2026-05-01 08:19
ftp://ftp.de.debian.org/debian/pool/main/c/cd-hit/cd-hit_4.8.1.orig.tar.gz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib --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 -j1
platform: Linux-6.8.0-1047-aws-aarch64-with-glibc2.35
python: 3.10.12
client-version: 1.4.0
compiler: g++ (Ubuntu 11.4.0-1ubuntu1~22.04.3) 11.4.0
cppcheck: head 2.20.0
head-info: 0fda84e (2026-05-01 02:32:52 +0200)
count: 469 431
elapsed-time: 7.3 6.0
head-timing-info:

old-timing-info:

head results:
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:236:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.hxx:67:3: warning: Class 'SequenceCache' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.hxx:67:3: warning: Class 'SequenceCache' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.hxx:66:2: style: Class 'SequenceCache' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:50:4: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:56:4: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:63:4: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:74:8: style: The scope of the variable 'res' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:133:8: style: The scope of the variable 'res' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:14:9: style: Local variable 'des' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.hxx:19:15: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:14:9: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:74:8: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:133:8: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:76:14: style: Variable 'ds' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:84:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:102:14: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:137:14: style: Variable 'ds' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:144:11: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:164:14: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:625:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:948:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable head [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:251:6: style:inconclusive: Technically the member function 'HashHit3::BestOffset' can be const. [functionConst]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:24:2: style: Class 'SequenceCluster' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:206:2: style: Struct 'ChimericSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:213:2: style: Struct 'HashHit' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:223:2: style: Struct 'HashHit3' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:523:2: style: Struct 'ParentInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:538:2: style: Struct 'OffsetCount' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:839:2: portability: %i in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:849:3: portability: %i in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:926:2: portability: %i in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:282:15: style: The scope of the variable 'hash' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:61:74: style:inconclusive: Function 'Write' argument 4 names different: declaration 'des' definition 'cdes'. [funcArgNamesDifferent]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:43:73: note: Function 'Write' argument 4 names different: declaration 'des' definition 'cdes'.
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:61:74: note: Function 'Write' argument 4 names different: declaration 'des' definition 'cdes'.
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:71:10: style: Local variable 'des' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:65:9: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:71:10: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:590:7: style: Local variable 'maxmm' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:552:22: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:590:7: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:591:7: style: Local variable 'maxmm2' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:552:33: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:591:7: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:624:9: style: Local variable 'hit' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:605:13: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:624:9: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:638:8: style: Local variable 'hit' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:605:13: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:638:8: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:872:8: style: Local variable 'i' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:785:6: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:872:8: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:872:14: style: Local variable 'm' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:785:12: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:872:14: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:902:8: style: Local variable 'i' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:785:6: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:902:8: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:902:14: style: Local variable 'm' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:785:12: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:902:14: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:706:17: style: Variable 'infoA' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:709:18: style: Variable 'infoB' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:900:13: style: Variable 'qs1' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:768:27: style: Parameter 'argv' can be declared as const array [constParameter]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:267:20: style: Variable 'hash' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:283:12: style: Unused variable: k [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:283:18: style: Unused variable: K2 [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:284:19: style: Variable 'count' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:551:15: style: Unused variable: K [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:551:18: style: Unused variable: K2 [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:552:33: style: Variable 'maxmm2' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:610:8: style: Variable 'duplicate' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:612:7: style: Variable 'dep' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:872:16: style: Variable 'm' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:872:8: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:872:11: style: Unused variable: j [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:902:8: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:902:11: style: Unused variable: j [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:902:14: style: Variable 'm' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:97:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seq [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:340:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:40:2: style: Struct 'ClusterMember' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:56:2: style: Class 'SequenceCluster' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:357:2: portability: %i in format string (no. 1) requires 'int' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:93:74: style:inconclusive: Function 'Write' argument 4 names different: declaration 'des' definition 'cdes'. [funcArgNamesDifferent]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:75:73: note: Function 'Write' argument 4 names different: declaration 'des' definition 'cdes'.
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:93:74: note: Function 'Write' argument 4 names different: declaration 'des' definition 'cdes'.
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:106:10: style: Local variable 'des' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:97:9: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:106:10: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:184:13: style: Local variable 'ss' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:178:11: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:184:13: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:195:19: style: Local variable 'm' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:165:19: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:195:19: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:216:14: style: Local variable 'ss' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:178:11: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:216:14: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:227:20: style: Local variable 'm' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:165:19: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:227:20: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:98:11: style: Variable 'rep' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:105:12: style: Variable 'seq' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:152:37: style: Parameter 'seqlist' can be declared as reference to const [constParameterReference]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:278:27: style: Parameter 'argv' can be declared as const array [constParameter]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:98:15: style: Variable 'rep' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:105:16: style: Variable 'seq' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:129:7: style: Unused variable: cdes [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:131:14: style: Variable 'k2' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:289:9: style: Unused variable: m [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:33:2: warning: Member variable 'DNode::color' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:33:2: warning: Member variable 'DNode::hash' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:33:2: warning: Member variable 'DNode::next' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:35:8: warning: Member variable 'DTree::first' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:35:8: warning: Member variable 'DTree::last' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:99:3: performance: Variable 'key' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:100:3: performance: Variable 'value' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:130:13: style: The member function 'Min::DTree::DeleteTree' can be static. [functionStatic]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:72:7: note: The member function 'Min::DTree::DeleteTree' can be static.
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:130:13: note: The member function 'Min::DTree::DeleteTree' can be static.
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:170:13: style: The member function 'Min::DMap::FindChild' can be static. [functionStatic]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:50:20: warning: Struct 'DTree' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:50:20: warning: Struct 'DTree' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:135:13: warning: The struct 'DMap' defines member function with name 'First' also defined in its parent struct 'DTree'. [duplInheritedMember]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:94:15: note: Parent function 'DTree::First'
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:135:13: note: Derived function 'DMap::First'
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:137:19: warning: The struct 'DMap' defines member function with name 'First' also defined in its parent struct 'DTree'. [duplInheritedMember]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:104:21: note: Parent function 'DTree::First'
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:137:19: note: Derived function 'DMap::First'
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:149:2: style: Struct 'DMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:103:7: style: The function 'HashKey' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:39:15: note: Virtual function in base class
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:103:7: note: Function in derived class
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:104:7: style: The function 'CopyValue' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:40:15: note: Virtual function in base class
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:104:7: note: Function in derived class
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:151:14: style: The function 'CompareNode' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:61:14: note: Virtual function in base class
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:151:14: note: Function in derived class
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:156:7: style: The function 'SwapNode' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:62:15: note: Virtual function in base class
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:156:7: note: Function in derived class
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:15:6: style: Condition 'p' is always true [knownConditionTrueFalse]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:129:44: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:14:13: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:20:13: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:44:11: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:59:11: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:375:16: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:504:31: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:104:43: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:129:10: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:135:29: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:136:51: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:137:40: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:138:62: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:152:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:153:22: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:158:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:159:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:184:23: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:187:24: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:194:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:198:11: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:507:21: warning: Potentially invalid type conversion in old-style C cast, clarify/fix with C++ cast [dangerousTypeCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:275:6: style: Variable 'parent' is assigned an expression that holds the same value. [redundantAssignment]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:264:20: note: parent is assigned 'node->parent' here.
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:275:6: note: Variable 'parent' is assigned an expression that holds the same value.
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:308:8: style: Variable 'parent' is assigned an expression that holds the same value. [redundantAssignment]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:275:13: note: parent is assigned 'node->parent' here.
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:277:10: note: Assuming condition is false
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:308:8: note: Variable 'parent' is assigned an expression that holds the same value.
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:174:7: style: The scope of the variable 'compare' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:195:7: style: The scope of the variable 'id' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:54:6: style: The scope of the variable 'i' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:107:6: style: The scope of the variable 'i' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:181:28: style: The scope of the variable 'uncle' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:383:6: style: The scope of the variable 'compare' can be reduced. [variableScope]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:35:20: style:inconclusive: Function 'DTree' argument 1 names different: declaration 'hashing' definition 'hs'. [funcArgNamesDifferent]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:53:14: note: Function 'DTree' argument 1 names different: declaration 'hashing' definition 'hs'.
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:35:20: note: Function 'DTree' argument 1 names different: declaration 'hashing' definition 'hs'.
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:371:9: style: Local variable 'tsize' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.hxx:50:10: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:371:9: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:463:20: style: Parameter 'left' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minMap.cxx:463:32: style: Parameter 'right' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.hxx:23:2: style: Class 'String' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.hxx:24:2: style: Class 'String' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:55:2: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:68:3: error: Common realloc mistake: 'data' nulled but not freed upon failure [memleakOnRealloc]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:84:15: warning: Either the condition 'data' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:86:6: note: Assuming that condition 'data' is not redundant
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:84:15: note: Null pointer addition
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:179:15: warning: Either the condition 'data' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:181:6: note: Assuming that condition 'data' is not redundant
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:179:15: note: Null pointer addition
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:186:15: warning: Either the condition 'data' is redundant or there is pointer arithmetic with NULL pointer. [nullPointerArithmeticRedundantCheck]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:188:6: note: Assuming that condition 'data' is not redundant
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:186:15: note: Null pointer addition
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:55:9: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:68:10: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:294:18: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:310:9: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:73:17: style: Variable 'bufsize' is reassigned a value before the old one has been used. [redundantAssignment]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:69:11: note: bufsize is assigned
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:73:17: note: bufsize is overwritten
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:294:11: style: Local variable 'data' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.hxx:17:8: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:294:11: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:300:13: style: Local variable 'm' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:293:16: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:300:13: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:331:13: style: Local variable 'm' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:293:16: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:331:13: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:96:28: style: Parameter 'chs' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:228:49: style: Parameter 'W' can be declared as const array [constParameter]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:228:65: style: Parameter 'K' can be declared as const array [constParameter]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:230:18: style: Variable 'R' can be declared as const array [constVariable]
cdhit-4.8.1/cd-hit-auxtools/mintlib/minString.cxx:318:4: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:19:2: style: Class 'SequenceLinker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:56:70: style: Condition 'second[j]=='N'' is always true [knownConditionTrueFalse]
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:56:50: note: Assuming that condition 'first[i]=='N'' is not redundant
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:56:23: note: Assuming that condition 'first[i]!=second[j]' is not redundant
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:56:70: note: Condition 'second[j]=='N'' is always true
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:237:11: style: Local variable 'i' shadows outer variable [shadowVariable]
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:181:6: note: Shadowed declaration
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:237:11: note: Shadow variable
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:173:27: style: Parameter 'argv' can be declared as const array [constParameter]
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:136:21: style: Variable 'qs1' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:140:14: style: Variable 'm' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:140:6: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cd-hit-auxtools/read-linker.cxx:140:9: style: Unused variable: j [unusedVariable]
cdhit-4.8.1/cdhit-2d.c++:59:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.h:313:2: warning: Member variable 'Options::NAAN' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:439:2: warning: Member variable 'WorkingParam::len_eff' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:439:2: warning: Member variable 'WorkingParam::aln_cover_flag' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:439:2: warning: Member variable 'WorkingParam::min_aln_lenS' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:439:2: warning: Member variable 'WorkingParam::min_aln_lenL' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:439:2: warning: Member variable 'WorkingParam::required_aa1' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:439:2: warning: Member variable 'WorkingParam::required_aas' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:439:2: warning: Member variable 'WorkingParam::required_aan' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:556:3: warning: Member variable 'SequenceDB::NAAN' is not initialized in the constructor. [uninitMemberVar]
cdhit-4.8.1/cdhit-common.h:129:33: warning: Class 'NVector < IndexCount >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cdhit-common.h:129:33: warning: Class 'NVector < uint32_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cdhit-common.h:129:33: warning: Class 'NVector < int64_t >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cdhit-common.h:129:33: warning: Class 'NVector < int >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cdhit-common.h:220:2: style: Struct 'IndexCount' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:238:3: style: Class 'WordTable' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:439:2: style: Struct 'WorkingParam' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:487:2: style: Struct 'WorkingBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:117:3: style: Class 'NVector < IndexCount >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:117:3: style: Class 'NVector < uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:117:3: style: Class 'NVector < int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:117:3: style: Class 'NVector < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < NVector < IndexCount > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < Sequence * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < unsigned int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < NVector < int64_t > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < NVector < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < char >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:144:13: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cdhit-common.h:152:13: style: C-style pointer casting [cstyleCast]
cdhit-4.8.1/cdhit-454.c++:94:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:454:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:461:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:469:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:475:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:1296:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:1386:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:1470:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:2253:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:2613:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:2677:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:2951:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:3023:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable frac [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:3070:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable total_bytes [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:3327:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable count [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:3630:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:3736:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:3857:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-common.c++:894:37: style:inconclusive: Boolean expression 'i==len1' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
cdhit-4.8.1/cdhit-common.c++:988:24: style:inconclusive: Boolean expression 'last!=back' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
cdhit-4.8.1/cdhit-common.c++:988:35: style:inconclusive: Boolean expression 'j!=len2' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
cdhit-4.8.1/cdhit-common.c++:1010:24: style:inconclusive: Boolean expression 'last!=back' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
cdhit-4.8.1/cdhit-common.c++:1010:35: style:inconclusive: Boolean expression 'i!=len1' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
cdhit-4.8.1/cdhit-common.c++:1317:16: style: The member function 'WordTable::AddWordCountsFrag' can be static. [functionStatic]
cdhit-4.8.1/cdhit-common.h:243:8: note: The member function 'WordTable::AddWordCountsFrag' can be static.
cdhit-4.8.1/cdhit-common.c++:1317:16: note: The member function 'WordTable::AddWordCountsFrag' can be static.
cdhit-4.8.1/cdhit-common.c++:1690:18: style: The member function 'SequenceDB::Readgz' can be static. [functionStatic]
cdhit-4.8.1/cdhit-common.h:566:8: note: The member function 'SequenceDB::Readgz' can be static.
cdhit-4.8.1/cdhit-common.c++:1690:18: note: The member function 'SequenceDB::Readgz' can be static.
cdhit-4.8.1/cdhit-common.c++:1883:18: style: The member function 'SequenceDB::Readgz' can be static. [functionStatic]
cdhit-4.8.1/cdhit-common.h:569:8: note: The member function 'SequenceDB::Readgz' can be static.
cdhit-4.8.1/cdhit-common.c++:1883:18: note: The member function 'SequenceDB::Readgz' can be static.
cdhit-4.8.1/cdhit-common.c++:2348:18: style: The member function 'SequenceDB::WriteClustersgz' can be static. [functionStatic]
cdhit-4.8.1/cdhit-common.h:572:8: note: The member function 'SequenceDB::WriteClustersgz' can be static.
cdhit-4.8.1/cdhit-common.c++:2348:18: note: The member function 'SequenceDB::WriteClustersgz' can be static.
cdhit-4.8.1/cdhit-common.c++:2426:18: style: The member function 'SequenceDB::WriteClustersgz' can be static. [functionStatic]
cdhit-4.8.1/cdhit-common.h:575:8: note: The member function 'SequenceDB::WriteClustersgz' can be static.
cdhit-4.8.1/cdhit-common.c++:2426:18: note: The member function 'SequenceDB::WriteClustersgz' can be static.
cdhit-4.8.1/cdhit-common.c++:3406:17: style: The member function 'SequenceDB::CheckOneEST' can be static. [functionStatic]
cdhit-4.8.1/cdhit-common.h:601:8: note: The member function 'SequenceDB::CheckOneEST' can be static.
cdhit-4.8.1/cdhit-common.c++:3406:17: note: The member function 'SequenceDB::CheckOneEST' can be static.
cdhit-4.8.1/cdhit-common.c++:3235:17: style: The member function 'SequenceDB::CheckOneAA' can be static. [functionStatic]
cdhit-4.8.1/cdhit-common.h:602:8: note: The member function 'SequenceDB::CheckOneAA' can be static.
cdhit-4.8.1/cdhit-common.c++:3235:17: note: The member function 'SequenceDB::CheckOneAA' can be static.
cdhit-4.8.1/cdhit-common.c++:131:12: warning: Struct 'TempFile' does not have a copy constructor which is recommended since it has dynamic memory/resource management. [noCopyConstructor]
cdhit-4.8.1/cdhit-common.c++:131:12: warning: Struct 'TempFile' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cdhit-common.h:129:33: warning: Class 'NVector < TempFile * >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cdhit-common.h:129:33: warning: Class 'NVector < float >' does not have a operator= which is recommended since it has dynamic memory/resource management. [noOperatorEq]
cdhit-4.8.1/cdhit-common.c++:113:2: style: Struct 'TempFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:117:3: style: Class 'NVector < TempFile * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:117:3: style: Class 'NVector < float >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < Vector < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < WorkingParam >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < WorkingBuffer >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.h:96:3: style: Class 'Vector < NVector < float > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
cdhit-4.8.1/cdhit-common.c++:3274:10: style: The if condition is the same as the previous if condition [duplicateCondition]
cdhit-4.8.1/cdhit-common.c++:3263:6: note: First condition
cdhit-4.8.1/cdhit-common.c++:3274:10: note: Second condition
cdhit-4.8.1/cdhit-common.c++:3442:14: style: The if condition is the same as the previous if condition [duplicateCondition]
cdhit-4.8.1/cdhit-common.c++:3430:6: note: First condition
cdhit-4.8.1/cdhit-common.c++:3442:14: note: Second condition
cdhit-4.8.1/cdhit-common.c++:3775:2: portability: %li in format string (no. 1) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
cdhit-4.8.1/cdhit-common.c++:118:17: warning: Possible null pointer dereference if the default parameter value is used: dir [nullPointerDefaultArg]
cdhit-4.8.1/cdhit-common.c++:1670:11: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:2665:15: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:2665:15: note: Assignment 'fout=std::fopen(db_clstr_bak.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:2668:37: note: Calling function 'PrintInfo', 2nd argument 'fout' value is 0
cdhit-4.8.1/cdhit-common.c++:1670:11: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:2342:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:2309:19: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:2309:19: note: Assignment 'fin=std::fopen(db,"rb")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:2317:13: note: Assuming condition is false
cdhit-4.8.1/cdhit-common.c++:2342:10: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:2343:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:2315:20: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:2315:20: note: Assignment 'fout=std::fopen(outfile,"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:2317:13: note: Assuming condition is false
cdhit-4.8.1/cdhit-common.c++:2343:10: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:2610:11: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:2605:15: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:2605:15: note: Assignment 'fout=std::fopen(db_clstr_bak.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:2610:11: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:2674:11: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:2665:15: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:2665:15: note: Assignment 'fout=std::fopen(db_clstr_bak.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:2674:11: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:2687:12: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:2684:14: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:2684:14: note: Assignment 'fout=std::fopen(db_clstr.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:2687:12: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:3651:11: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assignment 'fout=std::fopen(output.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:3651:11: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:3652:30: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assignment 'fout=std::fopen(output.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:3652:30: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:3653:11: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assignment 'fout=std::fopen(output.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:3653:11: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:3655:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assignment 'fout=std::fopen(output.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:3655:12: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:3656:31: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assignment 'fout=std::fopen(output.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:3656:31: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:3657:12: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assignment 'fout=std::fopen(output.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:3657:12: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:3659:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fout [nullPointerOutOfResources]
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assuming allocation function fails
cdhit-4.8.1/cdhit-common.c++:3650:20: note: Assignment 'fout=std::fopen(output.c_str(),"w+")', assigned value is 0
cdhit-4.8.1/cdhit-common.c++:3659:10: note: Null pointer dereference
cdhit-4.8.1/cdhit-common.c++:495:7: warning: Either the condition 'q' is redundant or there is overflow in pointer subtraction. [nullPointerArithmeticRedundantCheck]
cdhit-4.8.1/cdhit-common.c++:494:9: note: Assuming that condition 'q' is not redundant
cdhit-4.8.1/cdhit-common.c++:495:7: note: Null pointer subtraction
cdhit-4.8.1/cdhit-common.c++:3354:3: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
cdhit-4.8.1/cdhit-common.c++:3358:3: note: Found duplicate branches for 'if' and 'else'.
cdhit-4.8.1/cdhit-common.c++:3354:3: note: Found duplicate branches for 'if' and 'else'.
cdhit-4.8.1/cdhit-common.c++:923:5: style: Variable 'i' is reassigned a value before the old one has been used. [redundantAssignment]
cdhit-4.8.1/cdhit-common.c++:921:4: note: i is assigned
cdhit-4.8.1/cdhit-common.c++:923:5: note: i is overwritten
cdhit-4.8.1/cdhit-common.c++:3309:5: style: Redundant initialization for 'ic'. The initialized value is overwritten before it is read. [redundantInitialization]
cdhit-4.8.1/cdhit-common.c++:3308:17: note: ic is initialized
cdhit-4.8.1/cdhit-common.c++:3309:5: note: ic is overwritten
cdhit-4.8.1/cdhit-common.c++:3309:2: style: Variable 'ic' is assigned an expression that holds the same value. [redundantAssignment]
cdhit-4.8.1/cdhit-common.c++:3308:17: note: ic is assigned 'lookCounts.items' here.
cdhit-4.8.1/cdhit-common.c++:3309:2: note: Variable 'ic' is assigned an expression that holds the same value.
cdhit-4.8.1/cdhit-common.c++:3329:10: style: Redundant initialization for 'count'. The initialized value is overwritten before it is read. [redundantInitialization]
cdhit-4.8.1/cdhit-common.c++:3322:14: note: count is initialized
cdhit-4.8.1/cdhit-common.c++:3329:10: note: count is overwritten
cdhit-4.8.1/cdhit-common.c++:3494:6: style: Redundant initialization for 'ic'. The initialized value is overwritten before it is read. [redundantInitialization]
cdhit-4.8.1/cdhit-common.c++:3493:18: note: ic is initialized
cdhit-4.8.1/cdhit-common.c++:3494:6: note: ic is overwritten
cdhit-4.8.1/cdhit-common.c++:3494:3: style: Variable 'ic' is assigned an expression that holds the same value. [redundantAssignment]
cdhit-4.8.1/cdhit-common.c++:3493:18: note: ic is assigned 'lookCounts.items' here.
cdhit-4.8.1/cdhit-common.c++:3494:3: note: Variable 'ic' is assigned an expression that holds the same value.
cdhit-4.8.1/cdhit-common.c++:144:7: style: The scope of the variable 'i' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:481:7: style: The scope of the variable 'c1' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:533:6: style: The scope of the variable 'c22' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:533:11: style: The scope of the variable 'cpx' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:793:12: style: The scope of the variable 'k' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1302:9: style: The scope of the variable 'j' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1302:12: style: The scope of the variable 'k' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1323:9: style: The scope of the variable 'j' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1323:12: style: The scope of the variable 'k' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1342:19: style: The scope of the variable 'k1' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1342:23: style: The scope of the variable 'fra' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1436:17: style: The scope of the variable 'j1' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1579:9: style: The scope of the variable 'm' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1595:9: style: The scope of the variable 'm' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:1796:11: style: The scope of the variable 'res' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2039:9: style: The scope of the variable 'f_len2' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2052:11: style: The scope of the variable 'res' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2053:11: style: The scope of the variable 'res2' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2230:15: style: The scope of the variable 'len' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2313:12: style: The scope of the variable 'count' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2313:19: style: The scope of the variable 'rest' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2396:6: style: The scope of the variable 'count' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2396:13: style: The scope of the variable 'rest' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2522:6: style: The scope of the variable 'count' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2522:13: style: The scope of the variable 'rest' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2596:9: style: The scope of the variable 'i0' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2842:6: style: The scope of the variable 'i' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2842:12: style: The scope of the variable 'i0' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:2842:16: style: The scope of the variable 'i1' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:3426:6: style: The scope of the variable 'j' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:3966:6: style: The scope of the variable 'i' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:3966:15: style: The scope of the variable 'i0' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:3966:19: style: The scope of the variable 'i1' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:3997:15: style: The scope of the variable 'icomp' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:4023:7: style: The scope of the variable 'lo' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:4024:7: style: The scope of the variable 'hi' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:4025:7: style: The scope of the variable 'mid' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:4026:7: style: The scope of the variable 'tmp' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:4053:7: style: The scope of the variable 'lo' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:4054:7: style: The scope of the variable 'hi' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:4055:7: style: The scope of the variable 'mid' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:4056:7: style: The scope of the variable 'tmp' can be reduced. [variableScope]
cdhit-4.8.1/cdhit-common.c++:318:56: style:inconclusive: Function 'SetOptions' argument 3 names different: declaration 'twodata' definition 'twod'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:364:48: note: Function 'SetOptions' argument 3 names different: declaration 'twodata' definition 'twod'.
cdhit-4.8.1/cdhit-common.c++:318:56: note: Function 'SetOptions' argument 3 names different: declaration 'twodata' definition 'twod'.
cdhit-4.8.1/cdhit-common.c++:789:28: style:inconclusive: Function 'local_band_align' argument 1 names different: declaration 'query' definition 'iseq1'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:618:28: note: Function 'local_band_align' argument 1 names different: declaration 'query' definition 'iseq1'.
cdhit-4.8.1/cdhit-common.c++:789:28: note: Function 'local_band_align' argument 1 names different: declaration 'query' definition 'iseq1'.
cdhit-4.8.1/cdhit-common.c++:789:42: style:inconclusive: Function 'local_band_align' argument 2 names different: declaration 'ref' definition 'iseq2'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:618:42: note: Function 'local_band_align' argument 2 names different: declaration 'ref' definition 'iseq2'.
cdhit-4.8.1/cdhit-common.c++:789:42: note: Function 'local_band_align' argument 2 names different: declaration 'ref' definition 'iseq2'.
cdhit-4.8.1/cdhit-common.c++:789:55: style:inconclusive: Function 'local_band_align' argument 3 names different: declaration 'qlen' definition 'len1'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:618:53: note: Function 'local_band_align' argument 3 names different: declaration 'qlen' definition 'len1'.
cdhit-4.8.1/cdhit-common.c++:789:55: note: Function 'local_band_align' argument 3 names different: declaration 'qlen' definition 'len1'.
cdhit-4.8.1/cdhit-common.c++:789:65: style:inconclusive: Function 'local_band_align' argument 4 names different: declaration 'rlen' definition 'len2'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:618:63: note: Function 'local_band_align' argument 4 names different: declaration 'rlen' definition 'len2'.
cdhit-4.8.1/cdhit-common.c++:789:65: note: Function 'local_band_align' argument 4 names different: declaration 'rlen' definition 'len2'.
cdhit-4.8.1/cdhit-common.c++:1269:26: style:inconclusive: Function 'Init' argument 1 names different: declaration '<unnamed>' definition 'naa'. [funcArgNamesDifferentUnnamed]
cdhit-4.8.1/cdhit-common.c++:1269:35: style:inconclusive: Function 'Init' argument 2 names different: declaration '<unnamed>' definition 'naan'. [funcArgNamesDifferentUnnamed]
cdhit-4.8.1/cdhit-common.c++:1431:53: style:inconclusive: Function 'CountWords' argument 2 names different: declaration 'aan_list' definition 'word_encodes'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:249:44: note: Function 'CountWords' argument 2 names different: declaration 'aan_list' definition 'word_encodes'.
cdhit-4.8.1/cdhit-common.c++:1431:53: note: Function 'CountWords' argument 2 names different: declaration 'aan_list' definition 'word_encodes'.
cdhit-4.8.1/cdhit-common.c++:1431:82: style:inconclusive: Function 'CountWords' argument 3 names different: declaration 'aan_list_no' definition 'word_encodes_no'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:249:69: note: Function 'CountWords' argument 3 names different: declaration 'aan_list_no' definition 'word_encodes_no'.
cdhit-4.8.1/cdhit-common.c++:1431:82: note: Function 'CountWords' argument 3 names different: declaration 'aan_list_no' definition 'word_encodes_no'.
cdhit-4.8.1/cdhit-common.c++:2694:67: style:inconclusive: Function 'ControlShortCoverage' argument 2 names different: declaration 'option' definition 'options'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:458:54: note: Function 'ControlShortCoverage' argument 2 names different: declaration 'option' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:2694:67: note: Function 'ControlShortCoverage' argument 2 names different: declaration 'option' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:2706:45: style:inconclusive: Function 'ControlLongCoverage' argument 1 names different: declaration 'len' definition 'len2'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:459:32: note: Function 'ControlLongCoverage' argument 1 names different: declaration 'len' definition 'len2'.
cdhit-4.8.1/cdhit-common.c++:2706:45: note: Function 'ControlLongCoverage' argument 1 names different: declaration 'len' definition 'len2'.
cdhit-4.8.1/cdhit-common.c++:2706:67: style:inconclusive: Function 'ControlLongCoverage' argument 2 names different: declaration 'option' definition 'options'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:459:53: note: Function 'ControlLongCoverage' argument 2 names different: declaration 'option' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:2706:67: note: Function 'ControlLongCoverage' argument 2 names different: declaration 'option' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:2739:10: style:inconclusive: Function 'cal_aax_cutoff' argument 4 names different: declaration 'NR_clstr' definition 'cluster_thd'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:630:10: note: Function 'cal_aax_cutoff' argument 4 names different: declaration 'NR_clstr' definition 'cluster_thd'.
cdhit-4.8.1/cdhit-common.c++:2739:10: note: Function 'cal_aax_cutoff' argument 4 names different: declaration 'NR_clstr' definition 'cluster_thd'.
cdhit-4.8.1/cdhit-common.c++:2836:52: style:inconclusive: Function 'EncodeWords' argument 2 names different: declaration 'NA' definition 'NAA'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:529:38: note: Function 'EncodeWords' argument 2 names different: declaration 'NA' definition 'NAA'.
cdhit-4.8.1/cdhit-common.c++:2836:52: note: Function 'EncodeWords' argument 2 names different: declaration 'NA' definition 'NAA'.
cdhit-4.8.1/cdhit-common.c++:2912:41: style:inconclusive: Function 'ClusterOne' argument 5 names different: declaration 'buf' definition 'buffer'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:591:43: note: Function 'ClusterOne' argument 5 names different: declaration 'buf' definition 'buffer'.
cdhit-4.8.1/cdhit-common.c++:2912:41: note: Function 'ClusterOne' argument 5 names different: declaration 'buf' definition 'buffer'.
cdhit-4.8.1/cdhit-common.c++:3228:54: style:inconclusive: Function 'CheckOne' argument 2 names different: declaration 'tab' definition 'table'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:600:45: note: Function 'CheckOne' argument 2 names different: declaration 'tab' definition 'table'.
cdhit-4.8.1/cdhit-common.c++:3228:54: note: Function 'CheckOne' argument 2 names different: declaration 'tab' definition 'table'.
cdhit-4.8.1/cdhit-common.c++:3228:76: style:inconclusive: Function 'CheckOne' argument 3 names different: declaration 'par' definition 'param'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:600:65: note: Function 'CheckOne' argument 3 names different: declaration 'par' definition 'param'.
cdhit-4.8.1/cdhit-common.c++:3228:76: note: Function 'CheckOne' argument 3 names different: declaration 'par' definition 'param'.
cdhit-4.8.1/cdhit-common.c++:3228:120: style:inconclusive: Function 'CheckOne' argument 5 names different: declaration 'opt' definition 'options'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:600:107: note: Function 'CheckOne' argument 5 names different: declaration 'opt' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:3228:120: note: Function 'CheckOne' argument 5 names different: declaration 'opt' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:3235:56: style:inconclusive: Function 'CheckOneAA' argument 2 names different: declaration 'tab' definition 'table'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:602:47: note: Function 'CheckOneAA' argument 2 names different: declaration 'tab' definition 'table'.
cdhit-4.8.1/cdhit-common.c++:3235:56: note: Function 'CheckOneAA' argument 2 names different: declaration 'tab' definition 'table'.
cdhit-4.8.1/cdhit-common.c++:3235:78: style:inconclusive: Function 'CheckOneAA' argument 3 names different: declaration 'par' definition 'param'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:602:67: note: Function 'CheckOneAA' argument 3 names different: declaration 'par' definition 'param'.
cdhit-4.8.1/cdhit-common.c++:3235:78: note: Function 'CheckOneAA' argument 3 names different: declaration 'par' definition 'param'.
cdhit-4.8.1/cdhit-common.c++:3235:122: style:inconclusive: Function 'CheckOneAA' argument 5 names different: declaration 'opt' definition 'options'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:602:109: note: Function 'CheckOneAA' argument 5 names different: declaration 'opt' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:3235:122: note: Function 'CheckOneAA' argument 5 names different: declaration 'opt' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:3406:57: style:inconclusive: Function 'CheckOneEST' argument 2 names different: declaration 'tab' definition 'table'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:601:48: note: Function 'CheckOneEST' argument 2 names different: declaration 'tab' definition 'table'.
cdhit-4.8.1/cdhit-common.c++:3406:57: note: Function 'CheckOneEST' argument 2 names different: declaration 'tab' definition 'table'.
cdhit-4.8.1/cdhit-common.c++:3406:79: style:inconclusive: Function 'CheckOneEST' argument 3 names different: declaration 'par' definition 'param'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:601:68: note: Function 'CheckOneEST' argument 3 names different: declaration 'par' definition 'param'.
cdhit-4.8.1/cdhit-common.c++:3406:79: note: Function 'CheckOneEST' argument 3 names different: declaration 'par' definition 'param'.
cdhit-4.8.1/cdhit-common.c++:3406:123: style:inconclusive: Function 'CheckOneEST' argument 5 names different: declaration 'opt' definition 'options'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:601:110: note: Function 'CheckOneEST' argument 5 names different: declaration 'opt' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:3406:123: note: Function 'CheckOneEST' argument 5 names different: declaration 'opt' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:3786:65: style:inconclusive: Function 'ClusterTo' argument 2 names different: declaration 'optioins' definition 'options'. [funcArgNamesDifferent]
cdhit-4.8.1/cdhit-common.h:599:55: note: Function 'ClusterTo' argument 2 names different: declaration 'optioins' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:3786:65: note: Function 'ClusterTo' argument 2 names different: declaration 'optioins' definition 'options'.
cdhit-4.8.1/cdhit-common.c++:543:11: style: Local variable 'k' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:520:16: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:543:11: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:620:6: style: Local variable 'NAA2' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.h:196:12: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:620:6: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:621:6: style: Local variable 'NAA3' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.h:197:12: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:621:6: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:1383:7: style: Local variable 'size' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.h:234:11: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:1383:7: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:1456:15: style: Local variable 'ic' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:1440:14: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:1456:15: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:2277:8: style: Local variable 'len' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:2230:15: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:2277:8: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:2617:7: style: Local variable 'k' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:2596:13: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:2617:7: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3112:12: style: Local variable 'j' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3033:9: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3112:12: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3129:12: style: Local variable 'j' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3033:9: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3129:12: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3178:21: style: Local variable 'sum' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3083:10: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3178:21: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3758:8: style: Local variable 'len_bound' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3671:11: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3758:8: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3869:9: style: Local variable 'len' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3789:6: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3869:9: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3870:11: style: Local variable 'seqi' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3792:8: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3870:11: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3871:9: style: Local variable 'len_upper_bound' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3789:37: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3871:9: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3872:9: style: Local variable 'len_lower_bound' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3789:20: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3872:9: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3874:9: style: Local variable 'len_tmp' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3789:11: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3874:9: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:3886:9: style: Local variable 'flag' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.c++:3788:17: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:3886:9: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:4001:6: style: Local variable 'NAA1' shadows outer variable [shadowVariable]
cdhit-4.8.1/cdhit-common.h:195:12: note: Shadowed declaration
cdhit-4.8.1/cdhit-common.c++:4001:6: note: Shadow variable
cdhit-4.8.1/cdhit-common.c++:523:16: style: Variable 'taap' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:524:17: style: Variable 'aap_begin' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:525:17: style: Variable 'aap_list' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:622:16: style: Variable 'taap' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:623:17: style: Variable 'aap_begin' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:789:84: style: Parameter 'mat' can be declared as reference to const [constParameterReference]
cdhit-4.8.1/cdhit-common.c++:1299:53: style: Parameter 'counts' can be declared as reference to const [constParameterReference]
cdhit-4.8.1/cdhit-common.c++:1317:57: style: Parameter 'counts' can be declared as reference to const [constParameterReference]
cdhit-4.8.1/cdhit-common.c++:1321:56: style: Parameter 'word_encodes' can be declared as reference to const [constParameterReference]
cdhit-4.8.1/cdhit-common.c++:1321:85: style: Parameter 'word_encodes_no' can be declared as reference to const [constParameterReference]
cdhit-4.8.1/cdhit-common.c++:1454:25: style: Variable 'one' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:2652:45: style: Parameter 'other' can be declared as reference to const [constParameterReference]
cdhit-4.8.1/cdhit-common.c++:3240:17: style: Variable 'aap_list' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3241:17: style: Variable 'aap_begin' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3243:17: style: Variable 'taap' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3252:8: style: Variable 'aln_cover_flag' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3253:8: style: Variable 'required_aa1' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3254:8: style: Variable 'required_aa2' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3255:8: style: Variable 'required_aan' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3256:8: style: Variable 'min_aln_lenS' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3257:8: style: Variable 'min_aln_lenL' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3411:17: style: Variable 'aap_list' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3412:17: style: Variable 'aap_begin' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3414:17: style: Variable 'taap' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3418:8: style: Variable 'aln_cover_flag' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3422:8: style: Variable 'min_aln_lenS' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:3423:8: style: Variable 'min_aln_lenL' can be declared as reference to const [constVariableReference]
cdhit-4.8.1/cdhit-common.c++:205:53: style: Parameter 'iseq' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-common.c++:207:9: style: Variable 'c' can be declared as const array [constVariable]
cdhit-4.8.1/cdhit-common.c++:517:35: style: Parameter 'iseq2' can be declared as const array [constParameter]
cdhit-4.8.1/cdhit-common.c++:789:28: style: Parameter 'iseq1' can be declared as const array [constParameter]
cdhit-4.8.1/cdhit-common.c++:789:42: style: Parameter 'iseq2' can be declared as const array [constParameter]
cdhit-4.8.1/cdhit-common.c++:871:6: style: Variable 'gap_open' can be declared as const array [constVariable]
cdhit-4.8.1/cdhit-common.c++:873:6: style: Variable 'extra_score' can be declared as const array [constVariable]
cdhit-4.8.1/cdhit-common.c++:1223:35: style: Parameter 'mat1' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-common.c++:1672:8: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:1796:11: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:2052:11: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:2053:11: style: Variable 'res2' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:2318:13: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:2403:13: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:2552:13: style: Variable 'seq' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:2846:9: style: Variable 'word' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:3321:14: style: Variable 'ims' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:3870:11: style: Variable 'seqi' can be declared as pointer to const [constVariablePointer]
cdhit-4.8.1/cdhit-common.c++:3964:34: style: Parameter 'seqi' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-common.c++:3996:47: style: Parameter 'NAAN_array' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-common.c++:3998:6: style: Variable 'c' can be declared as const array [constVariable]
cdhit-4.8.1/cdhit-common.c++:557:15: style: Variable 'max_diag' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:565:13: style: Variable 'max_diag' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:585:14: style: Variable 'max_diag' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:534:8: style: Unused variable: bip [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:681:15: style: Variable 'max_diag' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:689:13: style: Variable 'max_diag' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:710:14: style: Variable 'max_diag' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:895:12: style: Variable 'gap' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:794:6: style: Unused variable: jj [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:794:10: style: Unused variable: kk [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:795:6: style: Unused variable: iden_no1 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:886:8: style: Unused variable: s1 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:886:12: style: Unused variable: k0 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:937:14: style: Variable 'letters' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:938:14: style: Variable 'letters2' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:1218:6: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1435:6: style: Variable 'S' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:1436:25: style: Unused variable: m [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1437:6: style: Unused variable: ix1 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1437:11: style: Unused variable: ix2 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1437:16: style: Unused variable: ix3 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1437:21: style: Unused variable: ix4 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1487:6: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1516:6: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1573:6: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1579:6: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1595:6: style: Unused variable: i [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:1816:22: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:1820:26: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:1848:26: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2083:22: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2087:26: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2104:23: style: Variable 'res2' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2108:27: style: Variable 'res2' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2146:26: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2170:26: style: Variable 'res' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2230:9: style: Unused variable: j [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:2230:12: style: Unused variable: k [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:2792:9: style: Variable 'k' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2797:11: style: Variable 'ks3' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:2798:11: style: Variable 'kn3' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:3021:15: style: Variable 'frac' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:3033:9: style: Unused variable: j [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3041:6: style: Unused variable: len [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3041:11: style: Unused variable: len_bound [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3042:6: style: Unused variable: flag [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3069:6: style: Variable 'K' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:3071:9: style: Variable 'mem_limit' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:3249:6: style: Unused variable: j [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3291:6: style: Variable 'M' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:3301:6: style: Unused variable: best1 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3302:8: style: Unused variable: lookptr [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3598:55: style: Unused variable: required_aa1 [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3671:6: style: Unused variable: len [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3671:11: style: Unused variable: len_bound [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3672:6: style: Unused variable: flag [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3700:9: style: Variable 'mem_limit' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-common.c++:3788:9: style: Unused variable: is [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3788:13: style: Unused variable: js [unusedVariable]
cdhit-4.8.1/cdhit-common.c++:3822:9: style: Variable 'mem_limit' is assigned a value that is never used. [unreadVariable]
cdhit-4.8.1/cdhit-div.c++:57:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-est-2d.c++:93:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-est.c++:81:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-utility.c++:152:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-utility.c++:191:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-utility.c++:231:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-utility.c++:280:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-utility.c++:329:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-utility.c++:349:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-utility.c++:381:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cdhit-utility.c++:151:24: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-utility.c++:190:27: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-utility.c++:230:28: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-utility.c++:279:31: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-utility.c++:328:28: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit-utility.c++:347:28: style: Parameter 'arg' can be declared as pointer to const [constParameterPointer]
cdhit-4.8.1/cdhit.c++:54:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:16:1: error: The one definition rule is violated, different classes/structs have the same name 'SequenceCluster' [ctuOneDefinitionRuleViolation]
cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:48:1: note: The one definition rule is violated, different classes/structs have the same name 'SequenceCluster'
cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:16:1: note: The one definition rule is violated, different classes/structs have the same name 'SequenceCluster'
diff:
head cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:133:8: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
head cdhit-4.8.1/cd-hit-auxtools/bioSequence.cxx:74:8: style: Variable 'res' can be declared as pointer to const [constVariablePointer]
head cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:706:17: style: Variable 'infoA' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:709:18: style: Variable 'infoB' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:768:27: style: Parameter 'argv' can be declared as const array [constParameter]
head cdhit-4.8.1/cd-hit-auxtools/cdhit-dup.cxx:900:13: style: Variable 'qs1' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:105:12: style: Variable 'seq' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:152:37: style: Parameter 'seqlist' can be declared as reference to const [constParameterReference]
head cdhit-4.8.1/cd-hit-auxtools/cdhit-lap.cxx:98:11: style: Variable 'rep' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:1269:26: style:inconclusive: Function 'Init' argument 1 names different: declaration '<unnamed>' definition 'naa'. [funcArgNamesDifferentUnnamed]
head cdhit-4.8.1/cdhit-common.c++:1269:35: style:inconclusive: Function 'Init' argument 2 names different: declaration '<unnamed>' definition 'naan'. [funcArgNamesDifferentUnnamed]
head cdhit-4.8.1/cdhit-common.c++:1299:53: style: Parameter 'counts' can be declared as reference to const [constParameterReference]
head cdhit-4.8.1/cdhit-common.c++:1321:56: style: Parameter 'word_encodes' can be declared as reference to const [constParameterReference]
head cdhit-4.8.1/cdhit-common.c++:1321:85: style: Parameter 'word_encodes_no' can be declared as reference to const [constParameterReference]
2.20.0 cdhit-4.8.1/cdhit-common.c++:2319:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
     cdhit-4.8.1/cdhit-common.c++:2309:19: note: Assuming allocation function fails
     cdhit-4.8.1/cdhit-common.c++:2309:19: note: Assignment 'fin=std::fopen(db,"rb")', assigned value is 0
     cdhit-4.8.1/cdhit-common.c++:2319:10: note: Null pointer dereference
2.20.0 cdhit-4.8.1/cdhit-common.c++:2334:38: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
     cdhit-4.8.1/cdhit-common.c++:2309:19: note: Assuming allocation function fails
     cdhit-4.8.1/cdhit-common.c++:2309:19: note: Assignment 'fin=std::fopen(db,"rb")', assigned value is 0
     cdhit-4.8.1/cdhit-common.c++:2334:38: note: Null pointer dereference
head cdhit-4.8.1/cdhit-common.c++:2342:10: warning: If resource allocation fails, then there is a possible null pointer dereference: fin [nullPointerOutOfResources]
     cdhit-4.8.1/cdhit-common.c++:2309:19: note: Assuming allocation function fails
     cdhit-4.8.1/cdhit-common.c++:2309:19: note: Assignment 'fin=std::fopen(db,"rb")', assigned value is 0
     cdhit-4.8.1/cdhit-common.c++:2317:13: note: Assuming condition is false
     cdhit-4.8.1/cdhit-common.c++:2342:10: note: Null pointer dereference
2.20.0 cdhit-4.8.1/cdhit-common.c++:2949:7: style: The scope of the variable 'size' can be reduced. [variableScope]
head cdhit-4.8.1/cdhit-common.c++:3240:17: style: Variable 'aap_list' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3241:17: style: Variable 'aap_begin' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3243:17: style: Variable 'taap' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3252:8: style: Variable 'aln_cover_flag' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3253:8: style: Variable 'required_aa1' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3254:8: style: Variable 'required_aa2' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3255:8: style: Variable 'required_aan' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3256:8: style: Variable 'min_aln_lenS' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3257:8: style: Variable 'min_aln_lenL' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3411:17: style: Variable 'aap_list' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3412:17: style: Variable 'aap_begin' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3414:17: style: Variable 'taap' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3418:8: style: Variable 'aln_cover_flag' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3422:8: style: Variable 'min_aln_lenS' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:3423:8: style: Variable 'min_aln_lenL' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:517:35: style: Parameter 'iseq2' can be declared as const array [constParameter]
head cdhit-4.8.1/cdhit-common.c++:523:16: style: Variable 'taap' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:524:17: style: Variable 'aap_begin' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:525:17: style: Variable 'aap_list' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:622:16: style: Variable 'taap' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:623:17: style: Variable 'aap_begin' can be declared as reference to const [constVariableReference]
head cdhit-4.8.1/cdhit-common.c++:789:28: style: Parameter 'iseq1' can be declared as const array [constParameter]
head cdhit-4.8.1/cdhit-common.c++:789:42: style: Parameter 'iseq2' can be declared as const array [constParameter]
head cdhit-4.8.1/cdhit-common.c++:789:84: style: Parameter 'mat' can be declared as reference to const [constParameterReference]
head cdhit-4.8.1/cdhit-common.c++:871:6: style: Variable 'gap_open' can be declared as const array [constVariable]
head cdhit-4.8.1/cdhit-common.c++:873:6: style: Variable 'extra_score' can be declared as const array [constVariable]


DONE