition 'bgnA_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:99:70: style:inconclusive: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:47:67: note: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:99:70: note: Function 'align' argument 4 names different: declaration 'endA' definition 'endA_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:27: style:inconclusive: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:48:30: note: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:27: note: Function 'align' argument 5 names different: declaration 'seqB' definition 'seqB_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:41: style:inconclusive: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:48:43: note: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:41: note: Function 'align' argument 6 names different: declaration 'lenB' definition 'seqlenB_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:57: style:inconclusive: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:48:55: note: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:57: note: Function 'align' argument 7 names different: declaration 'bgnB' definition 'bgnB_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:70: style:inconclusive: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:48:67: note: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:70: note: Function 'align' argument 8 names different: declaration 'endB' definition 'endB_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:82: style:inconclusive: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/align-ssw-driver.H:48:78: note: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:100:82: note: Function 'align' argument 9 names different: declaration 'verbose' definition 'verbose_'.
canu-2.2/src/utility/src/utility/align-ssw-driver.C:173:21: style: Variable 'nMismatch' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/align-ssw.C:134:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ssw.C:193:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ssw.C:354:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ssw.C:401:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ssw.C:586:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ssw.C:813:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/align-ssw.C:578:7: error: Common realloc mistake: 'h_b' nulled but not freed upon failure [memleakOnRealloc]
canu-2.2/src/utility/src/utility/align-ssw.C:579:7: error: Common realloc mistake: 'e_b' nulled but not freed upon failure [memleakOnRealloc]
canu-2.2/src/utility/src/utility/align-ssw.C:580:7: error: Common realloc mistake: 'h_c' nulled but not freed upon failure [memleakOnRealloc]
canu-2.2/src/utility/src/utility/align-ssw.C:589:7: error: Common realloc mistake: 'direction' nulled but not freed upon failure [memleakOnRealloc]
canu-2.2/src/utility/src/utility/align-ssw.C:691:9: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
canu-2.2/src/utility/src/utility/align-ssw.C:703:7: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
canu-2.2/src/utility/src/utility/align-ssw.C:711:7: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
canu-2.2/src/utility/src/utility/align-ssw.C:320:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:319:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:320:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:321:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:319:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:321:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:322:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:319:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:322:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:324:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:319:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:324:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:325:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:319:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:325:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:326:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:319:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:326:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:330:24: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:319:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:330:24: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:337:24: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:319:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:337:24: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:522:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:521:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:522:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:523:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:521:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:523:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:524:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:521:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:524:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:526:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:521:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:526:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:527:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:521:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:527:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:528:3: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:521:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:528:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:532:24: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:521:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:532:24: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:539:24: warning: If memory allocation fails, then there is a possible null pointer dereference: bests [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:521:49: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: note: Assignment 'bests=(struct alignment_end*)calloc(2,sizeof(struct alignment_end))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:539:24: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:722:5: warning: If memory allocation fails, then there is a possible null pointer dereference: c1 [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:718:25: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:718:8: note: Assignment 'c1=(uint32_t*)malloc(l*sizeof(uint32_t))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:722:5: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:723:5: warning: If memory allocation fails, then there is a possible null pointer dereference: c1 [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:718:25: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:718:8: note: Assignment 'c1=(uint32_t*)malloc(l*sizeof(uint32_t))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:723:5: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:743:5: warning: If memory allocation fails, then there is a possible null pointer dereference: reverse [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:740:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:740:21: note: Assignment 'reverse=(int8_t*)calloc(end+1,sizeof(int8_t))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:743:5: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:744:5: warning: If memory allocation fails, then there is a possible null pointer dereference: reverse [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:740:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:740:21: note: Assignment 'reverse=(int8_t*)calloc(end+1,sizeof(int8_t))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:744:5: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:753:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:753:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:754:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:754:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:755:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:755:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:763:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:763:5: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:764:5: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:764:5: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:766:43: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:766:43: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:767:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:767:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:768:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:768:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:769:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:769:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:770:3: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:752:36: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: note: Assignment 'p=(struct s_profile*)calloc(1,sizeof(struct _profile))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:770:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:796:3: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:795:32: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:795:16: note: Assignment 'r=(struct s_align*)calloc(1,sizeof(struct s_align))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:796:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:797:3: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:795:32: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:795:16: note: Assignment 'r=(struct s_align*)calloc(1,sizeof(struct s_align))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:797:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:798:3: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:795:32: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:795:16: note: Assignment 'r=(struct s_align*)calloc(1,sizeof(struct s_align))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:798:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:799:3: warning: If memory allocation fails, then there is a possible null pointer dereference: r [nullPointerOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:795:32: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:795:16: note: Assignment 'r=(struct s_align*)calloc(1,sizeof(struct s_align))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:799:3: note: Null pointer dereference
canu-2.2/src/utility/src/utility/align-ssw.C:240:30: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:195:35: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:195:18: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:240:30: note: Null pointer addition
canu-2.2/src/utility/src/utility/align-ssw.C:252:27: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:195:35: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:195:18: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:252:27: note: Null pointer addition
canu-2.2/src/utility/src/utility/align-ssw.C:446:30: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:403:35: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:403:18: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:446:30: note: Null pointer addition
canu-2.2/src/utility/src/utility/align-ssw.C:458:27: error:inconclusive: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:403:35: note: Assuming allocation function fails
canu-2.2/src/utility/src/utility/align-ssw.C:403:18: note: Assignment 'pvE=(__m128i*)calloc(segLen,sizeof(__m128i))', assigned value is 0
canu-2.2/src/utility/src/utility/align-ssw.C:458:27: note: Null pointer addition
canu-2.2/src/utility/src/utility/align-ssw.C:134:23: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:185:24: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:188:30: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:193:23: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:194:22: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:195:18: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:196:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:319:26: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:354:23: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:393:25: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:396:30: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:401:23: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:402:22: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:403:18: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:404:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:521:26: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:561:17: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:567:19: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:568:9: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:569:9: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:570:9: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:571:15: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:578:13: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:579:13: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:580:13: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:589:19: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:691:13: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:703:11: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:711:11: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:718:8: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:740:21: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:752:18: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:795:16: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:882:17: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:923:25: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/align-ssw.C:135:15: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
canu-2.2/src/utility/src/utility/align-ssw.C:303:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
canu-2.2/src/utility/src/utility/align-ssw.C:355:16: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
canu-2.2/src/utility/src/utility/align-ssw.C:505:17: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
canu-2.2/src/utility/src/utility/align-ssw.C:136:18: style: The scope of the variable 'j' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/align-ssw.C:306:13: style: The scope of the variable 'temp' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/align-ssw.C:356:18: style: The scope of the variable 'j' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/align-ssw.C:508:13: style: The scope of the variable 'temp' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/align-ssw.C:562:20: style: The scope of the variable 'f' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/align-ssw.C:565:11: style: The scope of the variable 'width' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/align-ssw.C:924:8: style: The scope of the variable 'op' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/align-ssw.C:188:48: style: Variable 'end_read_column' is allocated memory that is never used. [unusedAllocatedMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:396:48: style: Variable 'end_read_column' is allocated memory that is never used. [unusedAllocatedMemory]
canu-2.2/src/utility/src/utility/align-ssw.C:964:10: style: Variable 'length' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/bits.H:92:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uintType [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits.H:367:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits.H:383:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits.H:400:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits.H:677:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits-wordArray.H:38:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits-wordArray.H:78:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits-wordArray.H:111:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits-wordArray.C:58:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits-wordArray.C:129:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits.H:343:12: style:inconclusive: Technically the member function 'bitArray::isAllocated' can be const. [functionConst]
canu-2.2/src/utility/src/utility/bits.H:733:13: style: The member function 'stuffedBits::bitsToWords' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/bits-wordArray.C:50:3: warning: Class 'wordArray' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/bits-wordArray.C:50:3: warning: Class 'wordArray' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/bits.H:330:3: style: Class 'bitArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/bits.H:489:3: style: Class 'stuffedBits' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/bits.H:490:3: style: Class 'stuffedBits' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/bits.H:491:3: style: Class 'stuffedBits' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/bits.H:492:3: style: Class 'stuffedBits' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/bits-wordArray.C:42:71: error: Division by zero. [zerodiv]
canu-2.2/src/utility/src/utility/bits-wordArray.C:41:43: note: Assignment '_wordsPerLock=(useLocks==false)?(0):64', assigned value is 0
canu-2.2/src/utility/src/utility/bits-wordArray.C:42:71: note: Division by zero
canu-2.2/src/utility/src/utility/bits-wordArray.H:123:37: style:inconclusive: Function 'set' argument 2 names different: declaration 'v' definition 'value'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/bits.H:454:37: note: Function 'set' argument 2 names different: declaration 'v' definition 'value'.
canu-2.2/src/utility/src/utility/bits-wordArray.H:123:37: note: Function 'set' argument 2 names different: declaration 'v' definition 'value'.
canu-2.2/src/utility/src/utility/bits-wordArray.C:32:48: style:inconclusive: Function 'wordArray' argument 2 names different: declaration 'segmentsSizeInBits' definition 'segmentSizeInBits'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/bits.H:446:39: note: Function 'wordArray' argument 2 names different: declaration 'segmentsSizeInBits' definition 'segmentSizeInBits'.
canu-2.2/src/utility/src/utility/bits-wordArray.C:32:48: note: Function 'wordArray' argument 2 names different: declaration 'segmentsSizeInBits' definition 'segmentSizeInBits'.
canu-2.2/src/utility/src/utility/bits-wordArray.H:183:20: style: Variable 'lSize' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/bits.H:79:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable uintType [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/bits.C:409:35: style: Array index '_dataBlk' is used before limits check. [arrayIndexThenCheck]
canu-2.2/src/utility/src/utility/bits.C:73:14: warning: Member variable 'stuffedBits::_fibData' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/bits.C:98:14: warning: Member variable 'stuffedBits::_fibData' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/bits.C:121:14: warning: Member variable 'stuffedBits::_fibData' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/bits.C:423:14: style:inconclusive: Technically the member function 'stuffedBits::getPosition' can be const. [functionConst]
canu-2.2/src/utility/src/utility/bits.H:513:12: note: Technically the member function 'stuffedBits::getPosition' can be const.
canu-2.2/src/utility/src/utility/bits.C:423:14: note: Technically the member function 'stuffedBits::getPosition' can be const.
canu-2.2/src/utility/src/utility/bits.C:429:14: style:inconclusive: Technically the member function 'stuffedBits::getLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/bits.H:515:12: note: Technically the member function 'stuffedBits::getLength' can be const.
canu-2.2/src/utility/src/utility/bits.C:429:14: note: Technically the member function 'stuffedBits::getLength' can be const.
canu-2.2/src/utility/src/utility/bits.C:33:3: warning: Class 'stuffedBits' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/bits.C:33:3: warning: Class 'stuffedBits' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/bits.C:472:26: style:inconclusive: Function 'setBit' argument 1 names different: declaration 'on' definition 'bit'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/bits.H:523:24: note: Function 'setBit' argument 1 names different: declaration 'on' definition 'bit'.
canu-2.2/src/utility/src/utility/bits.C:472:26: note: Function 'setBit' argument 1 names different: declaration 'on' definition 'bit'.
canu-2.2/src/utility/src/utility/bits.C:632:46: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/bits.C:770:61: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/bits.C:834:51: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/bits.C:895:51: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/bits.C:1067:51: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/edlib.C:188:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/edlib.C:91:5: warning:inconclusive: Member variable 'Block::P' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/edlib.C:91:5: warning:inconclusive: Member variable 'Block::M' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/edlib.C:91:5: warning:inconclusive: Member variable 'Block::score' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/edlib.C:70:10: warning: Struct 'AlignmentData' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/edlib.C:70:10: warning: Struct 'AlignmentData' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/edlib.C:175:47: style:inconclusive: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/edlib.H:229:41: note: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'.
canu-2.2/src/utility/src/utility/edlib.C:175:47: note: Function 'edlibAlign' argument 1 names different: declaration 'query' definition 'queryOriginal'.
canu-2.2/src/utility/src/utility/edlib.C:176:47: style:inconclusive: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/edlib.H:230:41: note: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'.
canu-2.2/src/utility/src/utility/edlib.C:176:47: note: Function 'edlibAlign' argument 3 names different: declaration 'target' definition 'targetOriginal'.
canu-2.2/src/utility/src/utility/edlib.C:378:44: style:inconclusive: Function 'edlibAlignmentAnalyze' argument 1 names different: declaration 'alignment' definition 'a'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/edlib.H:256:49: note: Function 'edlibAlignmentAnalyze' argument 1 names different: declaration 'alignment' definition 'a'.
canu-2.2/src/utility/src/utility/edlib.C:378:44: note: Function 'edlibAlignmentAnalyze' argument 1 names different: declaration 'alignment' definition 'a'.
canu-2.2/src/utility/src/utility/edlib.C:379:32: style:inconclusive: Function 'edlibAlignmentAnalyze' argument 2 names different: declaration 'alignmentLength' definition 'aLength'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/edlib.H:257:37: note: Function 'edlibAlignmentAnalyze' argument 2 names different: declaration 'alignmentLength' definition 'aLength'.
canu-2.2/src/utility/src/utility/edlib.C:379:32: note: Function 'edlibAlignmentAnalyze' argument 2 names different: declaration 'alignmentLength' definition 'aLength'.
canu-2.2/src/utility/src/utility/edlib.C:1573:51: style:inconclusive: Function 'transformSequences' argument 7 names different: declaration 'equalityDefinitio' definition 'equalityDefinition'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/edlib.C:160:51: note: Function 'transformSequences' argument 7 names different: declaration 'equalityDefinitio' definition 'equalityDefinition'.
canu-2.2/src/utility/src/utility/edlib.C:1573:51: note: Function 'transformSequences' argument 7 names different: declaration 'equalityDefinitio' definition 'equalityDefinition'.
canu-2.2/src/utility/src/utility/edlib.C:590:18: style: Clarify calculation precedence for '%' and '?'. [clarifyCalculation]
canu-2.2/src/utility/src/utility/edlib.C:606:58: performance: Function parameter 'block' should be passed by const reference. [passedByValue]
canu-2.2/src/utility/src/utility/edlib.C:625:42: performance: Function parameter 'block' should be passed by const reference. [passedByValue]
canu-2.2/src/utility/src/utility/edlib.C:642:49: performance: Function parameter 'block' should be passed by const reference. [passedByValue]
canu-2.2/src/utility/src/utility/edlib.C:659:52: performance: Function parameter 'block' should be passed by const reference. [passedByValue]
canu-2.2/src/utility/src/utility/edlib.C:1630:44: performance: Function parameter 'result' should be passed by const reference. [passedByValue]
canu-2.2/src/utility/src/utility/edlib.C:662:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
canu-2.2/src/utility/src/utility/edlib.C:769:37: style: Variable 'Peq_c' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/edlib.C:953:18: style: Variable 'hout' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/files-buffered.C:34:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:53:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:102:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:160:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:187:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:266:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:407:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:428:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:599:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:649:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse41_128_32.c:101:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable __m128i [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-buffered.C:117:3: warning: Class 'readBuffer' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/files-buffered.C:117:3: warning: Class 'readBuffer' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/files-buffered.C:197:13: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
canu-2.2/src/utility/src/utility/files-buffered.C:194:17: note: outer condition: pos<_filePos
canu-2.2/src/utility/src/utility/files-buffered.C:197:13: note: identical inner condition: pos<_filePos
canu-2.2/src/utility/src/utility/files-buffered.C:239:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/files-buffered.C:294:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/files-buffered.C:668:15: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/files-buffered.C:630:4: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
canu-2.2/src/utility/src/utility/files-buffered.C:259:12: style: The scope of the variable 'bAct' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/files-buffered.C:100:30: style:inconclusive: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/files-buffered.H:31:20: note: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'.
canu-2.2/src/utility/src/utility/files-buffered.C:100:30: note: Function 'readBuffer' argument 1 names different: declaration 'F' definition 'file'.
canu-2.2/src/utility/src/utility/files-buffered.C:51:36: style: Argument 'filename' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/files-buffered.H:87:24: note: Shadowed function
canu-2.2/src/utility/src/utility/files-buffered.C:51:36: note: Shadow argument
canu-2.2/src/utility/src/utility/files-buffered.C:425:37: style: Argument 'filename' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/files-buffered.H:130:24: note: Shadowed function
canu-2.2/src/utility/src/utility/files-buffered.C:425:37: note: Shadow argument
canu-2.2/src/utility/src/utility/files-buffered.C:561:34: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/files-buffered.C:259:20: style: Variable 'bAct' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/files-compressed.C:97:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-compressed.C:171:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-compressed.C:239:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-compressed.C:86:12: warning: Class 'compressedFileReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/files-compressed.C:86:12: warning: Class 'compressedFileReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/files-compressed.C:220:7: warning: Class 'compressedFileWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/files-compressed.C:220:7: warning: Class 'compressedFileWriter' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/files-fasta-fastq.C:255:5: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
canu-2.2/src/utility/src/utility/files-fasta-fastq.C:39:34: warning: Either the condition 'bl==0' is redundant or there is division by zero at line 39. [zerodivcond]
canu-2.2/src/utility/src/utility/files-fasta-fastq.C:61:10: note: Assuming that condition 'bl==0' is not redundant
canu-2.2/src/utility/src/utility/files-fasta-fastq.C:39:34: note: Division by zero
canu-2.2/src/utility/src/utility/files-fasta-fastq.C:56:55: warning: Either the condition 'bl==0' is redundant or there is division by zero at line 56. [zerodivcond]
canu-2.2/src/utility/src/utility/files-fasta-fastq.C:61:10: note: Assuming that condition 'bl==0' is not redundant
canu-2.2/src/utility/src/utility/files-fasta-fastq.C:56:55: note: Division by zero
canu-2.2/src/utility/src/utility/files-fasta-fastq.C:255:13: style: Variable 'asFASTA' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/files-memoryMapped.C:30:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-memoryMapped.C:90:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files-memoryMapped.C:64:5: warning: Class 'memoryMappedFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/files-memoryMapped.C:64:5: warning: Class 'memoryMappedFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/files.C:72:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:105:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:246:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:274:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:288:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:310:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:336:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:348:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:369:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:399:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:433:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:455:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:485:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:520:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:534:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:547:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:565:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:581:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:626:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:655:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:722:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:743:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:776:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/files.C:819:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse41_128_32.c:235:19: warning: Uninitialized variable: vF_ext [uninitvar]
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse41_128_32.c:177:20: note: Assuming condition is false
canu-2.2/src/utility/src/parasail/sg_trace_striped_sse41_128_32.c:235:19: note: Uninitialized variable: vF_ext
canu-2.2/src/utility/src/utility/strings.H:110:10: style:inconclusive: Technically the member function 'splitToWords::issc' can be const. [functionConst]
canu-2.2/src/utility/src/utility/strings.H:115:11: style:inconclusive: Technically the member function 'splitToWords::numWords' can be const. [functionConst]
canu-2.2/src/utility/src/utility/strings.H:132:11: style:inconclusive: Technically the member function 'splitToWords::toint32' can be const. [functionConst]
canu-2.2/src/utility/src/utility/strings.H:133:11: style:inconclusive: Technically the member function 'splitToWords::touint32' can be const. [functionConst]
canu-2.2/src/utility/src/utility/strings.H:134:11: style:inconclusive: Technically the member function 'splitToWords::toint64' can be const. [functionConst]
canu-2.2/src/utility/src/utility/strings.H:135:11: style:inconclusive: Technically the member function 'splitToWords::touint64' can be const. [functionConst]
canu-2.2/src/utility/src/utility/strings.H:136:11: style:inconclusive: Technically the member function 'splitToWords::todouble' can be const. [functionConst]
canu-2.2/src/utility/src/utility/strings.H:56:3: style: Class 'KeyAndValue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/strings.H:86:3: style: Class 'splitToWords' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/files.C:585:23: style: Return value '((off_t)1)<42' is always true [knownConditionTrueFalse]
canu-2.2/src/utility/src/utility/files.C:73:30: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/files.C:106:28: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/files.C:716:70: style:inconclusive: Function 'AS_UTL_loadFileList' argument 2 names different: declaration 'FILE' definition 'fileList'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/files.H:75:78: note: Function 'AS_UTL_loadFileList' argument 2 names different: declaration 'FILE' definition 'fileList'.
canu-2.2/src/utility/src/utility/files.C:716:70: note: Function 'AS_UTL_loadFileList' argument 2 names different: declaration 'FILE' definition 'fileList'.
canu-2.2/src/utility/src/utility/files.C:817:40: style:inconclusive: Function 'AS_UTL_closeFile' argument 2 names different: declaration 'filename' definition 'prefix'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/files.H:80:48: note: Function 'AS_UTL_closeFile' argument 2 names different: declaration 'filename' definition 'prefix'.
canu-2.2/src/utility/src/utility/files.C:817:40: note: Function 'AS_UTL_closeFile' argument 2 names different: declaration 'filename' definition 'prefix'.
canu-2.2/src/utility/src/utility/files.C:656:12: style: Variable 'env' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/files.C:532:21: style: Variable 'size' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/files.C:563:21: style: Variable 'size' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/hexDump.C:35:19: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/kmers-tiny.H:62:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-files.H:126:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-exact.C:194:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-exact.C:374:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-exact.C:401:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-exact.C:494:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-exact.C:582:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-files.C:106:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-files.C:154:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-lookup.H:29:3: warning: Member variable 'merylExactLookup::_Kbits' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/kmers-tiny.H:82:15: style: The member function 'kmerTiny::addR' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/kmers-tiny.H:83:15: style: The member function 'kmerTiny::addL' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/kmers-tiny.H:89:15: style: The member function 'kmerTiny::reverseComplement' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/kmers-tiny.H:125:15: style: The member function 'kmerTiny::isFirst' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/kmers-tiny.H:126:15: style: The member function 'kmerTiny::isLast' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/kmers-tiny.H:138:12: style: The member function 'kmerTiny::toString' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/kmers-tiny.H:147:12: style:inconclusive: Technically the member function 'kmerTiny::recanonicalizeACGTorder' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-tiny.H:177:12: style: The member function 'kmerTiny::setPrefixSuffix' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/kmers-tiny.H:184:12: style:inconclusive: Technically the member function 'kmerTiny::operator>>=' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-tiny.H:185:12: style:inconclusive: Technically the member function 'kmerTiny::operator<<=' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-histogram.H:65:13: style:inconclusive: Technically the member function 'merylHistogram::numUnique' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-histogram.H:66:13: style:inconclusive: Technically the member function 'merylHistogram::numDistinct' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-histogram.H:67:13: style:inconclusive: Technically the member function 'merylHistogram::numTotal' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-histogram.H:69:13: style:inconclusive: Technically the member function 'merylHistogram::histogramLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-histogram.H:70:13: style:inconclusive: Technically the member function 'merylHistogram::histogramValue' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-histogram.H:71:13: style:inconclusive: Technically the member function 'merylHistogram::histogramOccurrences' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:93:14: style:inconclusive: Technically the member function 'kmerIterator::isValid' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:97:14: style:inconclusive: Technically the member function 'kmerIterator::isACGT' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:112:14: style:inconclusive: Technically the member function 'kmerIterator::getBaseBgn' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:113:14: style:inconclusive: Technically the member function 'kmerIterator::getBaseEnd' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:158:14: style:inconclusive: Technically the member function 'kmerIterator::fmer' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:159:14: style:inconclusive: Technically the member function 'kmerIterator::rmer' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:160:14: style:inconclusive: Technically the member function 'kmerIterator::position' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:162:14: style:inconclusive: Technically the member function 'kmerIterator::bgnPosition' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-iterator.H:163:14: style:inconclusive: Technically the member function 'kmerIterator::endPosition' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-files.H:70:13: style:inconclusive: Technically the member function 'merylFileBlockReader::prefix' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-files.H:71:13: style:inconclusive: Technically the member function 'merylFileBlockReader::nKmers' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-files.H:73:13: style: The member function 'merylFileBlockReader::suffixes' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/kmers-files.H:141:14: style:inconclusive: Technically the member function 'merylFileIndex::blockPrefix' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-files.H:142:14: style:inconclusive: Technically the member function 'merylFileIndex::blockPosition' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-files.H:143:14: style:inconclusive: Technically the member function 'merylFileIndex::numKmers' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-writer.H:54:11: style:inconclusive: Technically the member function 'merylFileWriter::numberOfFiles' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-writer.H:55:11: style:inconclusive: Technically the member function 'merylFileWriter::firstPrefixInFile' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:71:11: style:inconclusive: Technically the member function 'merylFileReader::theFMer' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:72:11: style:inconclusive: Technically the member function 'merylFileReader::theValue' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:74:11: style:inconclusive: Technically the member function 'merylFileReader::isMultiSet' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:85:11: style:inconclusive: Technically the member function 'merylFileReader::prefixSize' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:86:11: style:inconclusive: Technically the member function 'merylFileReader::suffixSize' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:88:11: style:inconclusive: Technically the member function 'merylFileReader::numFiles' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:89:11: style:inconclusive: Technically the member function 'merylFileReader::numBlocks' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:91:11: style:inconclusive: Technically the member function 'merylFileReader::numFilesBits' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-reader.H:92:11: style:inconclusive: Technically the member function 'merylFileReader::numBlocksBits' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-lookup.H:76:12: style:inconclusive: Technically the member function 'merylExactLookup::nKmers' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-lookup.H:152:19: style:inconclusive: Technically the member function 'merylExactLookup::value_value' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-lookup.H:108:12: note: Technically the member function 'merylExactLookup::value_value' can be const.
canu-2.2/src/utility/src/utility/kmers-lookup.H:152:19: note: Technically the member function 'merylExactLookup::value_value' can be const.
canu-2.2/src/utility/src/utility/kmers-files.C:45:13: warning: Class 'merylFileBlockReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/kmers-files.C:45:13: warning: Class 'merylFileBlockReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/kmers-lookup.H:35:15: warning: Class 'merylExactLookup' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/kmers-lookup.H:35:15: warning: Class 'merylExactLookup' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/kmers-iterator.H:38:3: style: Class 'kmerIterator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/kmers-writer-block.H:34:3: style: Class 'merylBlockWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/kmers-writer.H:39:3: style: Class 'merylFileWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/kmers-reader.H:37:3: style: Class 'merylFileReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/kmers-lookup.H:152:38: style: Argument 'value' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed function
canu-2.2/src/utility/src/utility/kmers-lookup.H:152:38: note: Shadow argument
canu-2.2/src/utility/src/utility/kmers-lookup.H:212:42: style: Argument 'value' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed function
canu-2.2/src/utility/src/utility/kmers-lookup.H:212:42: note: Shadow argument
canu-2.2/src/utility/src/utility/kmers-files.C:129:43: style: Argument 'suffixes' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/kmers-files.H:73:13: note: Shadowed function
canu-2.2/src/utility/src/utility/kmers-files.C:129:43: note: Shadow argument
canu-2.2/src/utility/src/utility/kmers-files.C:129:61: style: Argument 'values' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/kmers-files.H:74:13: note: Shadowed function
canu-2.2/src/utility/src/utility/kmers-files.C:129:61: note: Shadow argument
canu-2.2/src/utility/src/utility/kmers-lookup.H:152:19: style: Unused private function: 'merylExactLookup::value_value' [unusedPrivateFunction]
canu-2.2/src/utility/src/utility/kmers-lookup.H:108:12: note: Unused private function: 'merylExactLookup::value_value'
canu-2.2/src/utility/src/utility/kmers-lookup.H:152:19: note: Unused private function: 'merylExactLookup::value_value'
canu-2.2/src/utility/src/utility/kmers-exact.C:84:19: style: Variable '_prePtrBits' is reassigned a value before the old one has been used. [redundantAssignment]
canu-2.2/src/utility/src/utility/kmers-exact.C:83:19: note: _prePtrBits is assigned
canu-2.2/src/utility/src/utility/kmers-exact.C:84:19: note: _prePtrBits is overwritten
canu-2.2/src/utility/src/utility/kmers-exact.C:291:18: style: Local variable 'value' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed function
canu-2.2/src/utility/src/utility/kmers-exact.C:291:18: note: Shadow local variable
canu-2.2/src/utility/src/utility/kmers-exact.C:455:18: style: Local variable 'value' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed function
canu-2.2/src/utility/src/utility/kmers-exact.C:455:18: note: Shadow local variable
canu-2.2/src/utility/src/utility/bits.H:79:5: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 490. [shiftTooManyBits]
canu-2.2/src/utility/src/utility/kmers-exact.C:490:24: note: Assuming that condition '_valueBits>0' is not redundant
canu-2.2/src/utility/src/utility/kmers-exact.C:438:34: note: Calling function 'buildLowBitMask < uint32_t >', 1st argument '_valueBits' value is 0
canu-2.2/src/utility/src/utility/bits.H:79:5: note: Shift
canu-2.2/src/utility/src/utility/kmers-histogram.C:224:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-reader.C:131:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-reader.C:212:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-reader.C:221:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-reader.C:302:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-histogram.C:29:3: warning: Class 'merylHistogram' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/kmers-histogram.C:29:3: warning: Class 'merylHistogram' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:27:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:66:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:173:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:280:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-reader.C:235:13: warning: Class 'merylFileReader' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/kmers-reader.C:235:13: warning: Class 'merylFileReader' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/kmers-reader.C:367:3: style: Variable 'D' is assigned an expression that holds the same value. [redundantAssignment]
canu-2.2/src/utility/src/utility/kmers-reader.C:324:5: note: D is assigned 'new stuffedBits' here.
canu-2.2/src/utility/src/utility/kmers-reader.C:348:39: note: Assuming condition is false
canu-2.2/src/utility/src/utility/kmers-reader.C:367:3: note: Variable 'D' is assigned an expression that holds the same value.
canu-2.2/src/utility/src/utility/kmers-reader.C:129:50: style: Argument 'loadStatistics' shadows outer function [shadowFunction]
canu-2.2/src/utility/src/utility/kmers-reader.H:60:11: note: Shadowed function
canu-2.2/src/utility/src/utility/kmers-reader.C:129:50: note: Shadow argument
canu-2.2/src/utility/src/utility/kmers-reader.C:294:25: style: Parameter 'name' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:43:3: warning: Class 'merylBlockWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:43:3: warning: Class 'merylBlockWriter' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/kmers-reader.C:370:23: style: Variable 'position' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-reader.C:372:23: style: Variable 'm1' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-reader.C:373:23: style: Variable 'm2' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-reader.C:375:23: style: Variable 'prefix' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-reader.C:379:23: style: Variable 'unaryBits' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-reader.C:381:23: style: Variable 'k1' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-reader.C:384:23: style: Variable 'c1' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-reader.C:385:23: style: Variable 'c2' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:181:11: style: The scope of the variable 'oldName' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:182:11: style: The scope of the variable 'newName' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:243:23: style: Variable 'kmersIn' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:244:23: style: Variable 'kmersOut' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:357:14: style: Variable 'kmersIn' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-writer-block.C:358:14: style: Variable 'kmersOut' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-writer-stream.C:27:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-writer.C:31:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-writer.C:95:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-writer.C:141:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-writer.C:167:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/kmers-writer-stream.C:46:3: warning: Class 'merylStreamWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/kmers-writer-stream.C:46:3: warning: Class 'merylStreamWriter' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/kmers-writer.C:182:18: style:inconclusive: Technically the member function 'merylFileWriter::writeBlockToFile' can be const. [functionConst]
canu-2.2/src/utility/src/utility/kmers-writer.H:61:11: note: Technically the member function 'merylFileWriter::writeBlockToFile' can be const.
canu-2.2/src/utility/src/utility/kmers-writer.C:182:18: note: Technically the member function 'merylFileWriter::writeBlockToFile' can be const.
canu-2.2/src/utility/src/utility/kmers-writer.C:45:20: style: Condition '_initialized==false' is always true [knownConditionTrueFalse]
canu-2.2/src/utility/src/utility/kmers-writer.C:33:20: note: Assuming that condition '_initialized==true' is not redundant
canu-2.2/src/utility/src/utility/kmers-writer.C:38:23: note: Assuming condition is false
canu-2.2/src/utility/src/utility/kmers-writer.C:45:20: note: Condition '_initialized==false' is always true
canu-2.2/src/utility/src/utility/kmers-writer.C:246:11: style: The scope of the variable 'thisPrefix' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/kmers-writer.C:187:52: style: Parameter 'values' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/kmers-writer.C:246:22: style: Variable 'thisPrefix' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-writer.C:268:21: style: Variable 'lastValue' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers-writer.C:269:21: style: Variable 'thisValue' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/kmers.C:35:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/logging.C:89:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/logging.C:116:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/logging.C:130:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FILENAME_MAX [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/logging.C:150:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/logging.C:180:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/logging.C:474:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/logging.C:487:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/logging.C:170:16: error: Buffer is accessed out of bounds: rotmes [bufferAccessOutOfBounds]
canu-2.2/src/utility/src/utility/logging.C:282:10: style:inconclusive: Technically the member function 'logFile::getPrefix' can be const. [functionConst]
canu-2.2/src/utility/src/utility/logging.H:64:15: note: Technically the member function 'logFile::getPrefix' can be const.
canu-2.2/src/utility/src/utility/logging.C:282:10: note: Technically the member function 'logFile::getPrefix' can be const.
canu-2.2/src/utility/src/utility/logging.C:288:10: style:inconclusive: Technically the member function 'logFile::getLogName' can be const. [functionConst]
canu-2.2/src/utility/src/utility/logging.H:65:15: note: Technically the member function 'logFile::getLogName' can be const.
canu-2.2/src/utility/src/utility/logging.C:288:10: note: Technically the member function 'logFile::getLogName' can be const.
canu-2.2/src/utility/src/utility/logging.C:473:10: style: The member function 'logFile::writeStatus' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/logging.H:133:15: note: The member function 'logFile::writeStatus' can be static.
canu-2.2/src/utility/src/utility/logging.C:473:10: note: The member function 'logFile::writeStatus' can be static.
canu-2.2/src/utility/src/utility/logging.C:557:10: style:inconclusive: Technically the member function 'logFile::verbosityEnabled' can be const. [functionConst]
canu-2.2/src/utility/src/utility/logging.H:136:15: note: Technically the member function 'logFile::verbosityEnabled' can be const.
canu-2.2/src/utility/src/utility/logging.C:557:10: note: Technically the member function 'logFile::verbosityEnabled' can be const.
canu-2.2/src/utility/src/utility/logging.C:357:10: style:inconclusive: Technically the member function 'logFile::findLevelIndex' can be const. [functionConst]
canu-2.2/src/utility/src/utility/logging.H:163:33: note: Technically the member function 'logFile::findLevelIndex' can be const.
canu-2.2/src/utility/src/utility/logging.C:357:10: note: Technically the member function 'logFile::findLevelIndex' can be const.
canu-2.2/src/utility/src/utility/logging.C:40:10: style:inconclusive: Technically the member function 'logFileLevel::isEnabled' can be const. [functionConst]
canu-2.2/src/utility/src/utility/logging.C:45:10: style:inconclusive: Technically the member function 'logFileLevel::verbosity' can be const. [functionConst]
canu-2.2/src/utility/src/utility/logging.C:238:3: warning: Class 'logFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/logging.C:238:3: warning: Class 'logFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/logging.C:110:12: warning: Class 'logFileInstance' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/logging.C:110:12: warning: Class 'logFileInstance' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/logging.H:38:3: style: Class 'logFileHandle' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/logging.H:51:3: style: Class 'logFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/logging.C:31:3: style: Class 'logFileLevel' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/logging.C:372:31: style: Redundant condition: The condition '*optionString != 0' is redundant since '*optionString == '-'' is sufficient. [redundantCondition]
canu-2.2/src/utility/src/utility/logging.C:150:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/logging.C:155:7: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint32 {aka unsigned int}'. [invalidPrintfArgType_sint]
canu-2.2/src/utility/src/utility/logging.C:167:11: style: The scope of the variable 'rotmes' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/logging.C:534:21: style: The scope of the variable 'ap' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/logging.C:545:21: style: The scope of the variable 'ap' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/logging.C:576:21: style: The scope of the variable 'ap' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/logging.C:587:21: style: The scope of the variable 'ap' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/logging.C:598:21: style: The scope of the variable 'ap' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/logging.C:609:21: style: The scope of the variable 'ap' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/kmers.C:30:28: style: Parameter 'nameprefix' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/md5.C:340:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/md5.C:372:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/mt19937ar.H:45:3: style: Class 'mtRandom' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/mt19937ar.C:166:17: style: The scope of the variable 'x2' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/mt19937ar.C:192:38: warning: Function 'mtRandomExponential' argument order different: declaration 'lambda, tau' definition 'mode, lambda' [funcArgOrderDifferent]
canu-2.2/src/utility/src/utility/mt19937ar.H:72:39: note: Function 'mtRandomExponential' argument order different: declaration 'lambda, tau' definition 'mode, lambda'
canu-2.2/src/utility/src/utility/mt19937ar.C:192:38: note: Function 'mtRandomExponential' argument order different: declaration 'lambda, tau' definition 'mode, lambda'
canu-2.2/src/utility/src/utility/mt19937ar.C:93:28: style: Parameter 'init_key' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/mt19937ar.C:166:19: style: Variable 'x2' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/md5.C:309:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:310:20: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:349:19: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:384:11: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:400:15: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:413:13: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:413:36: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:420:25: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:425:15: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/md5.C:118:24: style:inconclusive: Function 'MD5Init' argument 1 names different: declaration '<unnamed>' definition 'context'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:131:26: style:inconclusive: Function 'MD5Update' argument 1 names different: declaration '<unnamed>' definition 'context'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:131:56: style:inconclusive: Function 'MD5Update' argument 2 names different: declaration '<unnamed>' definition 'input'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:131:70: style:inconclusive: Function 'MD5Update' argument 3 names different: declaration '<unnamed>' definition 'inputLen'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:165:30: style:inconclusive: Function 'MD5Final' argument 1 names different: declaration '<unnamed>' definition 'digest'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:165:51: style:inconclusive: Function 'MD5Final' argument 2 names different: declaration '<unnamed>' definition 'context'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:277:36: style:inconclusive: Function 'Encode' argument 1 names different: declaration '<unnamed>' definition 'output'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:277:52: style:inconclusive: Function 'Encode' argument 2 names different: declaration '<unnamed>' definition 'input'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:277:72: style:inconclusive: Function 'Encode' argument 3 names different: declaration '<unnamed>' definition 'len'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:291:29: style:inconclusive: Function 'Decode' argument 1 names different: declaration '<unnamed>' definition 'output'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:291:58: style:inconclusive: Function 'Decode' argument 2 names different: declaration '<unnamed>' definition 'input'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:291:78: style:inconclusive: Function 'Decode' argument 3 names different: declaration '<unnamed>' definition 'len'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/md5.C:277:52: style: Parameter 'input' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/md5.C:322:20: style: Parameter 'm' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/runtime.C:117:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sequence.C:277:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sequence.C:314:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sequence.C:357:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sequence.C:404:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sequence.C:682:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sequence.C:739:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/speedCounter.H:43:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/speedCounter.H:60:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/speedCounter.H:73:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sequence.C:213:16: style: Array index 'cc' is used before limits check. [arrayIndexThenCheck]
canu-2.2/src/utility/src/utility/sequence.C:502:9: style:inconclusive: Technically the member function 'dnaSeq::copy' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:119:21: note: Technically the member function 'dnaSeq::copy' can be const.
canu-2.2/src/utility/src/utility/sequence.C:502:9: note: Technically the member function 'dnaSeq::copy' can be const.
canu-2.2/src/utility/src/utility/sequence.C:519:9: style:inconclusive: Technically the member function 'dnaSeq::copy' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:122:21: note: Technically the member function 'dnaSeq::copy' can be const.
canu-2.2/src/utility/src/utility/sequence.C:519:9: note: Technically the member function 'dnaSeq::copy' can be const.
canu-2.2/src/utility/src/utility/sequence.C:631:13: style:inconclusive: Technically the member function 'dnaSeqFile::sequenceLength' can be const. [functionConst]
canu-2.2/src/utility/src/utility/sequence.H:206:15: note: Technically the member function 'dnaSeqFile::sequenceLength' can be const.
canu-2.2/src/utility/src/utility/sequence.C:631:13: note: Technically the member function 'dnaSeqFile::sequenceLength' can be const.
canu-2.2/src/utility/src/utility/sequence.C:581:13: warning: Class 'dnaSeqFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
canu-2.2/src/utility/src/utility/sequence.C:581:13: warning: Class 'dnaSeqFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
canu-2.2/src/utility/src/utility/sequence.C:156:25: warning: Either the condition 'qlt==NULL' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
canu-2.2/src/utility/src/utility/sequence.C:158:11: note: Assuming that condition 'qlt==NULL' is not redundant
canu-2.2/src/utility/src/utility/sequence.C:156:25: note: Null pointer addition
canu-2.2/src/utility/src/utility/sequence.C:115:10: style: The scope of the variable 'c' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/sequence.C:380:13: style: The scope of the variable 'c3' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/sequence.C:154:11: style: The scope of the variable 'c' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/sequence.C:984:80: style:inconclusive: Function 'loadSequence' argument 7 names different: declaration 'errorCode' definition 'error'. [funcArgNamesDifferent]
canu-2.2/src/utility/src/utility/sequence.H:222:78: note: Function 'loadSequence' argument 7 names different: declaration 'errorCode' definition 'error'.
canu-2.2/src/utility/src/utility/sequence.C:984:80: note: Function 'loadSequence' argument 7 names different: declaration 'errorCode' definition 'error'.
canu-2.2/src/utility/src/utility/sequence.C:368:13: style: Local variable 'c1' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/sequence.C:363:12: note: Shadowed variable
canu-2.2/src/utility/src/utility/sequence.C:368:13: note: Shadow local variable
canu-2.2/src/utility/src/utility/sequence.C:369:13: style: Local variable 'c2' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/sequence.C:364:12: note: Shadowed variable
canu-2.2/src/utility/src/utility/sequence.C:369:13: note: Shadow local variable
canu-2.2/src/utility/src/utility/sequence.C:370:13: style: Local variable 'c3' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/sequence.C:365:12: note: Shadowed variable
canu-2.2/src/utility/src/utility/sequence.C:370:13: note: Shadow local variable
canu-2.2/src/utility/src/utility/sequence.C:378:13: style: Local variable 'c1' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/sequence.C:363:12: note: Shadowed variable
canu-2.2/src/utility/src/utility/sequence.C:378:13: note: Shadow local variable
canu-2.2/src/utility/src/utility/sequence.C:379:13: style: Local variable 'c2' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/sequence.C:364:12: note: Shadowed variable
canu-2.2/src/utility/src/utility/sequence.C:379:13: note: Shadow local variable
canu-2.2/src/utility/src/utility/sequence.C:380:13: style: Local variable 'c3' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/sequence.C:365:12: note: Shadowed variable
canu-2.2/src/utility/src/utility/sequence.C:380:13: note: Shadow local variable
canu-2.2/src/utility/src/utility/sequence.C:671:13: style: Local variable 'indexFile' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/sequence.C:668:16: note: Shadowed variable
canu-2.2/src/utility/src/utility/sequence.C:671:13: note: Shadow local variable
canu-2.2/src/utility/src/utility/sequence.C:136:29: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/sequence.C:208:24: style: Parameter 'bases' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/sequence.C:270:27: style: Parameter 'chunk' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/sequence.C:305:41: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/sequence.C:350:27: style: Parameter 'chunk' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/sequence.C:394:41: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/sequence.C:438:27: style: Parameter 'chunk' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/sequence.C:451:41: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
canu-2.2/src/utility/src/utility/sequence.C:668:16: style: Variable 'indexFile' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/sequence.C:115:11: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sequence.C:363:17: style: Variable 'c1' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sequence.C:364:17: style: Variable 'c2' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sequence.C:365:17: style: Variable 'c3' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sequence.C:668:16: style: Variable 'indexFile' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sequence.C:1026:19: style: Variable 'lastWhite' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sequence.C:154:12: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sweatShop.C:142:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sweatShop.C:176:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sweatShop.C:275:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sweatShop.C:432:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/sweatShop.C:510:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/system-stackTrace.C:293:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/system-stackTrace.C:328:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SA_RESTART [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/system-stackTrace.C:287:13: style: Variable 'name' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/sweatShop.C:95:12: warning: Member variable 'sweatShop::_stateMutex' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/sweatShop.C:28:3: warning: Member variable 'sweatShopWorker::threadID' is not initialized in the constructor. [uninitMemberVar]
canu-2.2/src/utility/src/utility/sweatShop.C:200:12: style: Unused private function: 'sweatShop::loader' [unusedPrivateFunction]
canu-2.2/src/utility/src/utility/sweatShop.H:64:11: note: Unused private function: 'sweatShop::loader'
canu-2.2/src/utility/src/utility/sweatShop.C:200:12: note: Unused private function: 'sweatShop::loader'
canu-2.2/src/utility/src/utility/sweatShop.C:252:12: style: Unused private function: 'sweatShop::worker' [unusedPrivateFunction]
canu-2.2/src/utility/src/utility/sweatShop.H:65:11: note: Unused private function: 'sweatShop::worker'
canu-2.2/src/utility/src/utility/sweatShop.C:252:12: note: Unused private function: 'sweatShop::worker'
canu-2.2/src/utility/src/utility/sweatShop.C:339:12: style: Unused private function: 'sweatShop::writer' [unusedPrivateFunction]
canu-2.2/src/utility/src/utility/sweatShop.H:66:11: note: Unused private function: 'sweatShop::writer'
canu-2.2/src/utility/src/utility/sweatShop.C:339:12: note: Unused private function: 'sweatShop::writer'
canu-2.2/src/utility/src/utility/sweatShop.C:398:12: style: Unused private function: 'sweatShop::status' [unusedPrivateFunction]
canu-2.2/src/utility/src/utility/sweatShop.H:67:11: note: Unused private function: 'sweatShop::status'
canu-2.2/src/utility/src/utility/sweatShop.C:398:12: note: Unused private function: 'sweatShop::status'
canu-2.2/src/utility/src/utility/sweatShop.C:152:12: style: The member function 'sweatShop::loaderAddToLocal' can be static. [functionStatic]
canu-2.2/src/utility/src/utility/sweatShop.H:70:11: note: The member function 'sweatShop::loaderAddToLocal' can be static.
canu-2.2/src/utility/src/utility/sweatShop.C:152:12: note: The member function 'sweatShop::loaderAddToLocal' can be static.
canu-2.2/src/utility/src/utility/sweatShop.C:50:3: style: Class 'sweatShopState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
canu-2.2/src/utility/src/utility/sweatShop.C:71:19: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/sweatShop.C:77:25: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/sweatShop.C:83:19: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/sweatShop.C:89:19: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/sweatShop.C:185:19: style: Variable '_loaderP' is reassigned a value before the old one has been used. [redundantAssignment]
canu-2.2/src/utility/src/utility/sweatShop.C:181:19: note: _loaderP is assigned
canu-2.2/src/utility/src/utility/sweatShop.C:185:19: note: _loaderP is overwritten
canu-2.2/src/utility/src/utility/sweatShop.C:259:11: style: The scope of the variable 'err' can be reduced. [variableScope]
canu-2.2/src/utility/src/utility/sweatShop.C:96:29: style:inconclusive: Function 'sweatShop' argument 2 names different: declaration '<unnamed>' definition 'workerfcn'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/sweatShop.C:97:29: style:inconclusive: Function 'sweatShop' argument 3 names different: declaration '<unnamed>' definition 'writerfcn'. [funcArgNamesDifferentUnnamed]
canu-2.2/src/utility/src/utility/sweatShop.C:340:20: style: Variable 'deleteState' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/sweatShop.C:340:20: style: Variable 'deleteState' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sweatShop.C:405:21: style: Variable 'thisTime' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/sweatShop.C:410:21: style: Variable 'cpuPerSec' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/system.C:51:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/system.C:68:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/system.C:167:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SC_PHYS_PAGES [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/system.C:213:12: style: Variable 'env' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/system.C:213:18: style: Variable 'cpu' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/system.C:277:12: style: Variable 'env' can be declared as pointer to const [constVariablePointer]
canu-2.2/src/utility/src/utility/system.C:144:20: style: Variable 'epoch' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/system.C:145:20: style: Variable 'epochLen' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/system.C:147:20: style: Variable 'activeLen' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/types.C:182:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
canu-2.2/src/utility/src/utility/types.C:294:21: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
canu-2.2/src/utility/src/utility/types.C:310:21: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
canu-2.2/src/utility/src/utility/types.C:57:15: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/types.C:91:15: style: C-style pointer casting [cstyleCast]
canu-2.2/src/utility/src/utility/types.H:177:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:177:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:178:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:178:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:179:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:179:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:180:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:180:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:181:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:181:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:182:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:182:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:183:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:183:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:184:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:184:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:185:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:185:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:186:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:186:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:187:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:187:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:188:41: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:188:41: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:190:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:190:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:191:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:191:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:192:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:192:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:193:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:193:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:194:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:194:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:195:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:195:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:196:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:196:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:197:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:197:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:198:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:198:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:199:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:199:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:200:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:200:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:201:44: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:201:44: note: Shadow argument
canu-2.2/src/utility/src/utility/types.H:203:38: style: Argument 'str' shadows outer variable [shadowVariable]
canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
canu-2.2/src/utility/src/utility/types.H:203:38: note: Shadow argument
canu-2.2/src/utility/src/utility/types.C:294:23: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
canu-2.2/src/utility/src/utility/types.C:310:23: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
diff:
head canu-2.2/src/bogart/AS_BAT_Unitig.H:165:31: style: Argument 'ahang' shadows outer member [shadowMember]
     canu-2.2/src/bogart/AS_BAT_Unitig.H:200:20: note: Shadowed member
     canu-2.2/src/bogart/AS_BAT_Unitig.H:165:31: note: Shadow argument
head canu-2.2/src/bogart/AS_BAT_Unitig.H:165:44: style: Argument 'bhang' shadows outer member [shadowMember]
     canu-2.2/src/bogart/AS_BAT_Unitig.H:201:20: note: Shadowed member
     canu-2.2/src/bogart/AS_BAT_Unitig.H:165:44: note: Shadow argument
head canu-2.2/src/bogart/AS_BAT_Unitig.H:172:31: style: Argument 'ahang' shadows outer member [shadowMember]
     canu-2.2/src/bogart/AS_BAT_Unitig.H:200:20: note: Shadowed member
     canu-2.2/src/bogart/AS_BAT_Unitig.H:172:31: note: Shadow argument
head canu-2.2/src/bogart/AS_BAT_Unitig.H:172:44: style: Argument 'bhang' shadows outer member [shadowMember]
     canu-2.2/src/bogart/AS_BAT_Unitig.H:201:20: note: Shadowed member
     canu-2.2/src/bogart/AS_BAT_Unitig.H:172:44: note: Shadow argument
2.20.0 canu-2.2/src/correction/falconsense.C:631:21: style: Local variable 'ii' shadows outer variable [shadowVariable]
     canu-2.2/src/correction/falconsense.C:590:17: note: Shadowed declaration
     canu-2.2/src/correction/falconsense.C:631:21: note: Shadow variable
head canu-2.2/src/correction/falconsense.C:631:21: style: Local variable 'ii' shadows outer variable [shadowVariable]
     canu-2.2/src/correction/falconsense.C:590:17: note: Shadowed variable
     canu-2.2/src/correction/falconsense.C:631:21: note: Shadow local variable
2.20.0 canu-2.2/src/meryl/src/meryl/merylOp.C:48:11: style: Variable 'pre' can be declared as pointer to const [constVariablePointer]
head canu-2.2/src/overlapAlign/clearRangeFile.H:49:45: style: Argument 'bgn' shadows outer function [shadowFunction]
     canu-2.2/src/overlapAlign/clearRangeFile.H:44:13: note: Shadowed function
     canu-2.2/src/overlapAlign/clearRangeFile.H:49:45: note: Shadow argument
head canu-2.2/src/overlapAlign/clearRangeFile.H:49:57: style: Argument 'end' shadows outer function [shadowFunction]
     canu-2.2/src/overlapAlign/clearRangeFile.H:45:13: note: Shadowed function
     canu-2.2/src/overlapAlign/clearRangeFile.H:49:57: note: Shadow argument
head canu-2.2/src/overlapAlign/clearRangeFile.H:49:67: style: Argument 'deleted' shadows outer function [shadowFunction]
     canu-2.2/src/overlapAlign/clearRangeFile.H:47:13: note: Shadowed function
     canu-2.2/src/overlapAlign/clearRangeFile.H:49:67: note: Shadow argument
2.20.0 canu-2.2/src/overlapAlign/computeAlignments.C:164:15: style: Condition 'ashift3<bshift3' is always false [knownConditionTrueFalse]
     canu-2.2/src/overlapAlign/computeAlignments.C:141:18: note: bshift3 is assigned '(double)((bclrend>bovlend)?(0):(bovlend-bclrend))' here.
     canu-2.2/src/overlapAlign/computeAlignments.C:138:18: note: ashift3 is assigned '(double)((aclrend>aovlend)?(0):(aovlend-aclrend))' here.
     canu-2.2/src/overlapAlign/computeAlignments.C:164:15: note: Condition 'ashift3<bshift3' is always false
2.20.0 canu-2.2/src/overlapAlign/computeAlignments.C:278:15: style: Condition 'ashift5<bshift5' is always false [knownConditionTrueFalse]
     canu-2.2/src/overlapAlign/computeAlignments.C:259:18: note: bshift5 is assigned '(double)((bovl5<bclrend)?(0):(bovl5-bclrend))' here.
     canu-2.2/src/overlapAlign/computeAlignments.C:256:18: note: ashift5 is assigned '(double)((aclrbgn<aovl5)?(0):(aclrbgn-aovl5))' here.
     canu-2.2/src/overlapAlign/computeAlignments.C:278:15: note: Condition 'ashift5<bshift5' is always false
2.20.0 canu-2.2/src/overlapAlign/computeAlignments.C:287:15: style: Condition 'ashift3<bshift3' is always false [knownConditionTrueFalse]
     canu-2.2/src/overlapAlign/computeAlignments.C:260:18: note: bshift3 is assigned '(double)((bovl3>bclrbgn)?(0):(bclrbgn-bovl3))' here.
     canu-2.2/src/overlapAlign/computeAlignments.C:257:18: note: ashift3 is assigned '(double)((aclrend>aovl3)?(0):(aovl3-aclrend))' here.
     canu-2.2/src/overlapAlign/computeAlignments.C:287:15: note: Condition 'ashift3<bshift3' is always false
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:115:48: style: Parameter 'aend' can be declared as reference to const [constParameterReference]
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:564:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:564:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:564:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:564:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:565:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:565:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:565:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:565:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:567:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:567:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:567:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:567:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:568:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:568:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:568:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:568:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:609:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:609:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:609:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:609:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:610:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:610:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:610:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:610:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:612:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:612:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:612:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:612:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:613:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:613:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:613:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:613:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:657:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:657:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:657:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:657:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:658:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:658:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:658:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:658:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:660:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:660:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:660:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:660:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:661:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:661:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:661:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:661:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:702:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:702:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:702:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:702:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:703:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:703:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:703:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:703:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:705:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:705:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:705:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:705:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:706:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:706:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:706:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:706:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:739:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:739:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:739:13: style: Local variable 'abgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:533:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:739:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:740:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:740:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:740:13: style: Local variable 'aend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:534:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:740:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:742:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:742:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:742:13: style: Local variable 'bbgn' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:537:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:742:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:743:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:743:13: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:743:13: style: Local variable 'bend' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:538:11: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:743:13: note: Shadow local variable
2.20.0 canu-2.2/src/overlapAlign/computeOverlapAlignment.C:748:22: style: Local variable 'result' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:543:21: note: Shadowed declaration
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:748:22: note: Shadow variable
head canu-2.2/src/overlapAlign/computeOverlapAlignment.C:748:22: style: Local variable 'result' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:543:21: note: Shadowed variable
     canu-2.2/src/overlapAlign/computeOverlapAlignment.C:748:22: note: Shadow local variable
head canu-2.2/src/overlapErrorAdjustment/computeDiff.C:50:25: style: Condition 'i<-prefix_len' is always false [knownConditionTrueFalse]
head canu-2.2/src/overlapErrorAdjustment/correctionOutput.H:96:9: warning: Member variable 'Correction_Output_t::keep_left' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapErrorAdjustment/correctionOutput.H:97:9: warning: Member variable 'Correction_Output_t::keep_right' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapErrorAdjustment/correctionOutput.H:98:17: warning: Member variable 'Correction_Output_t::type' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:103:27: style: Parameter 'a_part' can be declared as pointer to const [constParameterPointer]
head canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:104:27: style: Parameter 'b_part' can be declared as pointer to const [constParameterPointer]
2.20.0 canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:248:18: style: Local variable 'p' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:124:10: note: Shadowed declaration
     canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:248:18: note: Shadow variable
head canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:248:18: style: Local variable 'p' shadows outer variable [shadowVariable]
     canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:124:10: note: Shadowed variable
     canu-2.2/src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C:248:18: note: Shadow local variable
head canu-2.2/src/overlapErrorAdjustment/findErrors.H:169:17: warning: Member variable 'Vote_t::vote_val' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapErrorAdjustment/findErrors.H:312:17: warning: Member variable 'Thread_Work_Area_t::rev_seq' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapErrorAdjustment/findErrors.H:315:17: warning: Member variable 'Thread_Work_Area_t::globalvote' has no initializer. [uninitMemberVarNoCtor]
2.20.0 canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:116:50: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:108:22: note: Assuming allocation function fails
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:108:22: note: Assignment 'F=fopen(N,"r")', assigned value is 0
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:109:11: note: Assuming condition is false
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:116:50: note: Null pointer dereference
2.20.0 canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:117:50: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:108:22: note: Assuming allocation function fails
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:108:22: note: Assignment 'F=fopen(N,"r")', assigned value is 0
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:109:11: note: Assuming condition is false
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:117:50: note: Null pointer dereference
2.20.0 canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:122:14: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:108:22: note: Assuming allocation function fails
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:108:22: note: Assignment 'F=fopen(N,"r")', assigned value is 0
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:109:11: note: Assuming condition is false
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:122:14: note: Null pointer dereference
2.20.0 canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:145:55: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:140:22: note: Assuming allocation function fails
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:140:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:141:11: note: Assuming condition is false
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:145:55: note: Null pointer dereference
2.20.0 canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:146:55: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:140:22: note: Assuming allocation function fails
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:140:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:141:11: note: Assuming condition is false
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:146:55: note: Null pointer dereference
2.20.0 canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:148:14: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:140:22: note: Assuming allocation function fails
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:140:22: note: Assignment 'F=fopen(O,"w")', assigned value is 0
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:141:11: note: Assuming condition is false
     canu-2.2/src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C:148:14: note: Null pointer dereference
head canu-2.2/src/overlapInCore/overlapInCore.H:198:11: warning: Member variable 'String_Olap_Node::diag_sum' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:200:11: warning: Member variable 'String_Olap_Node::diag_bgn' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:201:11: warning: Member variable 'String_Olap_Node::diag_end' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:202:15: warning: Member variable 'String_Olap_Node::Next' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:203:13: warning: Member variable 'String_Olap_Node::Full' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:204:13: warning: Member variable 'String_Olap_Node::consistent' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:227:20: warning: Member variable 'Work_Area::String_Olap_Space' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:231:19: warning: Member variable 'Work_Area::Match_Node_Space' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:240:13: warning: Member variable 'Work_Area::readStore' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:241:13: warning: Member variable 'Work_Area::readCache' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:243:10: warning: Member variable 'Work_Area::left_end_screened' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:244:10: warning: Member variable 'Work_Area::right_end_screened' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:246:10: warning: Member variable 'Work_Area::status' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:247:10: warning: Member variable 'Work_Area::thread_id' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:256:18: warning: Member variable 'Work_Area::overlaps' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:270:24: warning: Member variable 'Work_Area::editDist' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:273:11: warning: Member variable 'Work_Area::q_diff' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:274:18: warning: Member variable 'Work_Area::distinct_olap' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:319:18: warning: Member variable 'Hash_Bucket::Check' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/overlapInCore/overlapInCore.H:320:18: warning: Member variable 'Hash_Bucket::Hits' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/stores/sqLibrary.H:116:19: warning: Member variable 'sqLibrary::_libraryName' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/stores/sqLibrary.H:119:19: warning: Member variable 'sqLibrary::_techType' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/stores/sqLibrary.H:127:19: warning: Member variable 'sqLibrary::_U_keys' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/stores/sqLibrary.H:128:19: warning: Member variable 'sqLibrary::_U_values' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/stores/sqLibrary.H:132:19: warning: Member variable 'sqLibrary::_U_kvData' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/stores/tgTig.H:107:41: style: Argument 'anchor' shadows outer function [shadowFunction]
     canu-2.2/src/stores/tgTig.H:81:24: note: Shadowed function
     canu-2.2/src/stores/tgTig.H:107:41: note: Shadow argument
head canu-2.2/src/stores/tgTig.H:114:46: style: Argument 'anchor' shadows outer function [shadowFunction]
     canu-2.2/src/stores/tgTig.H:81:24: note: Shadowed function
     canu-2.2/src/stores/tgTig.H:114:46: note: Shadow argument
head canu-2.2/src/stores/tgTig.H:114:87: style: Argument 'bgn' shadows outer function [shadowFunction]
     canu-2.2/src/stores/tgTig.H:90:24: note: Shadowed function
     canu-2.2/src/stores/tgTig.H:114:87: note: Shadow argument
head canu-2.2/src/stores/tgTig.H:114:99: style: Argument 'end' shadows outer function [shadowFunction]
     canu-2.2/src/stores/tgTig.H:91:24: note: Shadowed function
     canu-2.2/src/stores/tgTig.H:114:99: note: Shadow argument
head canu-2.2/src/stores/tgTig.H:144:40: style: Argument 'min' shadows outer function [shadowFunction]
     canu-2.2/src/stores/tgTig.H:93:24: note: Shadowed function
     canu-2.2/src/stores/tgTig.H:144:40: note: Shadow argument
head canu-2.2/src/stores/tgTig.H:144:51: style: Argument 'max' shadows outer function [shadowFunction]
     canu-2.2/src/stores/tgTig.H:94:24: note: Shadowed function
     canu-2.2/src/stores/tgTig.H:144:51: note: Shadow argument
2.20.0 canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:219:11: style: Variable 'ul' is assigned an expression that holds the same value. [redundantAssignment]
     canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:206:17: note: ul is assigned 'lastCol[j-1]+((stringA[i-1]==stringB[j-1])?3:-4)' here.
     canu-2.2/src/utgcns/libNNalign/NNalgorithm.C:219:11: note: Variable 'ul' is assigned an expression that holds the same value.
head canu-2.2/src/utgcns/libNNalign/NNalign.C:27:16: warning: Member variable 'Optimal_Overlap_Data::h_alignA' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/utgcns/libNNalign/NNalign.C:28:16: warning: Member variable 'Optimal_Overlap_Data::h_alignB' has no initializer. [uninitMemberVarNoCtor]
head canu-2.2/src/utgcns/libNNalign/NNalign.C:29:16: warning: Member variable 'Optimal_Overlap_Data::h_trace' has no initializer. [uninitMemberVarNoCtor]
2.20.0 canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:24: style: Local variable 'ii' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:224:16: note: Shadowed declaration
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:24: note: Shadow variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:24: style: Local variable 'ii' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:224:16: note: Shadowed variable
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:24: note: Shadow local variable
2.20.0 canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:28: style: Local variable 'ie' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:224:20: note: Shadowed declaration
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:28: note: Shadow variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:28: style: Local variable 'ie' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:224:20: note: Shadowed variable
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:256:28: note: Shadow local variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:257:21: style: Local variable 'n' shadows outer argument [shadowArgument]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:222:42: note: Shadowed argument
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:257:21: note: Shadow local variable
2.20.0 canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:257:21: style: Local variable 'n' shadows outer argument [shadowArgument]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:222:42: note: Shadowed declaration
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:257:21: note: Shadow variable
2.20.0 canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:25: style: Local variable 'oi' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:279:17: note: Shadowed declaration
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:25: note: Shadow variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:25: style: Local variable 'oi' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:279:17: note: Shadowed variable
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:25: note: Shadow local variable
2.20.0 canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:29: style: Local variable 'oe' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:279:21: note: Shadowed declaration
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:29: note: Shadow variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:29: style: Local variable 'oe' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:279:21: note: Shadowed variable
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:309:29: note: Shadow local variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:310:21: style: Local variable 'n' shadows outer argument [shadowArgument]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:277:43: note: Shadowed argument
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:310:21: note: Shadow local variable
2.20.0 canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:310:21: style: Local variable 'n' shadows outer argument [shadowArgument]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:277:43: note: Shadowed declaration
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:310:21: note: Shadow variable
2.20.0 canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:25: style: Local variable 'oi' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:458:21: note: Shadowed declaration
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:25: note: Shadow variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:25: style: Local variable 'oi' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:458:21: note: Shadowed variable
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:25: note: Shadow local variable
2.20.0 canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:29: style: Local variable 'oe' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:458:25: note: Shadowed declaration
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:29: note: Shadow variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:29: style: Local variable 'oe' shadows outer variable [shadowVariable]
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:458:25: note: Shadowed variable
     canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.C:484:29: note: Shadow local variable
head canu-2.2/src/utgcns/libpbutgcns/AlnGraphBoost.H:120:9: warning: Member variable 'CnsResult::range' has no initializer. [uninitMemberVarNoCtor]
2.20.0 canu-2.2/src/utility/src/parasail/cigar_template.c:108:16: style: Local variable 'i' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/parasail/cigar_template.c:77:13: note: Shadowed declaration
     canu-2.2/src/utility/src/parasail/cigar_template.c:108:16: note: Shadow variable
head canu-2.2/src/utility/src/parasail/cigar_template.c:108:16: style: Local variable 'i' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/parasail/cigar_template.c:77:13: note: Shadowed variable
     canu-2.2/src/utility/src/parasail/cigar_template.c:108:16: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/parasail/cigar_template.c:172:28: style: Local variable 'i' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/parasail/cigar_template.c:77:13: note: Shadowed declaration
     canu-2.2/src/utility/src/parasail/cigar_template.c:172:28: note: Shadow variable
head canu-2.2/src/utility/src/parasail/cigar_template.c:172:28: style: Local variable 'i' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/parasail/cigar_template.c:77:13: note: Shadowed variable
     canu-2.2/src/utility/src/parasail/cigar_template.c:172:28: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/tests/fasta-fastq.C:109:11: style: Local variable 'F' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/tests/fasta-fastq.C:90:11: note: Shadowed declaration
     canu-2.2/src/utility/src/tests/fasta-fastq.C:109:11: note: Shadow variable
head canu-2.2/src/utility/src/tests/fasta-fastq.C:109:11: style: Local variable 'F' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/tests/fasta-fastq.C:90:11: note: Shadowed variable
     canu-2.2/src/utility/src/tests/fasta-fastq.C:109:11: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/tests/fasta-fastq.C:138:11: style: Local variable 'F' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/tests/fasta-fastq.C:90:11: note: Shadowed declaration
     canu-2.2/src/utility/src/tests/fasta-fastq.C:138:11: note: Shadow variable
head canu-2.2/src/utility/src/tests/fasta-fastq.C:138:11: style: Local variable 'F' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/tests/fasta-fastq.C:90:11: note: Shadowed variable
     canu-2.2/src/utility/src/tests/fasta-fastq.C:138:11: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/tests/magicNumber.C:43:10: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/utility/src/tests/magicNumber.C:41:12: note: Assuming allocation function fails
     canu-2.2/src/utility/src/tests/magicNumber.C:41:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
     canu-2.2/src/utility/src/tests/magicNumber.C:43:10: note: Null pointer dereference
2.20.0 canu-2.2/src/utility/src/tests/magicNumber.C:49:36: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/utility/src/tests/magicNumber.C:45:12: note: Assuming allocation function fails
     canu-2.2/src/utility/src/tests/magicNumber.C:45:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
     canu-2.2/src/utility/src/tests/magicNumber.C:49:36: note: Null pointer dereference
head canu-2.2/src/utility/src/tests/magicNumber.C:63:10: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/utility/src/tests/magicNumber.C:45:12: note: Assuming allocation function fails
     canu-2.2/src/utility/src/tests/magicNumber.C:45:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
     canu-2.2/src/utility/src/tests/magicNumber.C:46:29: note: Assuming condition is false
     canu-2.2/src/utility/src/tests/magicNumber.C:63:10: note: Null pointer dereference
2.20.0 canu-2.2/src/utility/src/tests/magicNumber.C:63:10: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/utility/src/tests/magicNumber.C:45:12: note: Assuming allocation function fails
     canu-2.2/src/utility/src/tests/magicNumber.C:45:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
     canu-2.2/src/utility/src/tests/magicNumber.C:63:10: note: Null pointer dereference
2.20.0 canu-2.2/src/utility/src/tests/magicNumber.C:69:36: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/utility/src/tests/magicNumber.C:65:12: note: Assuming allocation function fails
     canu-2.2/src/utility/src/tests/magicNumber.C:65:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
     canu-2.2/src/utility/src/tests/magicNumber.C:69:36: note: Null pointer dereference
head canu-2.2/src/utility/src/tests/magicNumber.C:79:10: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/utility/src/tests/magicNumber.C:65:12: note: Assuming allocation function fails
     canu-2.2/src/utility/src/tests/magicNumber.C:65:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
     canu-2.2/src/utility/src/tests/magicNumber.C:66:29: note: Assuming condition is false
     canu-2.2/src/utility/src/tests/magicNumber.C:79:10: note: Null pointer dereference
2.20.0 canu-2.2/src/utility/src/tests/magicNumber.C:79:10: warning: If resource allocation fails, then there is a possible null pointer dereference: F [nullPointerOutOfResources]
     canu-2.2/src/utility/src/tests/magicNumber.C:65:12: note: Assuming allocation function fails
     canu-2.2/src/utility/src/tests/magicNumber.C:65:12: note: Assignment 'F=fopen(argv[1],"r")', assigned value is 0
     canu-2.2/src/utility/src/tests/magicNumber.C:79:10: note: Null pointer dereference
2.20.0 canu-2.2/src/utility/src/utility/files-buffered.C:34:9: style: Local variable 'filename' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/files-buffered.H:87:24: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/files-buffered.C:34:9: note: Shadow variable
2.20.0 canu-2.2/src/utility/src/utility/files-buffered.C:407:9: style: Local variable 'filename' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/files-buffered.H:130:24: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/files-buffered.C:407:9: note: Shadow variable
head canu-2.2/src/utility/src/utility/files-buffered.C:425:37: style: Argument 'filename' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/files-buffered.H:130:24: note: Shadowed function
     canu-2.2/src/utility/src/utility/files-buffered.C:425:37: note: Shadow argument
head canu-2.2/src/utility/src/utility/files-buffered.C:51:36: style: Argument 'filename' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/files-buffered.H:87:24: note: Shadowed function
     canu-2.2/src/utility/src/utility/files-buffered.C:51:36: note: Shadow argument
2.20.0 canu-2.2/src/utility/src/utility/kmers-exact.C:291:18: style: Local variable 'value' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/kmers-exact.C:291:18: note: Shadow variable
head canu-2.2/src/utility/src/utility/kmers-exact.C:291:18: style: Local variable 'value' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed function
     canu-2.2/src/utility/src/utility/kmers-exact.C:291:18: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/utility/kmers-exact.C:455:18: style: Local variable 'value' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/kmers-exact.C:455:18: note: Shadow variable
head canu-2.2/src/utility/src/utility/kmers-exact.C:455:18: style: Local variable 'value' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed function
     canu-2.2/src/utility/src/utility/kmers-exact.C:455:18: note: Shadow local variable
head canu-2.2/src/utility/src/utility/kmers-files.C:129:43: style: Argument 'suffixes' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-files.H:73:13: note: Shadowed function
     canu-2.2/src/utility/src/utility/kmers-files.C:129:43: note: Shadow argument
head canu-2.2/src/utility/src/utility/kmers-files.C:129:61: style: Argument 'values' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-files.H:74:13: note: Shadowed function
     canu-2.2/src/utility/src/utility/kmers-files.C:129:61: note: Shadow argument
head canu-2.2/src/utility/src/utility/kmers-lookup.H:152:38: style: Argument 'value' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed function
     canu-2.2/src/utility/src/utility/kmers-lookup.H:152:38: note: Shadow argument
head canu-2.2/src/utility/src/utility/kmers-lookup.H:212:42: style: Argument 'value' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-lookup.H:86:12: note: Shadowed function
     canu-2.2/src/utility/src/utility/kmers-lookup.H:212:42: note: Shadow argument
head canu-2.2/src/utility/src/utility/kmers-reader.C:129:50: style: Argument 'loadStatistics' shadows outer function [shadowFunction]
     canu-2.2/src/utility/src/utility/kmers-reader.H:60:11: note: Shadowed function
     canu-2.2/src/utility/src/utility/kmers-reader.C:129:50: note: Shadow argument
2.20.0 canu-2.2/src/utility/src/utility/kmers-tiny.H:132:15: style:inconclusive: Technically the member function 'kmerTiny::operator++' can be const. [functionConst]
2.20.0 canu-2.2/src/utility/src/utility/kmers-tiny.H:135:15: style:inconclusive: Technically the member function 'kmerTiny::operator--' can be const. [functionConst]
head canu-2.2/src/utility/src/utility/md5.C:118:24: style:inconclusive: Function 'MD5Init' argument 1 names different: declaration '<unnamed>' definition 'context'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:131:26: style:inconclusive: Function 'MD5Update' argument 1 names different: declaration '<unnamed>' definition 'context'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:131:56: style:inconclusive: Function 'MD5Update' argument 2 names different: declaration '<unnamed>' definition 'input'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:131:70: style:inconclusive: Function 'MD5Update' argument 3 names different: declaration '<unnamed>' definition 'inputLen'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:165:30: style:inconclusive: Function 'MD5Final' argument 1 names different: declaration '<unnamed>' definition 'digest'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:165:51: style:inconclusive: Function 'MD5Final' argument 2 names different: declaration '<unnamed>' definition 'context'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:277:36: style:inconclusive: Function 'Encode' argument 1 names different: declaration '<unnamed>' definition 'output'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:277:52: style:inconclusive: Function 'Encode' argument 2 names different: declaration '<unnamed>' definition 'input'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:277:72: style:inconclusive: Function 'Encode' argument 3 names different: declaration '<unnamed>' definition 'len'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:291:29: style:inconclusive: Function 'Decode' argument 1 names different: declaration '<unnamed>' definition 'output'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:291:58: style:inconclusive: Function 'Decode' argument 2 names different: declaration '<unnamed>' definition 'input'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/md5.C:291:78: style:inconclusive: Function 'Decode' argument 3 names different: declaration '<unnamed>' definition 'len'. [funcArgNamesDifferentUnnamed]
2.20.0 canu-2.2/src/utility/src/utility/md5.C:388:3: error: Memory leak: m.context [memleak]
2.20.0 canu-2.2/src/utility/src/utility/mt19937ar.C:143:18: error: Array 'mt[624]' accessed at index 4294967691, which is out of bounds. [arrayIndexOutOfBounds]
     canu-2.2/src/utility/src/utility/mt19937ar.C:141:15: note: Assuming that condition 'kk<MT_N-1' is not redundant
     canu-2.2/src/utility/src/utility/mt19937ar.C:143:18: note: Array index out of bounds
2.20.0 canu-2.2/src/utility/src/utility/sequence.C:368:13: style: Local variable 'c1' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:363:12: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/sequence.C:368:13: note: Shadow variable
head canu-2.2/src/utility/src/utility/sequence.C:368:13: style: Local variable 'c1' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:363:12: note: Shadowed variable
     canu-2.2/src/utility/src/utility/sequence.C:368:13: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/utility/sequence.C:369:13: style: Local variable 'c2' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:364:12: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/sequence.C:369:13: note: Shadow variable
head canu-2.2/src/utility/src/utility/sequence.C:369:13: style: Local variable 'c2' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:364:12: note: Shadowed variable
     canu-2.2/src/utility/src/utility/sequence.C:369:13: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/utility/sequence.C:370:13: style: Local variable 'c3' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:365:12: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/sequence.C:370:13: note: Shadow variable
head canu-2.2/src/utility/src/utility/sequence.C:370:13: style: Local variable 'c3' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:365:12: note: Shadowed variable
     canu-2.2/src/utility/src/utility/sequence.C:370:13: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/utility/sequence.C:378:13: style: Local variable 'c1' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:363:12: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/sequence.C:378:13: note: Shadow variable
head canu-2.2/src/utility/src/utility/sequence.C:378:13: style: Local variable 'c1' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:363:12: note: Shadowed variable
     canu-2.2/src/utility/src/utility/sequence.C:378:13: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/utility/sequence.C:379:13: style: Local variable 'c2' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:364:12: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/sequence.C:379:13: note: Shadow variable
head canu-2.2/src/utility/src/utility/sequence.C:379:13: style: Local variable 'c2' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:364:12: note: Shadowed variable
     canu-2.2/src/utility/src/utility/sequence.C:379:13: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/utility/sequence.C:380:13: style: Local variable 'c3' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:365:12: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/sequence.C:380:13: note: Shadow variable
head canu-2.2/src/utility/src/utility/sequence.C:380:13: style: Local variable 'c3' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:365:12: note: Shadowed variable
     canu-2.2/src/utility/src/utility/sequence.C:380:13: note: Shadow local variable
2.20.0 canu-2.2/src/utility/src/utility/sequence.C:671:13: style: Local variable 'indexFile' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:668:16: note: Shadowed declaration
     canu-2.2/src/utility/src/utility/sequence.C:671:13: note: Shadow variable
head canu-2.2/src/utility/src/utility/sequence.C:671:13: style: Local variable 'indexFile' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/sequence.C:668:16: note: Shadowed variable
     canu-2.2/src/utility/src/utility/sequence.C:671:13: note: Shadow local variable
head canu-2.2/src/utility/src/utility/sweatShop.C:96:29: style:inconclusive: Function 'sweatShop' argument 2 names different: declaration '<unnamed>' definition 'workerfcn'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/sweatShop.C:97:29: style:inconclusive: Function 'sweatShop' argument 3 names different: declaration '<unnamed>' definition 'writerfcn'. [funcArgNamesDifferentUnnamed]
head canu-2.2/src/utility/src/utility/types.H:177:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:177:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:178:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:178:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:179:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:179:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:180:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:180:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:181:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:181:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:182:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:182:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:183:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:183:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:184:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:184:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:185:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:185:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:186:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:186:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:187:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:187:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:188:41: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:188:41: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:190:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:190:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:191:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:191:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:192:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:192:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:193:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:193:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:194:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:194:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:195:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:195:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:196:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:196:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:197:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:197:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:198:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:198:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:199:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:199:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:200:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:200:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:201:44: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:201:44: note: Shadow argument
head canu-2.2/src/utility/src/utility/types.H:203:38: style: Argument 'str' shadows outer variable [shadowVariable]
     canu-2.2/src/utility/src/utility/types.C:334:10: note: Shadowed variable
     canu-2.2/src/utility/src/utility/types.H:203:38: note: Shadow argument


DONE