2024-04-25 09:22 ftp://ftp.de.debian.org/debian/pool/main/k/kallisto/kallisto_0.48.0+dfsg.orig.tar.xz cppcheck-options: --library=posix --library=gnu --library=bsd --library=zlib --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j1 platform: Linux-5.15.0-105-generic-x86_64-with-glibc2.35 python: 3.10.12 client-version: 1.3.56 compiler: g++ (Ubuntu 12.3.0-1ubuntu1~22.04) 12.3.0 cppcheck: head 2.14.0 head-info: da380ea (2024-04-25 10:28:43 +0200) count: 467 467 elapsed-time: 38.1 38.0 head-timing-info: old-timing-info: head results: kallisto-0.48.0/src/BUSTools.cpp:27:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/BUSTools.cpp:7:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/BUSTools.cpp:8:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/BUSTools.cpp:9:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/BUSTools.cpp:12:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/BUSTools.cpp:19:17: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/BUSTools.cpp:40:20: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/BUSTools.cpp:25:67: style: Parameter 'data' can be declared as reference to const [constParameterReference] kallisto-0.48.0/src/EMAlgorithm.h:64:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/EMAlgorithm.h:199:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/EMAlgorithm.h:217:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.h:81:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/Bootstrap.cpp:81:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/KmerHashTable.h:135:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/KmerHashTable.h:150:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/KmerHashTable.h:191:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/KmerHashTable.h:224:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/KmerHashTable.h:51:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/KmerHashTable.h:70:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/common.h:119:1: warning: Member variable 'ProgramOptions::busOptions' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/EMAlgorithm.h:279:7: style:inconclusive: Member variable 'EMAlgorithm::num_trans_' uses an uninitialized argument 'target_names_' due to the order of declarations. [initializerList] kallisto-0.48.0/src/EMAlgorithm.h:33:5: note: Member variable 'EMAlgorithm::num_trans_' uses an uninitialized argument 'target_names_' due to the order of declarations. kallisto-0.48.0/src/EMAlgorithm.h:279:7: note: Member variable 'EMAlgorithm::num_trans_' uses an uninitialized argument 'target_names_' due to the order of declarations. kallisto-0.48.0/src/EMAlgorithm.h:279:7: style:inconclusive: Member variable 'EMAlgorithm::num_trans_' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/EMAlgorithm.h:33:5: note: Member variable 'EMAlgorithm::num_trans_' is in the wrong place in the initializer list. kallisto-0.48.0/src/EMAlgorithm.h:279:7: note: Member variable 'EMAlgorithm::num_trans_' is in the wrong place in the initializer list. kallisto-0.48.0/src/EMAlgorithm.h:285:30: style:inconclusive: Member variable 'EMAlgorithm::all_fl_means' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/EMAlgorithm.h:41:5: note: Member variable 'EMAlgorithm::all_fl_means' is in the wrong place in the initializer list. kallisto-0.48.0/src/EMAlgorithm.h:285:30: note: Member variable 'EMAlgorithm::all_fl_means' is in the wrong place in the initializer list. kallisto-0.48.0/src/Bootstrap.h:87:25: style:inconclusive: Member variable 'BootstrapThreadPool::seeds_' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/Bootstrap.cpp:27:3: note: Member variable 'BootstrapThreadPool::seeds_' is in the wrong place in the initializer list. kallisto-0.48.0/src/Bootstrap.h:87:25: note: Member variable 'BootstrapThreadPool::seeds_' is in the wrong place in the initializer list. kallisto-0.48.0/src/MinCollector.h:58:8: style:inconclusive: Technically the member function 'MinCollector::write' can be const. [functionConst] kallisto-0.48.0/src/Multinomial.hpp:54:33: style:inconclusive: Technically the member function 'Multinomial::counts' can be const. [functionConst] kallisto-0.48.0/src/Bootstrap.h:83:12: style:inconclusive: Technically the member function 'BootstrapThreadPool::num_threads' can be const. [functionConst] kallisto-0.48.0/src/KmerHashTable.h:233:10: performance:inconclusive: Technically the member function 'KmerHashTable < KmerEntry , KmerHash >::rndup' can be static (but you may consider moving to unnamed namespace). [functionStatic] kallisto-0.48.0/src/KmerIterator.hpp:16:3: style: Class 'KmerIterator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/KmerIndex.h:96:3: style: Struct 'KmerIndex' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/Multinomial.hpp:9:9: style: Class 'Multinomial' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/KmerHashTable.h:89:3: style: Struct 'KmerHashTable < KmerEntry , KmerHash >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/KmerHashTable.h:95:3: style: Struct 'KmerHashTable < KmerEntry , KmerHash >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/KmerHashTable.h:40:5: style: Class 'iterator_ < false >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/KmerHashTable.h:40:5: style: Class 'iterator_ < true >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/KmerHashTable.h:42:5: style: Class 'iterator_ < true >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/KmerIndex.h:22:39: performance: Function parameter 's' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.h:68:94: performance: Function parameter 'v1' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.h:68:142: performance: Function parameter 'v2' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.h:69:94: performance: Function parameter 'v1' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.h:69:142: performance: Function parameter 'v2' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/KmerHashTable.h:161:33: performance:inconclusive: Function parameter 'pos' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/common.h:34:18: style: Variable 'b' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/common.h:50:18: style: Variable 'u' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/EMAlgorithm.h:90:15: style: Variable 'wv' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/EMAlgorithm.h:99:15: style: Variable 'v' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/KmerHashTable.h:51:15: style: Variable 'km' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/KmerHashTable.h:70:15: style: Variable 'km' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/EMAlgorithm.h:208:9: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/Multinomial.hpp:16:20: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/KmerIndex.h:41:22: error: Shifting 32-bit value by 64 bits is undefined behaviour [shiftTooManyBits] kallisto-0.48.0/src/KmerIndex.h:37:11: note: Assignment 'i=0', assigned value is 0 kallisto-0.48.0/src/KmerIndex.h:38:19: note: Assuming container is not empty kallisto-0.48.0/src/KmerIndex.h:41:22: note: Shift kallisto-0.48.0/src/EMAlgorithm.h:255:20: style: Variable 'sum_big' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/EMAlgorithm.h:259:17: style: Variable 'sum_big' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/GeneModel.cpp:55:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_SHIFT [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/GeneModel.cpp:356:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/GeneModel.cpp:516:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/GeneModel.cpp:607:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/GeneModel.cpp:352:7: style: The scope of the variable 's' can be reduced. [variableScope] kallisto-0.48.0/src/GeneModel.cpp:509:7: style: The scope of the variable 'buf_end' can be reduced. [variableScope] kallisto-0.48.0/src/GeneModel.cpp:510:7: style: The scope of the variable 'bufread' can be reduced. [variableScope] kallisto-0.48.0/src/GeneModel.cpp:34:80: style:inconclusive: Function 'translateTrPosition' argument 3 names different: declaration 'length' definition 'rlen'. [funcArgNamesDifferent] kallisto-0.48.0/src/GeneModel.h:100:67: note: Function 'translateTrPosition' argument 3 names different: declaration 'length' definition 'rlen'. kallisto-0.48.0/src/GeneModel.cpp:34:80: note: Function 'translateTrPosition' argument 3 names different: declaration 'length' definition 'rlen'. kallisto-0.48.0/src/GeneModel.cpp:268:85: style:inconclusive: Function 'addGTFLine' argument 3 names different: declaration 'guessChromosome' definition 'guessChromosomes'. [funcArgNamesDifferent] kallisto-0.48.0/src/GeneModel.h:103:72: note: Function 'addGTFLine' argument 3 names different: declaration 'guessChromosome' definition 'guessChromosomes'. kallisto-0.48.0/src/GeneModel.cpp:268:85: note: Function 'addGTFLine' argument 3 names different: declaration 'guessChromosome' definition 'guessChromosomes'. kallisto-0.48.0/src/GeneModel.cpp:22:61: performance: Function parameter 'chr' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/GeneModel.cpp:60:13: style: Variable 'exon' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/GeneModel.cpp:98:13: style: Variable 'exon' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/GeneModel.cpp:623:28: warning:inconclusive: Access of moved variable 'gmodel'. [accessMoved] kallisto-0.48.0/src/GeneModel.cpp:622:27: note: Calling std::move(gmodel) kallisto-0.48.0/src/GeneModel.cpp:623:28: note: Access of moved variable 'gmodel'. kallisto-0.48.0/src/GeneModel.cpp:500:37: error: Uninitialized variables: tr.start, tr.stop, tr.length [uninitvar] kallisto-0.48.0/src/GeneModel.cpp:592:37: error: Uninitialized variables: tr.start, tr.stop, tr.length [uninitvar] kallisto-0.48.0/src/GeneModel.cpp:622:37: error: Uninitialized variables: gmodel.chr, gmodel.start, gmodel.stop, gmodel.strand [uninitvar] kallisto-0.48.0/src/GeneModel.cpp:627:44: error: Uninitialized variables: tmodel.chr, tmodel.start, tmodel.stop, tmodel.strand [uninitvar] kallisto-0.48.0/src/GeneModel.cpp:465:35: error: Uninitialized struct member: tmodel.chr [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:465:35: error: Uninitialized struct member: tmodel.start [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:465:35: error: Uninitialized struct member: tmodel.stop [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:465:35: error: Uninitialized struct member: tmodel.strand [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:465:35: error: Uninitialized struct member: tmodel.gene_id [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:482:38: error: Uninitialized struct member: emodel.chr [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:482:38: error: Uninitialized struct member: emodel.start [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:482:38: error: Uninitialized struct member: emodel.stop [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:482:38: error: Uninitialized struct member: emodel.strand [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:500:37: error: Uninitialized struct member: tr.start [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:500:37: error: Uninitialized struct member: tr.stop [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:500:37: error: Uninitialized struct member: tr.length [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:592:37: error: Uninitialized struct member: tr.start [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:592:37: error: Uninitialized struct member: tr.stop [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:592:37: error: Uninitialized struct member: tr.length [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:627:44: error: Uninitialized struct member: tmodel.chr [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:627:44: error: Uninitialized struct member: tmodel.start [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:627:44: error: Uninitialized struct member: tmodel.stop [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:627:44: error: Uninitialized struct member: tmodel.strand [uninitStructMember] kallisto-0.48.0/src/GeneModel.cpp:293:10: style: Variable 'type' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/GeneModel.cpp:352:9: style: Variable 's' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/GeneModel.cpp:509:15: style: Variable 'buf_end' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/GeneModel.cpp:510:15: style: Variable 'bufread' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/Kmer.cpp:279:31: error: Array 'km.longs[1]' accessed at index 1, which is out of bounds. [arrayIndexOutOfBounds] kallisto-0.48.0/src/Kmer.cpp:281:13: error: Array 'km.longs[1]' accessed at index 1, which is out of bounds. [arrayIndexOutOfBounds] kallisto-0.48.0/src/Kmer.cpp:367:31: error: Array 'km.longs[1]' accessed at index 1, which is out of bounds. [arrayIndexOutOfBounds] kallisto-0.48.0/src/Kmer.cpp:368:13: error: Array 'km.longs[1]' accessed at index 1, which is out of bounds. [arrayIndexOutOfBounds] kallisto-0.48.0/src/Kmer.cpp:221:23: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/Kmer.cpp:193:12: style: The scope of the variable 'j' can be reduced. [variableScope] kallisto-0.48.0/src/Kmer.cpp:193:14: style: The scope of the variable 'l' can be reduced. [variableScope] kallisto-0.48.0/src/Kmer.cpp:459:12: style: The scope of the variable 'j' can be reduced. [variableScope] kallisto-0.48.0/src/Kmer.cpp:459:14: style: The scope of the variable 'l' can be reduced. [variableScope] kallisto-0.48.0/src/Kmer.cpp:342:16: style: Unsigned expression 'index' can't be negative so it is unnecessary to test it. [unsignedPositive] kallisto-0.48.0/src/KmerIndex.cpp:12:1: error: There is an unknown macro here somewhere. Configuration is required. If KSEQ_INIT is a macro then please configure it. [unknownMacro] kallisto-0.48.0/src/KmerIterator.cpp:14:7: style: The scope of the variable 'pos_' can be reduced. [variableScope] kallisto-0.48.0/src/KmerIterator.cpp:98:22: style: Variable 'last_valid' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/Merge.cpp:89:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/Merge.cpp:36:38: performance: Function parameter 'name' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.cpp:163:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable contig [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/MinCollector.cpp:224:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/MinCollector.cpp:250:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/MinCollector.cpp:291:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/MinCollector.cpp:344:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/MinCollector.cpp:415:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/MinCollector.cpp:144:8: style:inconclusive: Technically the member function 'ComparePairsBySecond::operator()' can be const. [functionConst] kallisto-0.48.0/src/MinCollector.cpp:215:7: style: The scope of the variable 'i' can be reduced. [variableScope] kallisto-0.48.0/src/MinCollector.cpp:245:45: style:inconclusive: Function 'write' argument 1 names different: declaration 'index_out' definition 'pseudoprefix'. [funcArgNamesDifferent] kallisto-0.48.0/src/MinCollector.h:63:33: note: Function 'write' argument 1 names different: declaration 'index_out' definition 'pseudoprefix'. kallisto-0.48.0/src/MinCollector.cpp:245:45: note: Function 'write' argument 1 names different: declaration 'index_out' definition 'pseudoprefix'. kallisto-0.48.0/src/MinCollector.cpp:326:20: style: Local variable 'counts' shadows outer variable [shadowVariable] kallisto-0.48.0/src/MinCollector.h:82:20: note: Shadowed declaration kallisto-0.48.0/src/MinCollector.cpp:326:20: note: Shadow variable kallisto-0.48.0/src/MinCollector.cpp:376:106: performance: Function parameter 'v1' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.cpp:376:154: performance: Function parameter 'v2' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.cpp:380:106: performance: Function parameter 'v1' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.cpp:380:154: performance: Function parameter 'v2' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/MinCollector.cpp:198:14: style: Variable 'x' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/MinCollector.cpp:211:47: style: Parameter 'opt' can be declared as reference to const [constParameterReference] kallisto-0.48.0/src/MinCollector.cpp:417:14: style: Variable 'x' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/MinCollector.cpp:307:14: style: Variable 'tmp' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/PlaintextWriter.cpp:16:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.cpp:41:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.cpp:79:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.cpp:170:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.cpp:231:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.cpp:263:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.cpp:278:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.cpp:291:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PlaintextWriter.cpp:141:24: style:inconclusive: Function 'plaintext_aux' argument 1 names different: declaration 'out_fname' definition 'out_name'. [funcArgNamesDifferent] kallisto-0.48.0/src/PlaintextWriter.h:36:24: note: Function 'plaintext_aux' argument 1 names different: declaration 'out_fname' definition 'out_name'. kallisto-0.48.0/src/PlaintextWriter.cpp:141:24: note: Function 'plaintext_aux' argument 1 names different: declaration 'out_fname' definition 'out_name'. kallisto-0.48.0/src/ProcessReads.h:197:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/Fusion.hpp:62:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable contig [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/Fusion.hpp:331:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:65:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:99:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:155:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:235:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:388:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:632:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:1130:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:1547:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:1984:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:2423:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:2960:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CSOFT_CLIP [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:3038:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CMATCH [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:3201:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable l [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.cpp:3319:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FSECONDARY [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/ProcessReads.h:44:3: warning: Member variable 'SequenceReader::state' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::fp' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::head' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::rec' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::eseq' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::l_seq' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::bc' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::l_bc' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::umi' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::l_umi' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:139:3: warning: Member variable 'BamSequenceReader::err' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.h:172:3: warning: Member variable 'MasterProcessor::parallel_bus_read' is not initialized in the constructor. [uninitMemberVar] kallisto-0.48.0/src/ProcessReads.cpp:1015:16: warning:inconclusive: Member variable 'ReadProcessor::ec_umi' is not assigned in the move constructor. Should it be moved? [missingMemberCopy] kallisto-0.48.0/src/ProcessReads.cpp:1015:16: warning:inconclusive: Member variable 'ReadProcessor::new_ec_umi' is not assigned in the move constructor. Should it be moved? [missingMemberCopy] kallisto-0.48.0/src/ProcessReads.cpp:1387:15: warning:inconclusive: Member variable 'BUSProcessor::newB' is not assigned in the move constructor. Should it be moved? [missingMemberCopy] kallisto-0.48.0/src/ProcessReads.cpp:1868:15: warning:inconclusive: Member variable 'AlnProcessor::ec_umi' is not assigned in the move constructor. Should it be moved? [missingMemberCopy] kallisto-0.48.0/src/PseudoBam.h:27:8: style:inconclusive: Member variable 'PseudoAlignmentInfo::paired' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/PseudoBam.h:37:66: note: Member variable 'PseudoAlignmentInfo::paired' is in the wrong place in the initializer list. kallisto-0.48.0/src/PseudoBam.h:27:8: note: Member variable 'PseudoAlignmentInfo::paired' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:104:8: style:inconclusive: Member variable 'FastqSequenceReader::paired' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.h:70:20: note: Member variable 'FastqSequenceReader::paired' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:104:8: note: Member variable 'FastqSequenceReader::paired' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:296:10: style:inconclusive: Member variable 'ReadProcessor::bufsize' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1022:3: note: Member variable 'ReadProcessor::bufsize' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:296:10: note: Member variable 'ReadProcessor::bufsize' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:303:23: style:inconclusive: Member variable 'ReadProcessor::batchSR' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1032:3: note: Member variable 'ReadProcessor::batchSR' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:303:23: note: Member variable 'ReadProcessor::batchSR' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:341:11: style:inconclusive: Member variable 'BUSProcessor::numreads' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1362:115: note: Member variable 'BUSProcessor::numreads' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:341:11: note: Member variable 'BUSProcessor::numreads' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:334:10: style:inconclusive: Member variable 'BUSProcessor::bufsize' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1396:3: note: Member variable 'BUSProcessor::bufsize' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:334:10: note: Member variable 'BUSProcessor::bufsize' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:345:23: style:inconclusive: Member variable 'BUSProcessor::batchSR' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1406:3: note: Member variable 'BUSProcessor::batchSR' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:345:23: note: Member variable 'BUSProcessor::batchSR' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:381:22: style:inconclusive: Member variable 'AlnProcessor::em' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1839:49: note: Member variable 'AlnProcessor::em' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:381:22: note: Member variable 'AlnProcessor::em' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:385:7: style:inconclusive: Member variable 'AlnProcessor::id' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1839:85: note: Member variable 'AlnProcessor::id' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:385:7: note: Member variable 'AlnProcessor::id' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:385:7: style:inconclusive: Member variable 'AlnProcessor::id' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1874:3: note: Member variable 'AlnProcessor::id' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:385:7: note: Member variable 'AlnProcessor::id' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:376:10: style:inconclusive: Member variable 'AlnProcessor::bufsize' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1876:3: note: Member variable 'AlnProcessor::bufsize' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:376:10: note: Member variable 'AlnProcessor::bufsize' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:383:23: style:inconclusive: Member variable 'AlnProcessor::batchSR' is in the wrong place in the initializer list. [initializerList] kallisto-0.48.0/src/ProcessReads.cpp:1884:3: note: Member variable 'AlnProcessor::batchSR' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:383:23: note: Member variable 'AlnProcessor::batchSR' is in the wrong place in the initializer list. kallisto-0.48.0/src/ProcessReads.h:178:9: warning: Class 'MasterProcessor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] kallisto-0.48.0/src/ProcessReads.h:178:9: warning: Class 'MasterProcessor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] kallisto-0.48.0/src/ProcessReads.cpp:993:4: warning: Class 'ReadProcessor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] kallisto-0.48.0/src/ProcessReads.cpp:993:4: warning: Class 'ReadProcessor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] kallisto-0.48.0/src/ProcessReads.cpp:1365:4: warning: Class 'BUSProcessor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] kallisto-0.48.0/src/ProcessReads.cpp:1365:4: warning: Class 'BUSProcessor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] kallisto-0.48.0/src/ProcessReads.cpp:1842:4: warning: Class 'AlnProcessor' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] kallisto-0.48.0/src/ProcessReads.cpp:1842:4: warning: Class 'AlnProcessor' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] kallisto-0.48.0/src/ProcessReads.h:69:3: style: Class 'FastqSequenceReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/ProcessReads.h:115:3: style: Class 'BamSequenceReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] kallisto-0.48.0/src/ProcessReads.h:86:4: style: The destructor '~FastqSequenceReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:47:12: note: Virtual destructor in base class kallisto-0.48.0/src/ProcessReads.h:86:4: note: Destructor in derived class kallisto-0.48.0/src/ProcessReads.h:88:8: style: The function 'empty' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:50:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:88:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.h:89:8: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:51:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:89:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.h:90:8: style: The function 'reserveNfiles' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:52:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:90:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.h:91:8: style: The function 'fetchSequences' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:53:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:91:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.h:141:4: style: The destructor '~BamSequenceReader' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:47:12: note: Virtual destructor in base class kallisto-0.48.0/src/ProcessReads.h:141:4: note: Destructor in derived class kallisto-0.48.0/src/ProcessReads.h:143:8: style: The function 'empty' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:50:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:143:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.h:144:8: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:51:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:144:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.h:145:8: style: The function 'reserveNfiles' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:52:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:145:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.h:146:8: style: The function 'fetchSequences' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] kallisto-0.48.0/src/ProcessReads.h:53:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:146:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.h:144:8: style: The function 'reset' overrides a function in a base class but just delegates back to the base class. [uselessOverride] kallisto-0.48.0/src/ProcessReads.h:51:16: note: Virtual function in base class kallisto-0.48.0/src/ProcessReads.h:144:8: note: Function in derived class kallisto-0.48.0/src/ProcessReads.cpp:2239:15: style: The if condition is the same as the previous if condition [duplicateCondition] kallisto-0.48.0/src/ProcessReads.cpp:2228:15: note: First condition kallisto-0.48.0/src/ProcessReads.cpp:2239:15: note: Second condition kallisto-0.48.0/src/ProcessReads.cpp:2755:15: style: The if condition is the same as the previous if condition [duplicateCondition] kallisto-0.48.0/src/ProcessReads.cpp:2745:15: note: First condition kallisto-0.48.0/src/ProcessReads.cpp:2755:15: note: Second condition kallisto-0.48.0/src/ProcessReads.cpp:2467:64: style: Condition 'pi.UMI!=-1' is always true [knownConditionTrueFalse] kallisto-0.48.0/src/ProcessReads.cpp:2502:49: style: Condition 'pi.UMI==-1' is always false [knownConditionTrueFalse] kallisto-0.48.0/src/ProcessReads.cpp:3108:3: warning: Either the condition 'f_umi' is redundant or there is possible null pointer dereference: f_umi. [nullPointerRedundantCheck] kallisto-0.48.0/src/ProcessReads.cpp:3104:7: note: Assuming that condition 'f_umi' is not redundant kallisto-0.48.0/src/ProcessReads.cpp:3108:3: note: Null pointer dereference kallisto-0.48.0/src/ProcessReads.cpp:2924:19: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/ProcessReads.cpp:2954:19: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/ProcessReads.cpp:3037:21: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/ProcessReads.cpp:3047:19: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/ProcessReads.cpp:1091:15: style: The scope of the variable 's1' can be reduced. [variableScope] kallisto-0.48.0/src/ProcessReads.cpp:1093:7: style: The scope of the variable 'l1' can be reduced. [variableScope] kallisto-0.48.0/src/ProcessReads.cpp:1560:10: style: The scope of the variable 'bad_umi' can be reduced. [variableScope] kallisto-0.48.0/src/ProcessReads.cpp:2049:14: style: The scope of the variable 'bestProb' can be reduced. [variableScope] kallisto-0.48.0/src/ProcessReads.cpp:2199:14: style: The scope of the variable 'bestTr' can be reduced. [variableScope] kallisto-0.48.0/src/ProcessReads.cpp:2863:13: style: The scope of the variable 'j' can be reduced. [variableScope] kallisto-0.48.0/src/ProcessReads.cpp:805:206: style:inconclusive: Function 'update' argument 10 names different: declaration 'newB' definition 'newBP'. [funcArgNamesDifferent] kallisto-0.48.0/src/ProcessReads.h:286:381: note: Function 'update' argument 10 names different: declaration 'newB' definition 'newBP'. kallisto-0.48.0/src/ProcessReads.cpp:805:206: note: Function 'update' argument 10 names different: declaration 'newB' definition 'newBP'. kallisto-0.48.0/src/ProcessReads.cpp:989:130: style:inconclusive: Function 'ReadProcessor' argument 5 names different: declaration 'id' definition '_id'. [funcArgNamesDifferent] kallisto-0.48.0/src/ProcessReads.h:291:117: note: Function 'ReadProcessor' argument 5 names different: declaration 'id' definition '_id'. kallisto-0.48.0/src/ProcessReads.cpp:989:130: note: Function 'ReadProcessor' argument 5 names different: declaration 'id' definition '_id'. kallisto-0.48.0/src/ProcessReads.cpp:989:139: style:inconclusive: Function 'ReadProcessor' argument 6 names different: declaration 'local_id' definition '_local_id'. [funcArgNamesDifferent] kallisto-0.48.0/src/ProcessReads.h:291:130: note: Function 'ReadProcessor' argument 6 names different: declaration 'local_id' definition '_local_id'. kallisto-0.48.0/src/ProcessReads.cpp:989:139: note: Function 'ReadProcessor' argument 6 names different: declaration 'local_id' definition '_local_id'. kallisto-0.48.0/src/ProcessReads.cpp:1361:128: style:inconclusive: Function 'BUSProcessor' argument 5 names different: declaration 'id' definition '_id'. [funcArgNamesDifferent] kallisto-0.48.0/src/ProcessReads.h:329:116: note: Function 'BUSProcessor' argument 5 names different: declaration 'id' definition '_id'. kallisto-0.48.0/src/ProcessReads.cpp:1361:128: note: Function 'BUSProcessor' argument 5 names different: declaration 'id' definition '_id'. kallisto-0.48.0/src/ProcessReads.cpp:1361:137: style:inconclusive: Function 'BUSProcessor' argument 6 names different: declaration 'local_id' definition '_local_id'. [funcArgNamesDifferent] kallisto-0.48.0/src/ProcessReads.h:329:129: note: Function 'BUSProcessor' argument 6 names different: declaration 'local_id' definition '_local_id'. kallisto-0.48.0/src/ProcessReads.cpp:1361:137: note: Function 'BUSProcessor' argument 6 names different: declaration 'local_id' definition '_local_id'. kallisto-0.48.0/src/ProcessReads.cpp:1838:167: style:inconclusive: Function 'AlnProcessor' argument 7 names different: declaration 'id' definition '_id'. [funcArgNamesDifferent] kallisto-0.48.0/src/ProcessReads.h:371:155: note: Function 'AlnProcessor' argument 7 names different: declaration 'id' definition '_id'. kallisto-0.48.0/src/ProcessReads.cpp:1838:167: note: Function 'AlnProcessor' argument 7 names different: declaration 'id' definition '_id'. kallisto-0.48.0/src/ProcessReads.cpp:3136:40: style:inconclusive: Function 'fetchSequences' argument 8 names different: declaration 'readbatch_id' definition 'read_id'. [funcArgNamesDifferent] kallisto-0.48.0/src/ProcessReads.h:95:60: note: Function 'fetchSequences' argument 8 names different: declaration 'readbatch_id' definition 'read_id'. kallisto-0.48.0/src/ProcessReads.cpp:3136:40: note: Function 'fetchSequences' argument 8 names different: declaration 'readbatch_id' definition 'read_id'. kallisto-0.48.0/src/ProcessReads.cpp:3303:40: style:inconclusive: Function 'fetchSequences' argument 8 names different: declaration 'readbatch_id' definition 'read_id'. [funcArgNamesDifferent] kallisto-0.48.0/src/ProcessReads.h:150:60: note: Function 'fetchSequences' argument 8 names different: declaration 'readbatch_id' definition 'read_id'. kallisto-0.48.0/src/ProcessReads.cpp:3303:40: note: Function 'fetchSequences' argument 8 names different: declaration 'readbatch_id' definition 'read_id'. kallisto-0.48.0/src/ProcessReads.cpp:510:16: style: Local variable 'id' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:439:9: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:510:16: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:527:16: style: Local variable 'id' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:439:9: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:527:16: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:549:16: style: Local variable 'id' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:439:9: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:549:16: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:565:16: style: Local variable 'id' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:439:9: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:565:16: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:1336:16: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:1129:12: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:1336:16: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:1508:8: style: Local variable 'buffer' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.h:332:9: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:1508:8: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:1815:18: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:1545:12: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:1815:18: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:2056:18: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:1980:12: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:2056:18: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:2065:20: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:1980:12: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:2065:20: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:2077:18: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:1980:12: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:2077:18: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:2553:18: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:2411:12: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:2553:18: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:2562:20: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:2411:12: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:2562:20: note: Shadow variable kallisto-0.48.0/src/ProcessReads.cpp:2570:18: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/ProcessReads.cpp:2411:12: note: Shadowed declaration kallisto-0.48.0/src/ProcessReads.cpp:2570:18: note: Shadow variable kallisto-0.48.0/src/Fusion.hpp:29:87: performance: Function parameter 's' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/Fusion.hpp:30:74: performance: Function parameter 'u' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/ProcessReads.cpp:67:16: style: Variable 'x' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:344:16: style: Variable 't' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:512:20: style: Variable 't' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:530:20: style: Variable 't' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:552:20: style: Variable 't' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:829:15: style: Variable 'u' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:834:17: style: Variable 'u' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:1567:18: style: Variable 'umic' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:1642:16: style: Variable 'bcc' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:2014:26: style: Variable 'pi' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:2354:14: style: Variable 'b' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:2720:22: style: Variable 'x' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:2892:14: style: Variable 'b' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:3072:14: style: Variable 'f' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:3163:20: style: Variable 'f' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/ProcessReads.cpp:742:18: style: Variable 'tmp_hdr' can be declared as pointer to const [constVariablePointer] kallisto-0.48.0/src/Fusion.hpp:221:28: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:594:19: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:650:11: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:1217:33: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:1241:33: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:1702:33: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:1725:33: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:2164:44: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:2643:44: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:3111:8: style: Consider using std::fill algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:3114:9: style: Consider using std::fill algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/ProcessReads.cpp:1984:17: warning:inconclusive: Array index -1 is out of bounds. [negativeContainerIndex] kallisto-0.48.0/src/ProcessReads.cpp:1980:16: note: Assignment 'i=0', assigned value is 0 kallisto-0.48.0/src/ProcessReads.cpp:1982:24: note: Assignment 'si1=(paired)?2*i:i', assigned value is -1 kallisto-0.48.0/src/ProcessReads.cpp:1984:17: note: Negative array index kallisto-0.48.0/src/ProcessReads.cpp:2017:32: warning:inconclusive: Array index -1 is out of bounds. [negativeContainerIndex] kallisto-0.48.0/src/ProcessReads.cpp:1980:16: note: Assignment 'i=0', assigned value is 0 kallisto-0.48.0/src/ProcessReads.cpp:1982:24: note: Assignment 'si1=(paired)?2*i:i', assigned value is -1 kallisto-0.48.0/src/ProcessReads.cpp:2017:32: note: Negative array index kallisto-0.48.0/src/Fusion.hpp:48:63: warning: Uninitialized variable: p [uninitvar] kallisto-0.48.0/src/Fusion.hpp:37:7: note: Assuming condition is false kallisto-0.48.0/src/Fusion.hpp:48:63: note: Uninitialized variable: p kallisto-0.48.0/src/ProcessReads.cpp:231:15: style: Variable 'paired' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:618:15: style: Variable 'r' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:624:13: style: Variable 'r' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:724:9: style: Variable 'r' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:734:9: style: Unused variable: tid [unusedVariable] kallisto-0.48.0/src/ProcessReads.cpp:742:18: style: Variable 'tmp_hdr' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:964:11: style: Variable 'r' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:975:13: style: Variable 'r' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:1091:18: style: Variable 's1' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:1112:20: style: Variable 'maxBiasCount' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:1151:11: style: Variable 'r' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:1204:13: style: Variable 'p' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:1683:11: style: Variable 'r' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:1689:13: style: Variable 'p' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:2981:12: style: Variable 'lseq' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:3152:17: style: Variable 'umis_read' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/ProcessReads.cpp:3334:17: style: Variable 'j' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/PseudoBam.cpp:95:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/PseudoBam.cpp:15:19: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:16:20: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:32:19: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:33:20: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:70:6: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:75:6: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:395:12: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:397:12: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:399:14: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:404:14: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:407:14: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:408:14: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:409:14: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:410:14: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:411:14: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:415:16: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:417:18: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:432:11: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:434:11: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:438:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:440:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:445:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:446:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:449:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:450:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:451:13: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:454:15: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:458:17: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/PseudoBam.cpp:428:8: style: The scope of the variable 'mark0' can be reduced. [variableScope] kallisto-0.48.0/src/PseudoBam.cpp:130:11: style: Local variable 'flag1' shadows outer variable [shadowVariable] kallisto-0.48.0/src/PseudoBam.cpp:66:7: note: Shadowed declaration kallisto-0.48.0/src/PseudoBam.cpp:130:11: note: Shadow variable kallisto-0.48.0/src/PseudoBam.cpp:131:11: style: Local variable 'flag2' shadows outer variable [shadowVariable] kallisto-0.48.0/src/PseudoBam.cpp:66:15: note: Shadowed declaration kallisto-0.48.0/src/PseudoBam.cpp:131:11: note: Shadow variable kallisto-0.48.0/src/PseudoBam.cpp:457:16: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/PseudoBam.cpp:436:12: note: Shadowed declaration kallisto-0.48.0/src/PseudoBam.cpp:457:16: note: Shadow variable kallisto-0.48.0/src/PseudoBam.cpp:163:20: style: Variable 'x' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/PseudoBam.cpp:175:20: style: Variable 'x' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/PseudoBam.cpp:303:18: style: Variable 'x' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/PseudoBam.cpp:66:12: style: Variable 'flag1' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/PseudoBam.cpp:66:20: style: Variable 'flag2' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/PseudoBam.cpp:71:11: style: Variable 'nlen1' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/PseudoBam.cpp:76:11: style: Variable 'nlen2' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/PseudoBam.cpp:157:16: style: Variable 'nmap' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/PseudoBam.cpp:232:16: style: Variable 'tlen' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/PseudoBam.cpp:288:16: style: Variable 'tlen' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/hash.cpp:20:14: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:21:15: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:29:19: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:34:19: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:104:26: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:116:29: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:128:26: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:167:4: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:168:4: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:180:4: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:190:4: style: C-style pointer casting [cstyleCast] kallisto-0.48.0/src/hash.cpp:10:24: style: The scope of the variable 'tmp' can be reduced. [variableScope] kallisto-0.48.0/src/Inspect.h:87:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/Inspect.h:100:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/Inspect.h:128:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:59:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:110:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:169:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:314:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:386:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:486:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:610:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:647:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:679:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:806:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:914:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_argument [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:953:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:1526:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:1563:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:1755:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:1911:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:1995:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2273:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2318:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2362:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2370:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2374:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2390:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2418:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2431:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2439:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2451:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2488:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2518:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2530:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2544:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2615:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] kallisto-0.48.0/src/main.cpp:2591:14: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] kallisto-0.48.0/src/main.cpp:2592:19: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] kallisto-0.48.0/src/main.cpp:1580:7: style: The if condition is the same as the previous if condition [duplicateCondition] kallisto-0.48.0/src/main.cpp:1565:7: note: First condition kallisto-0.48.0/src/main.cpp:1580:7: note: Second condition kallisto-0.48.0/src/main.cpp:1081:16: style: Condition 'opt.batch_mode' is always true [knownConditionTrueFalse] kallisto-0.48.0/src/main.cpp:1028:9: note: Assuming that condition '!opt.batch_mode' is not redundant kallisto-0.48.0/src/main.cpp:1081:16: note: Condition 'opt.batch_mode' is always true kallisto-0.48.0/src/main.cpp:2091:14: style: Condition 'opt.batch_mode' is always true [knownConditionTrueFalse] kallisto-0.48.0/src/main.cpp:2029:7: note: Assuming that condition '!opt.batch_mode' is not redundant kallisto-0.48.0/src/main.cpp:2091:14: note: Condition 'opt.batch_mode' is always true kallisto-0.48.0/src/Inspect.h:62:11: style: The scope of the variable 'pos' can be reduced. [variableScope] kallisto-0.48.0/src/Inspect.h:349:10: style: The scope of the variable 'guessChromosomes' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:66:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:117:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:194:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:327:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:400:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:506:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:614:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:700:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:920:7: style: The scope of the variable 'c' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:1039:26: style: The scope of the variable 'f2' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:2046:24: style: The scope of the variable 'f2' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:2722:21: style: The scope of the variable 'genelistname' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:2723:21: style: The scope of the variable 'busbarcodelistname' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:2775:14: style: The scope of the variable 'guessChromosomes' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:2843:26: style: The scope of the variable 'fld' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:2952:14: style: The scope of the variable 'guessChromosomes' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:2997:26: style: The scope of the variable 'preBias' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:3072:18: style: The scope of the variable 'n_threads' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:3149:26: style: The scope of the variable 'preBias' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:3217:18: style: The scope of the variable 'n_threads' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:3265:14: style: The scope of the variable 'firstline' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:3268:20: style: The scope of the variable 'prevRow' can be reduced. [variableScope] kallisto-0.48.0/src/main.cpp:3268:33: style: The scope of the variable 'prevCol' can be reduced. [variableScope] kallisto-0.48.0/src/Inspect.h:383:21: style: Local variable 'tra' shadows outer variable [shadowVariable] kallisto-0.48.0/src/Inspect.h:372:27: note: Shadowed declaration kallisto-0.48.0/src/Inspect.h:383:21: note: Shadow variable kallisto-0.48.0/src/Inspect.h:392:17: style: Local variable 'len' shadows outer variable [shadowVariable] kallisto-0.48.0/src/Inspect.h:374:11: note: Shadowed declaration kallisto-0.48.0/src/Inspect.h:392:17: note: Shadow variable kallisto-0.48.0/src/Inspect.h:457:28: style: Local variable 'x' shadows outer variable [shadowVariable] kallisto-0.48.0/src/Inspect.h:418:18: note: Shadowed declaration kallisto-0.48.0/src/Inspect.h:457:28: note: Shadow variable kallisto-0.48.0/src/Inspect.h:465:28: style: Local variable 'x' shadows outer variable [shadowVariable] kallisto-0.48.0/src/Inspect.h:418:18: note: Shadowed declaration kallisto-0.48.0/src/Inspect.h:465:28: note: Shadow variable kallisto-0.48.0/src/main.cpp:2298:19: style: Local variable 'stFileInfo' shadows outer variable [shadowVariable] kallisto-0.48.0/src/main.cpp:2290:17: note: Shadowed declaration kallisto-0.48.0/src/main.cpp:2298:19: note: Shadow variable kallisto-0.48.0/src/main.cpp:2299:12: style: Local variable 'intStat' shadows outer variable [shadowVariable] kallisto-0.48.0/src/main.cpp:2291:10: note: Shadowed declaration kallisto-0.48.0/src/main.cpp:2299:12: note: Shadow variable kallisto-0.48.0/src/main.cpp:3520:20: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/main.cpp:3268:13: note: Shadowed declaration kallisto-0.48.0/src/main.cpp:3520:20: note: Shadow variable kallisto-0.48.0/src/main.cpp:3523:20: style: Local variable 'i' shadows outer variable [shadowVariable] kallisto-0.48.0/src/main.cpp:3268:13: note: Shadowed declaration kallisto-0.48.0/src/main.cpp:3523:20: note: Shadow variable kallisto-0.48.0/src/main.cpp:46:34: performance: Function parameter 'fn' should be passed by const reference. [passedByValue] kallisto-0.48.0/src/Inspect.h:194:16: style: Variable 'eiv' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/Inspect.h:203:15: style: Variable 'v' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/Inspect.h:296:15: style: Variable 'ct' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/Inspect.h:309:13: style: Variable 'seq' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/Inspect.h:420:15: style: Variable 'ecv' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:974:16: style: Variable 'fn' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:1521:40: style: Parameter 'opt' can be declared as reference to const [constParameterReference] kallisto-0.48.0/src/main.cpp:1540:16: style: Variable 'fasta' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:1586:18: style: Variable 'fn' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:1751:43: style: Parameter 'opt' can be declared as reference to const [constParameterReference] kallisto-0.48.0/src/main.cpp:1931:16: style: Variable 'fn' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:2077:18: style: Variable 'fn' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:2314:41: style: Parameter 'opt' can be declared as reference to const [constParameterReference] kallisto-0.48.0/src/main.cpp:2349:16: style: Variable 'fn' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:3760:24: style: Variable 'p' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:3780:30: style: Variable 'g_id' can be declared as reference to const [constVariableReference] kallisto-0.48.0/src/main.cpp:57:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:108:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:167:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:312:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:385:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:484:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:609:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:678:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:912:24: style: Variable 'long_options' can be declared as const array [constVariable] kallisto-0.48.0/src/main.cpp:2574:44: style: Parameter 'argv' can be declared as const array [constParameter] kallisto-0.48.0/src/main.cpp:2588:15: style: Variable 'timeinfo' can be declared as pointer to const [constVariablePointer] kallisto-0.48.0/src/main.cpp:884:41: warning:inconclusive: Access of moved variable 'v'. [accessMoved] kallisto-0.48.0/src/main.cpp:882:15: note: Calling std::move(v) kallisto-0.48.0/src/main.cpp:884:41: note: Access of moved variable 'v'. kallisto-0.48.0/src/main.cpp:887:7: warning:inconclusive: Access of moved variable 'v'. [accessMoved] kallisto-0.48.0/src/main.cpp:882:15: note: Calling std::move(v) kallisto-0.48.0/src/main.cpp:884:7: note: Assuming condition is false kallisto-0.48.0/src/main.cpp:887:7: note: Access of moved variable 'v'. kallisto-0.48.0/src/main.cpp:894:41: warning:inconclusive: Access of moved variable 'v'. [accessMoved] kallisto-0.48.0/src/main.cpp:891:16: note: Calling std::move(v) kallisto-0.48.0/src/main.cpp:894:41: note: Access of moved variable 'v'. kallisto-0.48.0/src/main.cpp:897:7: warning:inconclusive: Access of moved variable 'v'. [accessMoved] kallisto-0.48.0/src/main.cpp:891:16: note: Calling std::move(v) kallisto-0.48.0/src/main.cpp:894:7: note: Assuming condition is false kallisto-0.48.0/src/main.cpp:897:7: note: Access of moved variable 'v'. kallisto-0.48.0/src/Inspect.h:68:14: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm] kallisto-0.48.0/src/main.cpp:2878:40: error: Uninitialized variable: num_trans [uninitvar] kallisto-0.48.0/src/main.cpp:2884:40: error: Uninitialized variable: index_version [uninitvar] kallisto-0.48.0/src/Inspect.h:417:12: style: Variable 'single_chrom' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/main.cpp:478:7: style: Variable 'gbam_flag' is assigned a value that is never used. [unreadVariable] kallisto-0.48.0/src/main.cpp:1273:21: style: Unused variable: files [unusedVariable] kallisto-0.48.0/src/main.cpp:1274:33: style: Unused variable: values [unusedVariable] kallisto-0.48.0/src/main.cpp:1275:33: style: Unused variable: bcValues [unusedVariable] kallisto-0.48.0/src/main.cpp:1413:21: style: Unused variable: files [unusedVariable] kallisto-0.48.0/src/main.cpp:1414:33: style: Unused variable: values [unusedVariable] kallisto-0.48.0/src/main.cpp:1415:33: style: Unused variable: bcValues [unusedVariable] kallisto-0.48.0/src/weights.cpp:155:15: warning: Identical inner 'if' condition is always true. [identicalInnerCondition] kallisto-0.48.0/src/weights.cpp:153:31: note: outer condition: j