2024-04-23 13:55
ftp://ftp.de.debian.org/debian/pool/main/a/anfo/anfo_0.98.orig.tar.gz
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: 24be0e5 (2024-04-23 14:04:36 +0200)
count: 466 466
elapsed-time: 25.7 25.2
head-timing-info:

old-timing-info:

head results:
anfo-0.98/src/sequence.h:199:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hex [valueFlowBailoutIncompleteVar]
anfo-0.98/src/sequence.h:243:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hex [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.h:41:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.h:106:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.h:119:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.h:129:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.h:164:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
anfo-0.98/src/index.h:349:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable digits [valueFlowBailoutIncompleteVar]
anfo-0.98/src/compress_stream.h:398:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_WRONLY [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:93:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:179:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Match [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:180:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Mismatch [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:181:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Insert [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:182:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Delete [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:279:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable False [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:361:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:363:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:436:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:752:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:778:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/align.h:64:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ambicode [valueFlowBailoutIncompleteVar]
anfo-0.98/src/align.cc:169:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
anfo-0.98/src/align.h:221:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
anfo-0.98/src/logdom.h:70:67: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
anfo-0.98/src/logdom.h:66:45: note: Calling function 'from_float', 1st argument '0' value is 0
anfo-0.98/src/logdom.h:70:67: note: Invalid argument
anfo-0.98/src/stream.h:820:3: warning: Member variable 'SffReader::remaining_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/stream.h:820:3: warning: Member variable 'SffReader::number_of_flows_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/align.h:123:3: warning:inconclusive: Member variable 'ExtendAlignment < FullCell >::width_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/align.h:123:3: warning:inconclusive: Member variable 'ExtendAlignment < FullCell >::max_s_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/align.h:123:3: warning:inconclusive: Member variable 'ExtendAlignment < FullCell >::max_x_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/align.h:123:3: warning:inconclusive: Member variable 'ExtendAlignment < FullCell >::max_y_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/align.h:123:3: warning:inconclusive: Member variable 'ExtendAlignment < FullCell >::max_tail_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/align.h:35:3: warning:inconclusive: Member variable 'Array < adna_parblock :: num_states , FullCell >::arr_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/align.h:147:24: style:inconclusive: Member variable 'ExtendBothEnds < FullCell >::forwards_' uses an uninitialized argument 'score_' due to the order of declarations. [initializerList]
anfo-0.98/src/align.h:345:2: note: Member variable 'ExtendBothEnds < FullCell >::forwards_' uses an uninitialized argument 'score_' due to the order of declarations.
anfo-0.98/src/align.h:147:24: note: Member variable 'ExtendBothEnds < FullCell >::forwards_' uses an uninitialized argument 'score_' due to the order of declarations.
anfo-0.98/src/align.h:147:35: style:inconclusive: Member variable 'ExtendBothEnds < FullCell >::backwards_' uses an uninitialized argument 'score_' due to the order of declarations. [initializerList]
anfo-0.98/src/align.h:350:2: note: Member variable 'ExtendBothEnds < FullCell >::backwards_' uses an uninitialized argument 'score_' due to the order of declarations.
anfo-0.98/src/align.h:147:35: note: Member variable 'ExtendBothEnds < FullCell >::backwards_' uses an uninitialized argument 'score_' due to the order of declarations.
anfo-0.98/src/align.cc:89:2: performance: Variable 'gap_ext_penalty' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
anfo-0.98/src/util.h:275:8: style:inconclusive: Technically the member function 'Chan::close' can be const. [functionConst]
anfo-0.98/src/util.h:276:8: style:inconclusive: Technically the member function 'Chan::operator()' can be const. [functionConst]
anfo-0.98/src/index.h:176:7: style:inconclusive: Technically the member function 'compare_match_lists::operator()' can be const. [functionConst]
anfo-0.98/src/index.h:202:9: style:inconclusive: Technically the member function 'PreSeeds::equal_match_lists::operator()' can be const. [functionConst]
anfo-0.98/src/sequence.h:257:2: style: Struct 'Sequ' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/sequence.h:332:3: style: Class 'QSequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/align_fwd.h:43:2: style: Struct 'adna_parblock' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/index.h:79:3: style: Class 'CompactGenome' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/index.h:285:3: style: Class 'FixedIndex' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/index.h:512:3: style: Class 'Metagenome' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/compress_stream.h:214:2: style: Struct 'BzipError' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:307:2: style: Struct 'ParseError' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:353:3: style: Class 'UniversalReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:490:3: style: Class 'OnlyGenome' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:549:3: style: Class 'QualFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:563:3: style: Class 'LengthFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:574:3: style: Class 'GcFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:610:3: style: Class 'Subsample' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:623:3: style: Class 'MultiFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:640:3: style: Class 'QualMasker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:882:3: style: Class 'zero_copy_output_buf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/stream.h:893:3: style: Class 'zero_copy_ostream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/align.h:36:3: style: Class 'Array < adna_parblock :: num_states , FullCell >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:286:26: style: Class 'Holder < const CompactGenome >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:287:26: style: Class 'Holder < const CompactGenome >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/compress_stream.h:215:15: style: The function 'print_to' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/util.h:33:33: note: Virtual function in base class
anfo-0.98/src/compress_stream.h:215:15: note: Function in derived class
anfo-0.98/src/stream.h:308:15: style: The function 'print_to' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/util.h:33:33: note: Virtual function in base class
anfo-0.98/src/stream.h:308:15: note: Function in derived class
anfo-0.98/src/stream.h:323:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:323:18: note: Function in derived class
anfo-0.98/src/stream.h:326:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/stream.h:326:18: note: Function in derived class
anfo-0.98/src/stream.h:361:17: style: The function 'get_state' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:238:17: note: Virtual function in base class
anfo-0.98/src/stream.h:361:17: note: Function in derived class
anfo-0.98/src/stream.h:362:18: style: The function 'fetch_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:243:18: note: Virtual function in base class
anfo-0.98/src/stream.h:362:18: note: Function in derived class
anfo-0.98/src/stream.h:363:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:363:18: note: Function in derived class
anfo-0.98/src/stream.h:364:18: style: The function 'fetch_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:255:18: note: Virtual function in base class
anfo-0.98/src/stream.h:364:18: note: Function in derived class
anfo-0.98/src/stream.h:365:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/stream.h:365:18: note: Function in derived class
anfo-0.98/src/stream.h:402:12: style: The destructor '~ChunkedWriter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:218:12: note: Virtual destructor in base class
anfo-0.98/src/stream.h:402:12: note: Destructor in derived class
anfo-0.98/src/stream.h:404:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/stream.h:404:16: note: Function in derived class
anfo-0.98/src/stream.h:405:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/stream.h:405:16: note: Function in derived class
anfo-0.98/src/stream.h:406:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/stream.h:406:16: note: Function in derived class
anfo-0.98/src/stream.h:407:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/stream.h:407:18: note: Function in derived class
anfo-0.98/src/stream.h:422:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:422:18: note: Function in derived class
anfo-0.98/src/stream.h:425:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/stream.h:425:18: note: Function in derived class
anfo-0.98/src/stream.h:436:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/stream.h:436:16: note: Function in derived class
anfo-0.98/src/stream.h:452:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/stream.h:452:16: note: Function in derived class
anfo-0.98/src/stream.h:459:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/stream.h:459:16: note: Function in derived class
anfo-0.98/src/stream.h:479:16: style: The function 'keep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:458:16: note: Virtual function in base class
anfo-0.98/src/stream.h:479:16: note: Function in derived class
anfo-0.98/src/stream.h:491:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:491:16: note: Function in derived class
anfo-0.98/src/stream.h:512:16: style: The function 'keep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:458:16: note: Virtual function in base class
anfo-0.98/src/stream.h:512:16: note: Function in derived class
anfo-0.98/src/stream.h:524:22: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:524:22: note: Function in derived class
anfo-0.98/src/stream.h:539:16: style: The function 'keep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:458:16: note: Virtual function in base class
anfo-0.98/src/stream.h:539:16: note: Function in derived class
anfo-0.98/src/stream.h:550:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:550:16: note: Function in derived class
anfo-0.98/src/stream.h:565:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:565:16: note: Function in derived class
anfo-0.98/src/stream.h:575:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:575:16: note: Function in derived class
anfo-0.98/src/stream.h:588:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:588:16: note: Function in derived class
anfo-0.98/src/stream.h:601:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:601:16: note: Function in derived class
anfo-0.98/src/stream.h:611:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:611:16: note: Function in derived class
anfo-0.98/src/stream.h:624:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:624:16: note: Function in derived class
anfo-0.98/src/stream.h:641:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/stream.h:641:16: note: Function in derived class
anfo-0.98/src/stream.h:720:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/stream.h:720:16: note: Function in derived class
anfo-0.98/src/stream.h:728:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/stream.h:728:16: note: Function in derived class
anfo-0.98/src/stream.h:729:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/stream.h:729:16: note: Function in derived class
anfo-0.98/src/stream.h:730:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:730:18: note: Function in derived class
anfo-0.98/src/stream.h:739:18: style: The function 'fetch_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:243:18: note: Virtual function in base class
anfo-0.98/src/stream.h:739:18: note: Function in derived class
anfo-0.98/src/stream.h:740:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:740:18: note: Function in derived class
anfo-0.98/src/stream.h:764:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:764:18: note: Function in derived class
anfo-0.98/src/stream.h:765:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/stream.h:765:18: note: Function in derived class
anfo-0.98/src/stream.h:797:18: style: The function 'fetch_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:243:18: note: Virtual function in base class
anfo-0.98/src/stream.h:797:18: note: Function in derived class
anfo-0.98/src/stream.h:798:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:798:18: note: Function in derived class
anfo-0.98/src/stream.h:799:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/stream.h:799:18: note: Function in derived class
anfo-0.98/src/stream.h:823:18: style: The function 'fetch_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:243:18: note: Virtual function in base class
anfo-0.98/src/stream.h:823:18: note: Function in derived class
anfo-0.98/src/stream.h:824:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:824:18: note: Function in derived class
anfo-0.98/src/stream.h:825:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/stream.h:825:18: note: Function in derived class
anfo-0.98/src/stream.h:846:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/stream.h:846:18: note: Function in derived class
anfo-0.98/src/stream.h:847:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/stream.h:847:18: note: Function in derived class
anfo-0.98/src/util.h:109:10: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/util.h:122:9: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.h:286:36: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.h:109:14: style: Unused variable: code [unusedVariable]
anfo-0.98/src/misc_streams.h:137:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable False [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo-elk.cc:73:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Void [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo-elk.cc:82:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Void [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo-elk.cc:96:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T_Symbol [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo-elk.cc:113:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_WRONLY [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo-elk.cc:166:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T_String [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:280:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hdr_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:291:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:294:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable foot_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:305:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hdr_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:394:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hdr_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:182:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hdr_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:198:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:518:3: warning: Member variable 'DivergenceStream::ancient_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/anfo_common.h:69:4: error: Member variable 'minscore_' is initialized by itself. [selfInitialization]
anfo-0.98/src/misc_streams.h:44:8: performance:inconclusive: Technically the member function 'streams::by_genome_coordinate::compare' can be static (but you may consider moving to unnamed namespace). [functionStatic]
anfo-0.98/src/misc_streams.h:100:7: style:inconclusive: Technically the member function 'streams::by_seqid::operator()' can be const. [functionConst]
anfo-0.98/src/misc_streams.h:104:7: performance:inconclusive: Technically the member function 'streams::by_seqid::tag_header' can be static (but you may consider moving to unnamed namespace). [functionStatic]
anfo-0.98/src/misc_streams.h:108:10: performance:inconclusive: Technically the member function 'streams::by_seqid::is_sorted' can be static (but you may consider moving to unnamed namespace). [functionStatic]
anfo-0.98/src/misc_streams.h:604:8: style:inconclusive: Technically the member function 'streams::RegionFilter::inside' can be const. [functionConst]
anfo-0.98/src/anfo_common.h:62:3: style: Class 'Housekeeper' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/ducttape.h:99:3: style: Class 'DuctTaper' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/ducttape.h:77:4: style: Struct 'Acc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/ducttape.h:121:3: style: Class 'GlzWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/ducttape.h:144:3: style: Class 'ThreeAlnWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/misc_streams.h:56:3: style: Class 'by_genome_coordinate' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/misc_streams.h:57:3: style: Class 'by_genome_coordinate' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/misc_streams.h:455:3: style: Class 'RepairHeaderStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/misc_streams.h:599:3: style: Class 'RegionFilter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/misc_streams.h:621:3: style: Class 'InsideRegion' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/misc_streams.h:627:3: style: Class 'OutsideRegion' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/output_streams.h:50:3: style: Class 'TextWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/output_streams.h:93:3: style: Class 'SamWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/output_streams.h:126:3: style: Class 'FastaAlnWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/output_streams.h:152:3: style: Class 'TableWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/output_streams.h:179:3: style: Class 'WigCoverageWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/anfo-elk.cc:66:2: style: Struct 'StreamWrapper' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/misc_streams.h:275:3: style: Class 'SortingStream < by_genome_coordinate >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/misc_streams.h:275:3: style: Class 'SortingStream < by_seqid >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:286:26: style: Class 'Holder < StreamBundle >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:287:26: style: Class 'Holder < StreamBundle >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:286:26: style: Class 'Holder < FanOut >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:287:26: style: Class 'Holder < FanOut >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:286:26: style: Class 'Holder < Compose >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:287:26: style: Class 'Holder < Compose >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:286:26: style: Class 'Holder < streams :: Stream >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:287:26: style: Class 'Holder < streams :: Stream >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:286:26: style: Class 'Holder < Stream >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:287:26: style: Class 'Holder < Stream >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:286:26: style: Class 'Holder < MergeStream >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/util.h:287:26: style: Class 'Holder < MergeStream >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/anfo_common.h:71:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/anfo_common.h:71:16: note: Function in derived class
anfo-0.98/src/anfo_common.h:88:12: style: The destructor '~Indexer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:218:12: note: Virtual destructor in base class
anfo-0.98/src/anfo_common.h:88:12: note: Destructor in derived class
anfo-0.98/src/anfo_common.h:90:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/anfo_common.h:90:16: note: Function in derived class
anfo-0.98/src/anfo_common.h:91:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/anfo_common.h:91:16: note: Function in derived class
anfo-0.98/src/anfo_common.h:109:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/anfo_common.h:109:16: note: Function in derived class
anfo-0.98/src/anfo_common.h:110:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/anfo_common.h:110:16: note: Function in derived class
anfo-0.98/src/ducttape.h:104:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/ducttape.h:104:16: note: Function in derived class
anfo-0.98/src/ducttape.h:105:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/ducttape.h:105:16: note: Function in derived class
anfo-0.98/src/ducttape.h:106:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/ducttape.h:106:16: note: Function in derived class
anfo-0.98/src/ducttape.h:107:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/ducttape.h:107:18: note: Function in derived class
anfo-0.98/src/ducttape.h:122:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/ducttape.h:122:16: note: Function in derived class
anfo-0.98/src/ducttape.h:145:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/ducttape.h:145:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:132:18: style: The function 'fetch_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:243:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:132:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:133:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:133:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:137:18: style: The function 'get_summary' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:279:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:137:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:138:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:138:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:162:18: style: The function 'fetch_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:243:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:162:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:163:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:163:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:456:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:456:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:462:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:462:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:463:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:463:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:464:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:464:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:465:18: style: The function 'fetch_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:255:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:465:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:471:17: style: The function 'get_state' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:238:17: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:471:17: note: Function in derived class
anfo-0.98/src/misc_streams.h:473:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:473:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:474:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:474:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:475:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:475:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:477:18: style: The function 'fetch_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:243:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:477:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:478:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:478:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:479:18: style: The function 'fetch_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:255:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:479:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:480:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:480:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:496:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:496:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:497:18: style: The function 'get_summary' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:279:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:497:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:522:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:522:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:523:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:523:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:524:18: style: The function 'get_summary' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:279:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:524:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:534:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:534:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:535:18: style: The function 'get_summary' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:279:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:535:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:584:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:584:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:622:16: style: The function 'keep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:458:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:622:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:628:16: style: The function 'keep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:458:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:628:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:634:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:634:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:635:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:635:16: note: Function in derived class
anfo-0.98/src/output_streams.h:52:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:52:16: note: Function in derived class
anfo-0.98/src/output_streams.h:53:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:53:16: note: Function in derived class
anfo-0.98/src/output_streams.h:54:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:54:16: note: Function in derived class
anfo-0.98/src/output_streams.h:55:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/output_streams.h:55:18: note: Function in derived class
anfo-0.98/src/output_streams.h:98:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:98:16: note: Function in derived class
anfo-0.98/src/output_streams.h:106:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:106:16: note: Function in derived class
anfo-0.98/src/output_streams.h:111:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:111:16: note: Function in derived class
anfo-0.98/src/output_streams.h:127:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:127:16: note: Function in derived class
anfo-0.98/src/output_streams.h:143:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:143:16: note: Function in derived class
anfo-0.98/src/output_streams.h:153:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:153:16: note: Function in derived class
anfo-0.98/src/output_streams.h:164:16: style: The function 'xform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:435:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:164:16: note: Function in derived class
anfo-0.98/src/output_streams.h:180:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/output_streams.h:180:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:268:12: style: The destructor '~SortingStream < by_genome_coordinate >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:218:12: note: Virtual destructor in base class
anfo-0.98/src/misc_streams.h:268:12: note: Destructor in derived class
anfo-0.98/src/misc_streams.h:280:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:280:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:281:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:281:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:282:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:282:16: note: Function in derived class
anfo-0.98/src/misc_streams.h:288:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:288:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:294:18: style: The function 'fetch_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:255:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:294:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:295:18: style: The function 'get_summary' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:279:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:295:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:268:12: style: The destructor '~SortingStream < by_seqid >' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:218:12: note: Virtual destructor in base class
anfo-0.98/src/misc_streams.h:268:12: note: Destructor in derived class
anfo-0.98/src/misc_streams.h:187:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:187:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:201:18: style: The function 'type_name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:282:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:201:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:137:18: style: The function 'get_summary' overrides a function in a base class but is identical to the overridden function [uselessOverride]
anfo-0.98/src/stream.h:279:18: note: Virtual function in base class
anfo-0.98/src/misc_streams.h:137:18: note: Function in derived class
anfo-0.98/src/anfo-elk.cc:71:6: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:78:21: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:158:21: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:205:21: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:208:9: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:423:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:424:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:425:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:426:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:427:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:429:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:430:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:431:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:432:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:433:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:434:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:435:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:436:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:437:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:438:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:440:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:441:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:442:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:443:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:445:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:446:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:447:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:448:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:449:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:450:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:451:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:452:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:453:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:454:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:455:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:456:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:457:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:458:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:459:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:460:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:461:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:462:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:464:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:465:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:467:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:468:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:469:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:471:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:472:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:473:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:475:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:476:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:477:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:478:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:481:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/anfo-elk.cc:482:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/misc_streams.h:343:22: style: Local variable 's' shadows outer argument [shadowArgument]
anfo-0.98/src/misc_streams.h:320:92: note: Shadowed declaration
anfo-0.98/src/misc_streams.h:343:22: note: Shadow variable
anfo-0.98/src/anfo_common.h:68:52: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
anfo-0.98/src/misc_streams.h:275:61: performance: Function parameter 'comp' should be passed by const reference. [passedByValue]
anfo-0.98/src/anfo-elk.cc:158:16: style: Variable 'h' can be declared as reference to const [constVariableReference]
anfo-0.98/src/anfo-tool.cc:107:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo-tool.cc:378:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GOOGLE_PROTOBUF_VERIFY_VERSION [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo-tool.cc:78:20: warning: Either the condition 'a' is redundant or there is possible null pointer dereference: a. [nullPointerRedundantCheck]
anfo-0.98/src/anfo-tool.cc:79:6: note: Assuming that condition 'a' is not redundant
anfo-0.98/src/anfo-tool.cc:78:20: note: Null pointer dereference
anfo-0.98/src/anfo-tool.cc:85:18: warning: Either the condition 'a' is redundant or there is possible null pointer dereference: a. [nullPointerRedundantCheck]
anfo-0.98/src/anfo-tool.cc:86:6: note: Assuming that condition 'a' is not redundant
anfo-0.98/src/anfo-tool.cc:85:18: note: Null pointer dereference
anfo-0.98/src/concurrent_stream.h:94:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/concurrent_stream.h:95:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size_ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:198:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:270:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Result [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:304:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable const_iterator [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:393:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable const_iterator [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo.cc:110:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GOOGLE_PROTOBUF_VERIFY_VERSION [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.h:275:3: style: Class 'SortingStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/concurrent_stream.h:117:4: style: The destructor '~ConcurrentStream' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:218:12: note: Virtual destructor in base class
anfo-0.98/src/concurrent_stream.h:117:4: note: Destructor in derived class
anfo-0.98/src/concurrent_stream.h:119:17: style: The function 'get_state' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:238:17: note: Virtual function in base class
anfo-0.98/src/concurrent_stream.h:119:17: note: Function in derived class
anfo-0.98/src/concurrent_stream.h:120:16: style: The function 'put_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:260:16: note: Virtual function in base class
anfo-0.98/src/concurrent_stream.h:120:16: note: Function in derived class
anfo-0.98/src/concurrent_stream.h:121:16: style: The function 'put_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:266:16: note: Virtual function in base class
anfo-0.98/src/concurrent_stream.h:121:16: note: Function in derived class
anfo-0.98/src/concurrent_stream.h:122:16: style: The function 'put_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:272:16: note: Virtual function in base class
anfo-0.98/src/concurrent_stream.h:122:16: note: Function in derived class
anfo-0.98/src/concurrent_stream.h:123:18: style: The function 'fetch_header' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:243:18: note: Virtual function in base class
anfo-0.98/src/concurrent_stream.h:123:18: note: Function in derived class
anfo-0.98/src/concurrent_stream.h:124:18: style: The function 'fetch_result' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:249:18: note: Virtual function in base class
anfo-0.98/src/concurrent_stream.h:124:18: note: Function in derived class
anfo-0.98/src/concurrent_stream.h:125:18: style: The function 'fetch_footer' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:255:18: note: Virtual function in base class
anfo-0.98/src/concurrent_stream.h:125:18: note: Function in derived class
anfo-0.98/src/misc_streams.h:268:12: style: The destructor '~SortingStream' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
anfo-0.98/src/stream.h:218:12: note: Virtual destructor in base class
anfo-0.98/src/misc_streams.h:268:12: note: Destructor in derived class
anfo-0.98/src/anfo.cc:121:6: style: The scope of the variable 'task_id' can be reduced. [variableScope]
anfo-0.98/src/conffile.h:66:43: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam]
anfo-0.98/src/anfo_common.cc:62:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo_common.cc:247:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable too_many_seeds [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo_common.cc:347:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_policy [valueFlowBailoutIncompleteVar]
anfo-0.98/src/anfo_common.cc:226:13: style: Local variable 'i' shadows outer variable [shadowVariable]
anfo-0.98/src/anfo_common.cc:212:11: note: Shadowed declaration
anfo-0.98/src/anfo_common.cc:226:13: note: Shadow variable
anfo-0.98/src/anfo_common.cc:421:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
anfo-0.98/src/util.h:292:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.h:295:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.h:298:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
anfo-0.98/src/concurrent_stream.cc:77:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid [valueFlowBailoutIncompleteVar]
anfo-0.98/src/concurrent_stream.cc:269:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GC_Node [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.h:287:26: style: Class 'Holder' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/concurrent_stream.cc:102:4: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/dnaindex.cc:144:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable G [valueFlowBailoutIncompleteVar]
anfo-0.98/src/dnaindex.cc:232:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GOOGLE_PROTOBUF_VERIFY_VERSION [valueFlowBailoutIncompleteVar]
anfo-0.98/src/dnaindex.cc:78:3: style: Struct 'mk_dense_word' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/dnaindex.cc:226:2: style: Struct 'put_gap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/dnaindex.cc:102:37: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
anfo-0.98/src/dnaindex.cc:105:37: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
anfo-0.98/src/dnaindex.cc:109:37: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
anfo-0.98/src/dnaindex.cc:113:37: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
anfo-0.98/src/dnaindex.cc:117:37: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
anfo-0.98/src/dnaindex.cc:122:37: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
anfo-0.98/src/dnaindex.cc:128:37: style: Operator '|' with one operand equal to zero is redundant. [badBitmaskCheck]
anfo-0.98/src/dnaindex.cc:293:19: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/dnaindex.cc:344:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/dnaindex.cc:294:23: error: Memory is allocated but not initialized: base [uninitdata]
anfo-0.98/src/dnaindex.cc:345:23: error: Memory is allocated but not initialized: lists [uninitdata]
anfo-0.98/src/ducttape.cc:39:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable need_input [valueFlowBailoutIncompleteVar]
anfo-0.98/src/ducttape.cc:139:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/ducttape.cc:144:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable need_input [valueFlowBailoutIncompleteVar]
anfo-0.98/src/ducttape.cc:151:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/ducttape.cc:208:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Delete [valueFlowBailoutIncompleteVar]
anfo-0.98/src/ducttape.cc:301:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable aln_i [valueFlowBailoutIncompleteVar]
anfo-0.98/src/ducttape.cc:470:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable aln_b [valueFlowBailoutIncompleteVar]
anfo-0.98/src/ducttape.cc:583:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable beg [valueFlowBailoutIncompleteVar]
anfo-0.98/src/ducttape.cc:200:8: style:inconclusive: Technically the member function 'streams::AlnIter::operator!=' can be const. [functionConst]
anfo-0.98/src/fa2dna.cc:133:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
anfo-0.98/src/fa2dna.cc:154:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
anfo-0.98/src/fa2dna.cc:324:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GOOGLE_PROTOBUF_VERIFY_VERSION [valueFlowBailoutIncompleteVar]
anfo-0.98/src/fa2dna.cc:117:3: warning: Member variable 'FastaDecoder::source_position_' is not initialized in the constructor. [uninitMemberVar]
anfo-0.98/src/fa2dna.cc:123:17: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/fa2dna.cc:124:17: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/fa2dna.cc:125:17: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/fa2dna.cc:140:16: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/fa2dna.cc:141:16: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/fastlz.c:425:13: style: Variable 'op_limit' can be declared as pointer to const [constVariablePointer]
anfo-0.98/src/file-info.cc:37:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GOOGLE_PROTOBUF_VERIFY_VERSION [valueFlowBailoutIncompleteVar]
anfo-0.98/src/file-info.cc:43:12: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/file-info.cc:48:13: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/file-info.cc:49:13: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/file-info.cc:52:13: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/file-info.cc:64:13: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/file-info.cc:66:13: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index-test.cc:61:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GOOGLE_PROTOBUF_VERIFY_VERSION [valueFlowBailoutIncompleteVar]
anfo-0.98/src/index.cc:48:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
anfo-0.98/src/index.cc:101:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable flush [valueFlowBailoutIncompleteVar]
anfo-0.98/src/index.cc:380:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GLOB_NOSORT [valueFlowBailoutIncompleteVar]
anfo-0.98/src/index.cc:472:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDWR [valueFlowBailoutIncompleteVar]
anfo-0.98/src/index.cc:483:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROT_READ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/index.cc:55:17: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:57:0: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:60:0: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:61:0: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:63:28: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:85:23: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:93:22: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:119:9: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:122:25: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:123:31: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:128:30: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:133:20: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:485:13: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:494:13: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/index.cc:248:50: style:inconclusive: Function 'lookupS' argument 1 names different: declaration 'seq' definition 'dna'. [funcArgNamesDifferent]
anfo-0.98/src/index.h:288:41: note: Function 'lookupS' argument 1 names different: declaration 'seq' definition 'dna'.
anfo-0.98/src/index.cc:248:50: note: Function 'lookupS' argument 1 names different: declaration 'seq' definition 'dna'.
anfo-0.98/src/index.cc:478:31: style: Parameter 'start' can be declared as pointer to const [constParameterPointer]
anfo-0.98/src/index.cc:40:53: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
anfo-0.98/src/misc_streams.cc:22:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:84:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:120:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:150:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:216:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable need_input [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:229:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable need_input [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:277:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable need_input [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:339:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Null [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:373:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GC_Node [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:475:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable False [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:561:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
anfo-0.98/src/misc_streams.cc:332:42: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
anfo-0.98/src/misc_streams.cc:523:98: style:inconclusive: Function 'AgreesWithChain' argument 3 names different: declaration 's' definition 'p'. [funcArgNamesDifferent]
anfo-0.98/src/misc_streams.h:583:83: note: Function 'AgreesWithChain' argument 3 names different: declaration 's' definition 'p'.
anfo-0.98/src/misc_streams.cc:523:98: note: Function 'AgreesWithChain' argument 3 names different: declaration 's' definition 'p'.
anfo-0.98/src/misc_streams.cc:164:26: style: Local variable 's' shadows outer variable [shadowVariable]
anfo-0.98/src/misc_streams.cc:149:11: note: Shadowed declaration
anfo-0.98/src/misc_streams.cc:164:26: note: Shadow variable
anfo-0.98/src/output_streams.cc:197:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable q [valueFlowBailoutIncompleteVar]
anfo-0.98/src/output_streams.cc:274:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable show [valueFlowBailoutIncompleteVar]
anfo-0.98/src/output_streams.cc:349:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TYPE_GROUP [valueFlowBailoutIncompleteVar]
anfo-0.98/src/output_streams.cc:447:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Match [valueFlowBailoutIncompleteVar]
anfo-0.98/src/output_streams.cc:596:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
anfo-0.98/src/output_streams.cc:69:13: style: Local variable 'i' shadows outer variable [shadowVariable]
anfo-0.98/src/output_streams.cc:40:11: note: Shadowed declaration
anfo-0.98/src/output_streams.cc:69:13: note: Shadow variable
anfo-0.98/src/output_streams.cc:77:12: style: Local variable 'i' shadows outer variable [shadowVariable]
anfo-0.98/src/output_streams.cc:40:11: note: Shadowed declaration
anfo-0.98/src/output_streams.cc:77:12: note: Shadow variable
anfo-0.98/src/output_streams.cc:111:12: style: Local variable 'i' shadows outer variable [shadowVariable]
anfo-0.98/src/output_streams.cc:40:11: note: Shadowed declaration
anfo-0.98/src/output_streams.cc:111:12: note: Shadow variable
anfo-0.98/src/output_streams.cc:197:23: style: Local variable 'r' shadows outer argument [shadowArgument]
anfo-0.98/src/output_streams.cc:187:52: note: Shadowed declaration
anfo-0.98/src/output_streams.cc:197:23: note: Shadow variable
anfo-0.98/src/output_streams.cc:510:17: style: Local variable 'i' shadows outer variable [shadowVariable]
anfo-0.98/src/output_streams.cc:486:11: note: Shadowed declaration
anfo-0.98/src/output_streams.cc:510:17: note: Shadow variable
anfo-0.98/src/output_streams.cc:522:16: style: Local variable 'i' shadows outer variable [shadowVariable]
anfo-0.98/src/output_streams.cc:486:11: note: Shadowed declaration
anfo-0.98/src/output_streams.cc:522:16: note: Shadow variable
anfo-0.98/src/output_streams.cc:535:17: style: Local variable 'i' shadows outer variable [shadowVariable]
anfo-0.98/src/output_streams.cc:486:11: note: Shadowed declaration
anfo-0.98/src/output_streams.cc:535:17: note: Shadow variable
anfo-0.98/src/output_streams.cc:128:87: style: Parameter 's' can be declared as reference to const. However it seems that 'show_noop' is a callback function, if 's' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
anfo-0.98/src/output_streams.cc:259:24: note: You might need to cast the function pointer here
anfo-0.98/src/output_streams.cc:128:87: note: Parameter 's' can be declared as reference to const
anfo-0.98/src/sequence.cc:288:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Match [valueFlowBailoutIncompleteVar]
anfo-0.98/src/sequence.cc:91:33: error: Invalid isspace() argument nr 1. A non-boolean value is required. [invalidFunctionArgBool]
anfo-0.98/src/sequence.cc:63:3: style: Class 'Reader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
anfo-0.98/src/sequence.cc:66:38: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/sequence.cc:81:38: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/sequence.cc:105:39: style:inconclusive: Function 'Base' argument 2 names different: declaration 'q_score' definition 'q'. [funcArgNamesDifferent]
anfo-0.98/src/sequence.h:298:25: note: Function 'Base' argument 2 names different: declaration 'q_score' definition 'q'.
anfo-0.98/src/sequence.cc:105:39: note: Function 'Base' argument 2 names different: declaration 'q_score' definition 'q'.
anfo-0.98/src/sequence.cc:111:27: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
anfo-0.98/src/sequence.cc:339:15: style: Variable 'junk' is assigned a value that is never used. [unreadVariable]
anfo-0.98/src/stream.cc:61:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:97:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:119:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Match [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:188:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:460:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:712:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:863:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable need_input [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:886:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:937:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable have_output [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:1047:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:1066:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:1232:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:1302:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:1341:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:1393:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.cc:1504:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_of_stream [valueFlowBailoutIncompleteVar]
anfo-0.98/src/stream.h:884:15: style: Virtual function 'sync' is called from destructor '~zero_copy_output_buf()' at line 1552. Dynamic binding is not used. [virtualCallInConstructor]
anfo-0.98/src/stream.cc:1552:49: note: Calling sync
anfo-0.98/src/stream.h:884:15: note: sync is a virtual function
anfo-0.98/src/stream.cc:1441:12: style: The if condition is the same as the previous if condition [duplicateCondition]
anfo-0.98/src/stream.cc:1439:12: note: First condition
anfo-0.98/src/stream.cc:1441:12: note: Second condition
anfo-0.98/src/stream.cc:1127:25: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1133:23: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1137:23: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1142:23: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1251:16: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1252:10: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1267:19: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1270:12: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1283:10: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1354:16: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1355:10: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1370:19: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:1373:12: style: C-style pointer casting [cstyleCast]
anfo-0.98/src/stream.cc:373:20: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
anfo-0.98/src/stream.cc:715:33: style:inconclusive: Function 'xform' argument 1 names different: declaration 'r' definition 'res'. [funcArgNamesDifferent]
anfo-0.98/src/stream.h:491:31: note: Function 'xform' argument 1 names different: declaration 'r' definition 'res'.
anfo-0.98/src/stream.cc:715:33: note: Function 'xform' argument 1 names different: declaration 'r' definition 'res'.
anfo-0.98/src/stream.cc:1445:16: style: Variable 'bases_rev' can be declared as const array [constVariable]
anfo-0.98/src/stream.cc:571:8: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
anfo-0.98/src/stream.cc:189:15: style: Variable 'tag' is assigned a value that is never used. [unreadVariable]
anfo-0.98/src/stream.cc:279:9: style: Unused variable: comp_size_l [unusedVariable]
anfo-0.98/src/stream.cc:381:9: style: Variable 'dlen' is assigned a value that is never used. [unreadVariable]
anfo-0.98/src/util.cc:98:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.cc:112:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TIOCGWINSZ [valueFlowBailoutIncompleteVar]
anfo-0.98/src/util.cc:55:9: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
anfo-0.98/src/util.cc:131:3: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
anfo-0.98/src/util.cc:146:3: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
diff:


DONE