2024-04-04 16:58 ftp://ftp.de.debian.org/debian/pool/main/t/tophat/tophat_2.1.1+dfsg1.orig.tar.xz cppcheck-options: --library=posix --library=gnu --library=bsd --library=boost --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 -j4 platform: Linux-6.1.0-18-amd64-x86_64-with-glibc2.36 python: 3.11.2 client-version: 1.3.55 compiler: g++ (Debian 12.2.0-14) 12.2.0 cppcheck: head 2.13.0 head-info: 3e22ef1 (2024-04-04 17:45:34 +0200) count: 1356 1103 elapsed-time: 28.1 97.1 head-timing-info: old-timing-info: head results: tophat-2.1.1/src/common.h:526:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.h:542:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.h:599:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CORE_SIZE [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/FastaTools.cpp:29:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/FastaTools.cpp:65:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/FastaTools.cpp:128:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/FastaTools.cpp:155:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.h:304:4: warning: Member variable 'GBamRecord::tag' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/common.h:304:4: warning: Member variable 'GBamRecord::abuf' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/common.h:327:10: performance:inconclusive: Technically the member function 'GBamRecord::parse_error' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/common.h:619:12: style:inconclusive: Technically the member function 'GBamWriter::writtenCount' can be const. [functionConst] tophat-2.1.1/src/common.h:200:3: style: Class 'FZPipe' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/common.h:304:4: style: Class 'GBamRecord' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/FastaTools.h:48:5: style: Class 'FastaReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/FastaTools.h:70:5: style: Class 'FastaWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/FastaTools.cpp:80:27: style: Condition 'line_buf_.length()>0' is always true [knownConditionTrueFalse] tophat-2.1.1/src/FastaTools.cpp:76:24: note: Assuming that condition 'line_buf_.empty()' is not redundant tophat-2.1.1/src/FastaTools.cpp:80:27: note: Condition 'line_buf_.length()>0' is always true tophat-2.1.1/src/common.h:377:19: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:58:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GBase.cpp:81:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.h:239:36: performance: Function parameter 'fname' should be passed by const reference. [passedByValue] tophat-2.1.1/src/GBase.cpp:105:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/FastaTools.cpp:15:38: performance: Function parameter 'fname' should be passed by const reference. [passedByValue] tophat-2.1.1/src/GBase.cpp:210:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/FastaTools.cpp:26:36: performance: Function parameter 'fname' should be passed by const reference. [passedByValue] tophat-2.1.1/src/GBase.cpp:220:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/FastaTools.cpp:113:38: performance: Function parameter 'fname' should be passed by const reference. [passedByValue] tophat-2.1.1/src/GBase.cpp:266:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/FastaTools.cpp:124:36: performance: Function parameter 'fname' should be passed by const reference. [passedByValue] tophat-2.1.1/src/GBase.cpp:453:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.h:429:48: style: Parameter 'idxfile' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/GBase.cpp:482:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.h:468:28: style: Parameter 'fname' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/common.h:468:48: style: Parameter 'idxfile' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/FastaTools.cpp:147:38: style: Parameter 'rec' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/common.h:365:67: style: Parameter 'data' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/common.h:567:12: style: Variable 'name' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/GStr.cpp:1255:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GStr.cpp:1270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:242:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:261:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:288:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:316:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:356:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:399:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:425:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:442:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:482:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:155:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:171:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:231:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:250:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:265:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:312:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:318:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:328:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:335:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:348:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:367:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:377:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:383:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:392:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:430:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:476:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:491:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:517:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:544:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:593:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:609:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:614:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:620:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:628:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:634:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GFaSeqGet.cpp:70:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GBase.h:298:8: style:inconclusive: Technically the member function 'GSeg::len' can be const. [functionConst] tophat-2.1.1/src/GBase.h:299:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst] tophat-2.1.1/src/GBase.h:304:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst] tophat-2.1.1/src/GBase.h:309:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst] tophat-2.1.1/src/GBase.h:314:8: style:inconclusive: Technically the member function 'GSeg::overlap' can be const. [functionConst] tophat-2.1.1/src/GBase.h:321:7: style:inconclusive: Technically the member function 'GSeg::overlapLen' can be const. [functionConst] tophat-2.1.1/src/GBase.h:331:7: style:inconclusive: Technically the member function 'GSeg::overlapLen' can be const. [functionConst] tophat-2.1.1/src/GBase.h:344:8: style:inconclusive: Technically the member function 'GSeg::coordMatch' can be const. [functionConst] tophat-2.1.1/src/GBase.h:351:8: style:inconclusive: Technically the member function 'GSeg::operator==' can be const. [functionConst] tophat-2.1.1/src/GBase.h:354:8: style:inconclusive: Technically the member function 'GSeg::operator<' can be const. [functionConst] tophat-2.1.1/src/GBase.h:378:8: style:inconclusive: Technically the member function 'GLineReader::readcount' can be const. [functionConst] tophat-2.1.1/src/GBase.h:380:8: style:inconclusive: Technically the member function 'GLineReader::length' can be const. [functionConst] tophat-2.1.1/src/GBase.h:381:8: style:inconclusive: Technically the member function 'GLineReader::size' can be const. [functionConst] tophat-2.1.1/src/GBase.h:382:9: style:inconclusive: Technically the member function 'GLineReader::isEof' can be const. [functionConst] tophat-2.1.1/src/GBase.h:383:9: style:inconclusive: Technically the member function 'GLineReader::eof' can be const. [functionConst] tophat-2.1.1/src/GBase.h:384:10: style:inconclusive: Technically the member function 'GLineReader::getfpos' can be const. [functionConst] tophat-2.1.1/src/GBase.h:385:10: style:inconclusive: Technically the member function 'GLineReader::getFpos' can be const. [functionConst] tophat-2.1.1/src/GBase.h:293:3: style: Class 'GSeg' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GBase.h:396:4: style: Class 'GLineReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GBase.h:402:4: style: Class 'GLineReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GBase.cpp:57:3: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/GBase.h:410:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.h:418:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:159:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:166:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:175:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:231:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:250:4: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:256:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:326:25: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:329:46: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:399:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:406:17: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:408:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:418:12: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:421:19: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:423:15: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:456:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:485:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:518:11: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:525:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:535:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:574:10: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:592:14: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:594:11: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:653:4: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:835:22: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GBase.cpp:637:8: style: The scope of the variable 'c' can be reduced. [variableScope] tophat-2.1.1/src/GBase.cpp:666:16: style: The scope of the variable 'g' can be reduced. [variableScope] tophat-2.1.1/src/GBase.cpp:448:34: style:inconclusive: Function 'fgetline' argument 2 names different: declaration 'buflen' definition 'buf_cap'. [funcArgNamesDifferent] tophat-2.1.1/src/GBase.h:428:34: note: Function 'fgetline' argument 2 names different: declaration 'buflen' definition 'buf_cap'. tophat-2.1.1/src/GBase.cpp:448:34: note: Function 'fgetline' argument 2 names different: declaration 'buflen' definition 'buf_cap'. tophat-2.1.1/src/GBase.h:304:22: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/GBase.h:309:22: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/GBase.h:351:25: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/GBase.h:354:24: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/GBase.cpp:208:9: style: Variable 'cdir' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/GBase.cpp:261:38: style: Parameter 'mode' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/GBase.cpp:405:36: style: Parameter 'newvalue' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/GBase.cpp:414:26: style: Parameter 'part' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/GBase.cpp:592:9: style: Variable 'smax' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/GBase.h:299:22: style: Parameter 'd' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/GBase.h:321:24: style: Parameter 'r' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/GBase.h:344:25: style: Parameter 's' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/GBase.cpp:248:17: style: Variable 'mkdir_err' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/GStr.cpp:836:26: warning: Either the condition 'idx<0' is redundant or the array 'data->chars[1]' is accessed at index -1, which is out of bounds. [negativeIndex] tophat-2.1.1/src/GStr.cpp:830:12: note: Assuming that condition 'idx<0' is not redundant tophat-2.1.1/src/GStr.cpp:836:26: note: Negative array index tophat-2.1.1/src/GStr.cpp:697:49: warning: Either the condition 'len<0' is redundant or ::memcpy() argument nr 3 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg] tophat-2.1.1/src/GStr.cpp:690:40: note: Assuming that condition 'len<0' is not redundant tophat-2.1.1/src/GStr.cpp:697:49: note: Invalid argument tophat-2.1.1/src/GStr.cpp:191:13: warning: Member variable 'GStr::fTokenDelimiter' is not assigned a value in 'GStr::operator='. [operatorEqVarError] tophat-2.1.1/src/GStr.cpp:191:13: warning: Member variable 'GStr::fLastTokenStart' is not assigned a value in 'GStr::operator='. [operatorEqVarError] tophat-2.1.1/src/GStr.cpp:191:13: warning: Member variable 'GStr::fTokenizeMode' is not assigned a value in 'GStr::operator='. [operatorEqVarError] tophat-2.1.1/src/GStr.cpp:191:13: warning: Member variable 'GStr::readbuf' is not assigned a value in 'GStr::operator='. [operatorEqVarError] tophat-2.1.1/src/GStr.cpp:191:13: warning: Member variable 'GStr::readbufsize' is not assigned a value in 'GStr::operator='. [operatorEqVarError] tophat-2.1.1/src/GStr.h:76:14: style:inconclusive: Technically the member function 'GStr::to' can be const. [functionConst] tophat-2.1.1/src/GStr.cpp:1328:12: note: Technically the member function 'GStr::to' can be const. tophat-2.1.1/src/GStr.h:76:14: note: Technically the member function 'GStr::to' can be const. tophat-2.1.1/src/GStr.h:78:14: style:inconclusive: Technically the member function 'GStr::from' can be const. [functionConst] tophat-2.1.1/src/GStr.cpp:1334:12: note: Technically the member function 'GStr::from' can be const. tophat-2.1.1/src/GStr.h:78:14: note: Technically the member function 'GStr::from' can be const. tophat-2.1.1/src/GStr.h:96:15: performance:inconclusive: Technically the member function 'GStr::append' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/GStr.cpp:290:13: note: Technically the member function 'GStr::append' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/GStr.h:96:15: note: Technically the member function 'GStr::append' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/GStr.h:109:13: style:inconclusive: Technically the member function 'GStr::count' can be const. [functionConst] tophat-2.1.1/src/GStr.cpp:1340:11: note: Technically the member function 'GStr::count' can be const. tophat-2.1.1/src/GStr.h:109:13: note: Technically the member function 'GStr::count' can be const. tophat-2.1.1/src/GStr.h:112:13: style:inconclusive: Technically the member function 'GStr::asInt' can be const. [functionConst] tophat-2.1.1/src/GStr.cpp:1250:11: note: Technically the member function 'GStr::asInt' can be const. tophat-2.1.1/src/GStr.h:112:13: note: Technically the member function 'GStr::asInt' can be const. tophat-2.1.1/src/GStr.h:113:16: style:inconclusive: Technically the member function 'GStr::asReal' can be const. [functionConst] tophat-2.1.1/src/GStr.cpp:1265:14: note: Technically the member function 'GStr::asReal' can be const. tophat-2.1.1/src/GStr.h:113:16: note: Technically the member function 'GStr::asReal' can be const. tophat-2.1.1/src/GStr.h:115:14: style:inconclusive: Technically the member function 'GStr::asReal' can be const. [functionConst] tophat-2.1.1/src/GStr.cpp:1269:12: note: Technically the member function 'GStr::asReal' can be const. tophat-2.1.1/src/GStr.h:115:14: note: Technically the member function 'GStr::asReal' can be const. tophat-2.1.1/src/GStr.h:117:14: style:inconclusive: Technically the member function 'GStr::asInt' can be const. [functionConst] tophat-2.1.1/src/GStr.cpp:1254:12: note: Technically the member function 'GStr::asInt' can be const. tophat-2.1.1/src/GStr.h:117:14: note: Technically the member function 'GStr::asInt' can be const. tophat-2.1.1/src/GStr.h:33:9: style: Class 'GStr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GStr.h:34:9: style: Class 'GStr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GStr.h:35:9: style: Class 'GStr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GStr.h:36:9: style: Class 'GStr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GStr.cpp:21:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:38:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:55:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:59:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:70:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:171:14: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:172:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:173:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:382:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:391:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:399:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:406:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:773:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:776:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:802:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:966:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:974:17: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1054:19: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1118:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1120:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1132:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1140:11: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1141:29: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1159:13: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1165:10: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1173:11: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1174:29: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1181:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1196:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1200:13: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1202:15: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1218:35: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1221:20: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:1237:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GStr.cpp:706:8: style: The scope of the variable 'c' can be reduced. [variableScope] tophat-2.1.1/src/GStr.cpp:747:16: style: The scope of the variable 'p' can be reduced. [variableScope] tophat-2.1.1/src/GStr.cpp:768:8: style: The scope of the variable 'dest' can be reduced. [variableScope] tophat-2.1.1/src/GStr.cpp:1282:7: style: The scope of the variable 'buf' can be reduced. [variableScope] tophat-2.1.1/src/GStr.cpp:1306:7: style: The scope of the variable 'buf' can be reduced. [variableScope] tophat-2.1.1/src/GStr.cpp:49:29: style:inconclusive: Function 'replace_data' argument 1 names different: declaration 'length' definition 'len'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:183:31: note: Function 'replace_data' argument 1 names different: declaration 'length' definition 'len'. tophat-2.1.1/src/GStr.cpp:49:29: note: Function 'replace_data' argument 1 names different: declaration 'length' definition 'len'. tophat-2.1.1/src/GStr.cpp:176:28: style:inconclusive: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:39:30: note: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:176:28: note: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:184:27: style:inconclusive: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:40:29: note: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:184:27: note: Function 'operator[]' argument 1 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:678:23: style:inconclusive: Function 'substr' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:75:25: note: Function 'substr' argument 1 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:678:23: note: Function 'substr' argument 1 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:720:29: style:inconclusive: Function 'tr' argument 1 names different: declaration 'from' definition 'rfrom'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:107:30: note: Function 'tr' argument 1 names different: declaration 'from' definition 'rfrom'. tophat-2.1.1/src/GStr.cpp:720:29: note: Function 'tr' argument 1 names different: declaration 'from' definition 'rfrom'. tophat-2.1.1/src/GStr.cpp:720:48: style:inconclusive: Function 'tr' argument 2 names different: declaration 'to' definition 'rto'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:107:48: note: Function 'tr' argument 2 names different: declaration 'to' definition 'rto'. tophat-2.1.1/src/GStr.cpp:720:48: note: Function 'tr' argument 2 names different: declaration 'to' definition 'rto'. tophat-2.1.1/src/GStr.cpp:761:34: style:inconclusive: Function 'replace' argument 1 names different: declaration 'from' definition 'rfrom'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:91:35: note: Function 'replace' argument 1 names different: declaration 'from' definition 'rfrom'. tophat-2.1.1/src/GStr.cpp:761:34: note: Function 'replace' argument 1 names different: declaration 'from' definition 'rfrom'. tophat-2.1.1/src/GStr.cpp:761:53: style:inconclusive: Function 'replace' argument 2 names different: declaration 'to' definition 'rto'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:91:53: note: Function 'replace' argument 2 names different: declaration 'to' definition 'rto'. tophat-2.1.1/src/GStr.cpp:761:53: note: Function 'replace' argument 2 names different: declaration 'to' definition 'rto'. tophat-2.1.1/src/GStr.cpp:815:22: style:inconclusive: Function 'cut' argument 1 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:83:23: note: Function 'cut' argument 1 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:815:22: note: Function 'cut' argument 1 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:844:39: style:inconclusive: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:89:40: note: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:844:39: note: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:874:38: style:inconclusive: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:90:40: note: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:874:38: note: Function 'paste' argument 2 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:907:39: style:inconclusive: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:92:41: note: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:907:39: note: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:931:39: style:inconclusive: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GStr.h:93:41: note: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:931:39: note: Function 'insert' argument 2 names different: declaration 'index' definition 'idx'. tophat-2.1.1/src/GStr.cpp:35:6: style: Local variable 'length' shadows outer function [shadowFunction] tophat-2.1.1/src/GStr.h:72:13: note: Shadowed declaration tophat-2.1.1/src/GStr.cpp:35:6: note: Shadow variable tophat-2.1.1/src/GStr.cpp:730:10: style: Variable 's' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/GStr.cpp:1172:10: style: Variable 'token_end' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/GStr.cpp:1138:10: style: Variable 'tlen' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/bam2fastx.cpp:117:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam2fastx.cpp:184:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FQCFAIL [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam2fastx.cpp:323:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam2fastx.cpp:330:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam2fastx.cpp:345:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam2fastx.cpp:370:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/reads.h:42:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/reads.h:169:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREAD1 [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/reads.h:244:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/reads.h:331:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/reads.h:358:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.h:618:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.h:778:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable observation_order [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/align_status.cpp:127:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam2fastx.cpp:424:10: error: Resource leak: fout2 [resourceLeak] tophat-2.1.1/src/bam2fastx.cpp:181:25: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bam2fastx.cpp:240:14: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bam2fastx.cpp:254:14: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bam2fastx.cpp:258:16: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bam2fastx.cpp:264:10: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bam2fastx.cpp:182:7: style: The scope of the variable 'i' can be reduced. [variableScope] tophat-2.1.1/src/bam2fastx.cpp:290:22: style: Parameter 'rd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/bam2fastx.cpp:329:24: style: Parameter 'last' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/bam2fastx.cpp:349:30: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr] tophat-2.1.1/src/bam_merge.h:47:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam_merge.cpp:7:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam_merge.cpp:28:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam_merge.h:22:1: style: Struct 'CBamLine' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/bam_merge.h:66:3: style: Struct 'less_bam' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/bam_merge.h:126:3: style: Class 'BamMerge' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:267:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.h:945:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.h:953:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.h:960:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GTFToFasta.cpp:37:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GTFToFasta.cpp:104:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GTFToFasta.cpp:154:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GTFToFasta.cpp:162:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GTFToFasta.cpp:171:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:343:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fUnique [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:363:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:376:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:382:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:391:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:419:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:431:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:441:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:468:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:608:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:613:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:633:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:432:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:172:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GList.hh:235:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:566:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:578:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:592:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:609:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:616:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:626:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:635:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:646:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:662:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:673:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:684:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:692:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:697:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:711:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:725:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:758:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:767:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:776:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:789:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:803:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:808:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:813:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:822:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:834:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:843:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:855:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:864:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:871:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:884:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:908:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:207:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:216:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:226:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:238:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:258:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:282:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:315:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:327:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:333:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:343:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:388:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:398:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:411:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:421:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:434:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:466:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:471:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:480:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:499:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:506:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:517:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:531:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:552:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bam_merge_impl.cpp:36:25: style: Checking if unsigned expression 'bam_fnames.size()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/bam_merge_impl.cpp:96:21: style: Checking if unsigned expression '_lines.size()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/bam_merge_impl.cpp:124:29: style: Checking if unsigned expression 'temp_bam_lines.size()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/bam_merge_impl.cpp:9:11: style: Variable 'name' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.h:844:5: warning: Member variable 'HitFactory::_hit_stream' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/bwt_map.h:894:2: warning: Member variable 'LineHitFactory::_hit_buf' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/bwt_map.h:894:2: warning: Member variable 'LineHitFactory::_line_num' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/bwt_map.h:930:2: warning: Member variable 'SplicedSAMHitFactory::_seg_offset' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/bwt_map.h:930:2: warning: Member variable 'SplicedSAMHitFactory::_size_buf' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/bwt_map.h:1009:2: warning: Member variable 'SplicedBAMHitFactory::_seg_offset' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/bwt_map.h:1009:2: warning: Member variable 'SplicedBAMHitFactory::_size_buf' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/reads.h:62:12: style:inconclusive: Technically the member function 'FLineReader::readcount' can be const. [functionConst] tophat-2.1.1/src/reads.h:63:7: style:inconclusive: Technically the member function 'FLineReader::length' can be const. [functionConst] tophat-2.1.1/src/reads.h:64:8: style:inconclusive: Technically the member function 'FLineReader::isEof' can be const. [functionConst] tophat-2.1.1/src/reads.h:127:7: style:inconclusive: Technically the member function 'Read::lengths_equal' can be const. [functionConst] tophat-2.1.1/src/reads.h:327:16: style:inconclusive: Technically the member function 'ReadStream::get_format' can be const. [functionConst] tophat-2.1.1/src/reads.h:382:10: style:inconclusive: Technically the member function 'ReadStream::isBam' can be const. [functionConst] tophat-2.1.1/src/reads.h:388:17: style:inconclusive: Technically the member function 'ReadStream::filename' can be const. [functionConst] tophat-2.1.1/src/reads.h:275:12: style:inconclusive: Technically the member function 'ReadStream::ReadOrdering::operator()' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:555:11: performance:inconclusive: Technically the member function 'ReadTable::observation_order' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/bwt_map.h:720:12: performance:inconclusive: Technically the member function 'RefSequenceTable::observation_order' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/bwt_map.h:1139:10: style:inconclusive: Technically the member function 'HitStream::eof' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:1140:10: style:inconclusive: Technically the member function 'HitStream::ready' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:1226:7: style:inconclusive: Technically the member function 'HitStream::fromBowtie' can be const. [functionConst] tophat-2.1.1/src/junctions.h:74:8: style:inconclusive: Technically the member function 'skip_count_lt::operator()' can be const. [functionConst] tophat-2.1.1/src/insertions.h:106:8: style:inconclusive: Technically the member function 'insertion_comparison::operator()' can be const. [functionConst] tophat-2.1.1/src/reads.h:316:9: warning: Class 'ReadStream' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] tophat-2.1.1/src/reads.h:316:9: warning: Class 'ReadStream' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] tophat-2.1.1/src/reads.h:69:3: style: Class 'FLineReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/reads.h:80:3: style: Class 'FLineReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/reads.h:224:2: style: Struct 'GetReadProc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/reads.h:291:5: style: Class 'ReadStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:121:10: style:inconclusive: Technically the member function 'GVec::Capacity' can be const. [functionConst] tophat-2.1.1/src/reads.h:295:5: style: Class 'ReadStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:124:10: style:inconclusive: Technically the member function 'GVec::Count' can be const. [functionConst] tophat-2.1.1/src/reads.h:300:5: style: Class 'ReadStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:134:10: style:inconclusive: Technically the member function 'GVec::isEmpty' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:604:2: style: Class 'RefSequenceTable' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:135:10: style:inconclusive: Technically the member function 'GVec::notEmpty' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:898:12: style: The function 'hitfile_rec' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:874:19: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:898:12: note: Function in derived class tophat-2.1.1/src/bwt_map.h:902:10: style: The function 'openStream' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:849:18: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:902:10: note: Function in derived class tophat-2.1.1/src/bwt_map.h:903:10: style: The function 'rewind' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:850:18: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:903:10: note: Function in derived class tophat-2.1.1/src/GVec.hh:184:10: style:inconclusive: Technically the member function 'GPVec::isEmpty' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:904:10: style: The function 'seek' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:851:18: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:904:10: note: Function in derived class tophat-2.1.1/src/GVec.hh:185:10: style:inconclusive: Technically the member function 'GPVec::notEmpty' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:905:10: style: The function 'closeStream' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:852:18: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:905:10: note: Function in derived class tophat-2.1.1/src/GVec.hh:186:9: style:inconclusive: Technically the member function 'GPVec::Capacity' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:906:10: style: The function 'next_record' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:875:17: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:906:10: note: Function in derived class tophat-2.1.1/src/GVec.hh:187:9: style:inconclusive: Technically the member function 'GPVec::Count' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:936:7: style: The function 'get_hit_from_buf' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:876:17: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:936:7: note: Function in derived class tophat-2.1.1/src/GVec.hh:199:9: style:inconclusive: Technically the member function 'GPVec::IndexOf' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:757:38: note: Technically the member function 'GPVec::IndexOf' can be const. tophat-2.1.1/src/GVec.hh:199:9: note: Technically the member function 'GPVec::IndexOf' can be const. tophat-2.1.1/src/bwt_map.h:956:7: style: The function 'get_hit_from_buf' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:876:17: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:956:7: note: Function in derived class tophat-2.1.1/src/bwt_map.h:980:10: style: The function 'openStream' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:849:18: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:980:10: note: Function in derived class tophat-2.1.1/src/bwt_map.h:981:10: style: The function 'rewind' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:850:18: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:981:10: note: Function in derived class tophat-2.1.1/src/bwt_map.h:982:10: style: The function 'seek' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:851:18: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:982:10: note: Function in derived class tophat-2.1.1/src/GList.hh:61:10: style:inconclusive: Technically the member function 'GArray::Sorted' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:983:10: style: The function 'closeStream' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:852:18: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:983:10: note: Function in derived class tophat-2.1.1/src/GList.hh:63:10: style:inconclusive: Technically the member function 'GArray::Unique' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:985:10: style: The function 'next_record' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:875:17: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:985:10: note: Function in derived class tophat-2.1.1/src/bwt_map.h:986:12: style: The function 'hitfile_rec' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:874:19: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:986:12: note: Function in derived class tophat-2.1.1/src/GList.hh:104:10: style:inconclusive: Technically the member function 'GList::Sorted' can be const. [functionConst] tophat-2.1.1/src/bwt_map.h:988:10: style: The function 'get_hit_from_buf' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:876:17: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:988:10: note: Function in derived class tophat-2.1.1/src/bwt_map.h:1018:10: style: The function 'get_hit_from_buf' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/bwt_map.h:988:10: note: Virtual function in base class tophat-2.1.1/src/bwt_map.h:1018:10: note: Function in derived class tophat-2.1.1/src/GList.hh:127:9: style:inconclusive: Technically the member function 'GList::Unique' can be const. [functionConst] tophat-2.1.1/src/GFaSeqGet.h:127:7: style:inconclusive: Technically the member function 'GFaSeqGet::getsublen' can be const. [functionConst] tophat-2.1.1/src/GFaSeqGet.h:128:7: style:inconclusive: Technically the member function 'GFaSeqGet::getseqlen' can be const. [functionConst] tophat-2.1.1/src/GFaSeqGet.h:129:9: style:inconclusive: Technically the member function 'GFaSeqGet::getseqofs' can be const. [functionConst] tophat-2.1.1/src/GFaSeqGet.h:130:7: style:inconclusive: Technically the member function 'GFaSeqGet::getLineLen' can be const. [functionConst] tophat-2.1.1/src/GFaSeqGet.h:131:7: style:inconclusive: Technically the member function 'GFaSeqGet::getLineBLen' can be const. [functionConst] tophat-2.1.1/src/GFaSeqGet.cpp:37:3: warning: Class 'GFaSeqGet' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] tophat-2.1.1/src/GFaSeqGet.cpp:37:3: warning: Class 'GFaSeqGet' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] tophat-2.1.1/src/GList.hh:224:39: warning: The class 'GArray' defines member function with name 'Add' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:386:37: note: Parent function 'GVec::Add' tophat-2.1.1/src/GList.hh:224:39: note: Derived function 'GArray::Add' tophat-2.1.1/src/GList.hh:51:9: warning: The class 'GArray' defines member function with name 'Add' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:88:9: note: Parent function 'GVec::Add' tophat-2.1.1/src/GList.hh:51:9: note: Derived function 'GArray::Add' tophat-2.1.1/src/GList.hh:53:9: warning: The class 'GArray' defines member function with name 'cAdd' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:89:9: note: Parent function 'GVec::cAdd' tophat-2.1.1/src/GList.hh:53:9: note: Derived function 'GArray::cAdd' tophat-2.1.1/src/GList.hh:54:9: warning: The class 'GArray' defines member function with name 'cPush' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:94:9: note: Parent function 'GVec::cPush' tophat-2.1.1/src/GList.hh:54:9: note: Derived function 'GArray::cPush' tophat-2.1.1/src/GList.hh:55:9: warning: The class 'GArray' defines member function with name 'Push' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:93:9: note: Parent function 'GVec::Push' tophat-2.1.1/src/GList.hh:55:9: note: Derived function 'GArray::Push' tophat-2.1.1/src/GList.hh:333:40: warning: The class 'GArray' defines member function with name 'Sort' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:556:38: note: Parent function 'GVec::Sort' tophat-2.1.1/src/GList.hh:333:40: note: Derived function 'GArray::Sort' tophat-2.1.1/src/GList.hh:326:40: warning: The class 'GArray' defines member function with name 'Replace' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:465:38: note: Parent function 'GVec::Replace' tophat-2.1.1/src/GList.hh:326:40: note: Derived function 'GArray::Replace' tophat-2.1.1/src/GList.hh:309:40: warning: The class 'GArray' defines member function with name 'Insert' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:430:38: note: Parent function 'GVec::Insert' tophat-2.1.1/src/GList.hh:309:40: note: Derived function 'GArray::Insert' tophat-2.1.1/src/GList.hh:73:10: warning: The class 'GArray' defines member function with name 'Insert' also defined in its parent class 'GVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:81:10: note: Parent function 'GVec::Insert' tophat-2.1.1/src/GList.hh:73:10: note: Derived function 'GArray::Insert' tophat-2.1.1/src/GList.hh:465:38: warning: The class 'GList' defines member function with name 'Add' also defined in its parent class 'GPVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:764:38: note: Parent function 'GPVec::Add' tophat-2.1.1/src/GList.hh:465:38: note: Derived function 'GList::Add' tophat-2.1.1/src/GList.hh:632:39: warning: The class 'GList' defines member function with name 'Sort' also defined in its parent class 'GPVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:913:39: note: Parent function 'GPVec::Sort' tophat-2.1.1/src/GList.hh:632:39: note: Derived function 'GList::Sort' tophat-2.1.1/src/GList.hh:606:39: warning: The class 'GList' defines member function with name 'Insert' also defined in its parent class 'GPVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:774:39: note: Parent function 'GPVec::Insert' tophat-2.1.1/src/GList.hh:606:39: note: Derived function 'GList::Insert' tophat-2.1.1/src/GList.hh:612:39: warning: The class 'GList' defines member function with name 'Move' also defined in its parent class 'GPVec'. [duplInheritedMember] tophat-2.1.1/src/GVec.hh:787:39: note: Parent function 'GPVec::Move' tophat-2.1.1/src/GList.hh:612:39: note: Derived function 'GList::Move' tophat-2.1.1/src/GVec.hh:75:5: style: Class 'GVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:159:5: style: Class 'GPVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:160:5: style: Class 'GPVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:162:5: style: Class 'GPVec' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:32:5: style: Class 'GArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:33:5: style: Class 'GArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:95:5: style: Class 'GList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:98:5: style: Class 'GList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GFaSeqGet.h:68:3: style: Class 'GFaSeqGet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GFaSeqGet.h:76:3: style: Class 'GFaSeqGet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:60:20: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:61:20: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:243:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:262:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:289:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:297:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:317:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:357:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:366:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:572:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:584:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:598:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:651:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:654:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:678:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:737:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:742:4: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:750:4: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:759:16: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:856:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GList.hh:26:13: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GList.hh:27:20: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GList.hh:84:13: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GList.hh:85:20: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GList.hh:351:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GList.hh:491:26: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GList.hh:517:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.h:32:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.h:80:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:7:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:11:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:16:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:17:10: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:18:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:238:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:240:10: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:271:22: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:286:22: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GFaSeqGet.cpp:306:22: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GVec.hh:570:8: style: Variable 'fCount' is reassigned a value before the old one has been used. [redundantAssignment] tophat-2.1.1/src/GVec.hh:566:8: note: fCount is assigned tophat-2.1.1/src/GVec.hh:570:8: note: fCount is overwritten tophat-2.1.1/src/GFaSeqGet.cpp:167:13: style: Redundant initialization for 'newstart'. The initialized value is overwritten before it is read. [redundantInitialization] tophat-2.1.1/src/GFaSeqGet.cpp:160:16: note: newstart is initialized tophat-2.1.1/src/GFaSeqGet.cpp:167:13: note: newstart is overwritten tophat-2.1.1/src/GFaSeqGet.cpp:196:10: style: Variable 'qlen' is reassigned a value before the old one has been used. [redundantAssignment] tophat-2.1.1/src/GFaSeqGet.cpp:173:9: note: qlen is assigned tophat-2.1.1/src/GFaSeqGet.cpp:196:10: note: qlen is overwritten tophat-2.1.1/src/GVec.hh:527:9: style: The scope of the variable 'j' can be reduced. [variableScope] tophat-2.1.1/src/GVec.hh:878:9: style: The scope of the variable 'J' can be reduced. [variableScope] tophat-2.1.1/src/GVec.hh:879:7: style: The scope of the variable 'P' can be reduced. [variableScope] tophat-2.1.1/src/GList.hh:279:8: style: The scope of the variable 'c' can be reduced. [variableScope] tophat-2.1.1/src/GList.hh:557:14: style: The scope of the variable 'c' can be reduced. [variableScope] tophat-2.1.1/src/GVec.hh:526:48: style:inconclusive: Function 'qSort' argument 1 names different: declaration 'L' definition 'l'. [funcArgNamesDifferent] tophat-2.1.1/src/GVec.hh:73:20: note: Function 'qSort' argument 1 names different: declaration 'L' definition 'l'. tophat-2.1.1/src/GVec.hh:526:48: note: Function 'qSort' argument 1 names different: declaration 'L' definition 'l'. tophat-2.1.1/src/GVec.hh:526:55: style:inconclusive: Function 'qSort' argument 2 names different: declaration 'R' definition 'r'. [funcArgNamesDifferent] tophat-2.1.1/src/GVec.hh:73:27: note: Function 'qSort' argument 2 names different: declaration 'R' definition 'r'. tophat-2.1.1/src/GVec.hh:526:55: note: Function 'qSort' argument 2 names different: declaration 'R' definition 'r'. tophat-2.1.1/src/GVec.hh:696:47: style:inconclusive: Function 'Get' argument 1 names different: declaration 'i' definition 'idx'. [funcArgNamesDifferent] tophat-2.1.1/src/GVec.hh:164:18: note: Function 'Get' argument 1 names different: declaration 'i' definition 'idx'. tophat-2.1.1/src/GVec.hh:696:47: note: Function 'Get' argument 1 names different: declaration 'i' definition 'idx'. tophat-2.1.1/src/GList.hh:347:52: style:inconclusive: Function 'GList' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent] tophat-2.1.1/src/GList.hh:98:23: note: Function 'GList' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/GList.hh:347:52: note: Function 'GList' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/junctions.h:67:56: style: Return value 'left!=right' is always true [knownConditionTrueFalse] tophat-2.1.1/src/junctions.h:67:39: note: Assuming that condition 'left2' is redundant or the array 'nuc[3]' is accessed at index 3, which is out of bounds. [arrayIndexOutOfBoundsCond] tophat-2.1.1/src/codons.h:32:20: note: Assuming that condition 'idx>2' is not redundant tophat-2.1.1/src/codons.h:34:14: note: Array index out of bounds tophat-2.1.1/src/codons.h:34:14: warning: Either the condition 'idx<0' is redundant or the array 'nuc[3]' is accessed at index -1, which is out of bounds. [negativeIndex] tophat-2.1.1/src/codons.h:32:11: note: Assuming that condition 'idx<0' is not redundant tophat-2.1.1/src/codons.h:34:14: note: Negative array index tophat-2.1.1/src/codons.h:40:14: warning: Either the condition 'idx>2' is redundant or the array 'nuc[3]' is accessed at index 3, which is out of bounds. [arrayIndexOutOfBoundsCond] tophat-2.1.1/src/codons.h:38:20: note: Assuming that condition 'idx>2' is not redundant tophat-2.1.1/src/codons.h:40:14: note: Array index out of bounds tophat-2.1.1/src/codons.h:40:14: warning: Either the condition 'idx<0' is redundant or the array 'nuc[3]' is accessed at index -1, which is out of bounds. [negativeIndex] tophat-2.1.1/src/codons.h:38:11: note: Assuming that condition 'idx<0' is not redundant tophat-2.1.1/src/codons.h:40:14: note: Negative array index tophat-2.1.1/src/codons.h:11:2: style: Struct 'Codon' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/codons.cpp:60:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/codons.cpp:83:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/codons.h:11:14: style: Parameter 'str' can be declared as pointer to const. However it seems that 'Codon' is a callback function, if 'str' is declared with const you might also need to cast function pointer(s). [constParameterCallback] tophat-2.1.1/src/codons.h:9:8: note: You might need to cast the function pointer here tophat-2.1.1/src/codons.h:11:14: note: Parameter 'str' can be declared as pointer to const tophat-2.1.1/src/common.cpp:193:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:215:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:430:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:455:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:492:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:728:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:815:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:831:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:839:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:848:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:941:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:980:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:1060:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CMATCH [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:1096:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_table [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:1148:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:1234:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_rev_table [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/common.cpp:1257:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/coverage.cpp:51:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/coverage.cpp:219:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/coverage.cpp:250:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.cpp:368:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.cpp:993:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.cpp:1162:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_rev_table [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.cpp:1459:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.cpp:1492:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_rev_table [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.cpp:1802:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.cpp:2359:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/coverage.h:49:8: performance:inconclusive: Technically the member function 'Coverage::print_info' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/coverage.cpp:248:16: note: Technically the member function 'Coverage::print_info' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/coverage.h:49:8: note: Technically the member function 'Coverage::print_info' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/coverage.h:52:8: performance:inconclusive: Technically the member function 'Coverage::merge_contig' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/coverage.cpp:127:16: note: Technically the member function 'Coverage::merge_contig' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/coverage.h:52:8: note: Technically the member function 'Coverage::merge_contig' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/coverage.h:53:25: performance:inconclusive: Technically the member function 'Coverage::get_contig' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/coverage.cpp:147:33: note: Technically the member function 'Coverage::get_contig' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/coverage.h:53:25: note: Technically the member function 'Coverage::get_contig' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/coverage.cpp:226:7: portability: %lu in format string (no. 2) requires 'unsigned long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_uint] tophat-2.1.1/src/coverage.cpp:230:3: portability: %lu in format string (no. 1) requires 'unsigned long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_uint] tophat-2.1.1/src/coverage.cpp:250:3: portability: %lu in format string (no. 2) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint] tophat-2.1.1/src/common.cpp:974:13: warning: Member variable 'GBamRecord::tag' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/common.cpp:974:13: warning: Member variable 'GBamRecord::abuf' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/common.h:363:10: style:inconclusive: Technically the member function 'GBamRecord::add_quals' can be const. [functionConst] tophat-2.1.1/src/common.cpp:1100:19: note: Technically the member function 'GBamRecord::add_quals' can be const. tophat-2.1.1/src/common.h:363:10: note: Technically the member function 'GBamRecord::add_quals' can be const. tophat-2.1.1/src/common.cpp:953:19: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:966:13: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:967:10: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1051:21: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1075:78: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1092:21: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1128:16: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1140:19: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1145:19: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1159:19: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1164:19: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1173:15: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1177:15: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1229:14: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1240:18: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1253:27: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1254:26: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/common.cpp:1173:15: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] tophat-2.1.1/src/common.cpp:1177:15: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast] tophat-2.1.1/src/common.cpp:232:5: style:inconclusive: Statements following 'return' will never be executed. [unreachableCode] tophat-2.1.1/src/common.cpp:1037:16: style: The scope of the variable 's' can be reduced. [variableScope] tophat-2.1.1/src/common.cpp:1039:8: style: The scope of the variable 'i' can be reduced. [variableScope] tophat-2.1.1/src/common.cpp:1039:11: style: The scope of the variable 'op' can be reduced. [variableScope] tophat-2.1.1/src/common.cpp:1040:9: style: The scope of the variable 'x' can be reduced. [variableScope] tophat-2.1.1/src/common.cpp:1255:8: style: The scope of the variable 'i' can be reduced. [variableScope] tophat-2.1.1/src/common.cpp:1259:8: style: The scope of the variable 'mate_num' can be reduced. [variableScope] tophat-2.1.1/src/common.cpp:426:34: style:inconclusive: Function 'str_replace' argument 1 names different: declaration 'str' definition 'base_str'. [funcArgNamesDifferent] tophat-2.1.1/src/common.h:176:44: note: Function 'str_replace' argument 1 names different: declaration 'str' definition 'base_str'. tophat-2.1.1/src/common.cpp:426:34: note: Function 'str_replace' argument 1 names different: declaration 'str' definition 'base_str'. tophat-2.1.1/src/common.cpp:451:27: style: Parameter 'str' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/common.cpp:737:51: style: Parameter 'popencmd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/common.cpp:754:52: style: Parameter 'popencmd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/common.cpp:1028:13: style: Variable 'after_cigar' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/common.cpp:1240:10: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/common.cpp:1253:19: style: Variable 'qual' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/common.cpp:1259:16: style: Variable 'mate_num' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/common.cpp:1262:19: style: Variable 'mate_num' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/common.cpp:1264:19: style: Variable 'mate_num' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/GHash.hh:299:22: style: Comparison of a variable having boolean value using relational (<, >, <= or >=) operator. [comparisonOfBoolWithBoolError] tophat-2.1.1/src/fix_map_ordering.cpp:81:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/fix_map_ordering.cpp:130:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FSECONDARY [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/fix_map_ordering.cpp:140:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/fix_map_ordering.cpp:155:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/fix_map_ordering.cpp:209:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/fix_map_ordering.cpp:405:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/fix_map_ordering.cpp:417:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GTFToFasta.cpp:33:5: performance: Variable 'gtf_fname_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] tophat-2.1.1/src/gff.h:210:8: style:inconclusive: Technically the member function 'GffAttr::operator==' can be const. [functionConst] tophat-2.1.1/src/gff.h:213:8: style:inconclusive: Technically the member function 'GffAttr::operator>' can be const. [functionConst] tophat-2.1.1/src/gff.h:216:8: style:inconclusive: Technically the member function 'GffAttr::operator<' can be const. [functionConst] tophat-2.1.1/src/gff.h:474:8: style:inconclusive: Technically the member function 'GffObj::hasErrors' can be const. [functionConst] tophat-2.1.1/src/gff.h:479:8: style:inconclusive: Technically the member function 'GffObj::hasGffID' can be const. [functionConst] tophat-2.1.1/src/gff.h:484:8: style:inconclusive: Technically the member function 'GffObj::createdByExon' can be const. [functionConst] tophat-2.1.1/src/gff.h:489:8: style:inconclusive: Technically the member function 'GffObj::isGene' can be const. [functionConst] tophat-2.1.1/src/gff.h:494:8: style:inconclusive: Technically the member function 'GffObj::isDiscarded' can be const. [functionConst] tophat-2.1.1/src/gff.h:500:8: style:inconclusive: Technically the member function 'GffObj::isUsed' can be const. [functionConst] tophat-2.1.1/src/gff.h:505:8: style:inconclusive: Technically the member function 'GffObj::isTranscript' can be const. [functionConst] tophat-2.1.1/src/gff.h:510:8: style:inconclusive: Technically the member function 'GffObj::promotedChildren' can be const. [functionConst] tophat-2.1.1/src/gff.h:525:8: style:inconclusive: Technically the member function 'GffObj::getLevel' can be const. [functionConst] tophat-2.1.1/src/gff.h:611:16: style:inconclusive: Technically the member function 'GffObj::getSubfName' can be const. [functionConst] tophat-2.1.1/src/gff.h:624:9: style:inconclusive: Technically the member function 'GffObj::hasCDS' can be const. [functionConst] tophat-2.1.1/src/gff.h:626:16: style:inconclusive: Technically the member function 'GffObj::getFeatureName' can be const. [functionConst] tophat-2.1.1/src/gff.h:654:10: performance:inconclusive: Technically the member function 'GffObj::getExonAttr' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/gff.h:668:16: style:inconclusive: Technically the member function 'GffObj::getGSeqName' can be const. [functionConst] tophat-2.1.1/src/gff.h:672:16: style:inconclusive: Technically the member function 'GffObj::getRefName' can be const. [functionConst] tophat-2.1.1/src/gff.h:677:16: style:inconclusive: Technically the member function 'GffObj::getTrackName' can be const. [functionConst] tophat-2.1.1/src/gff.h:779:9: style:inconclusive: Technically the member function 'GffObj::xcoordseg' can be const. [functionConst] tophat-2.1.1/src/gff.h:812:9: style:inconclusive: Technically the member function 'GffObj::unxcoordseg' can be const. [functionConst] tophat-2.1.1/src/gff.h:888:9: style:inconclusive: Technically the member function 'GffObj::empty' can be const. [functionConst] tophat-2.1.1/src/gff.h:919:9: style:inconclusive: Technically the member function 'GSeqStat::operator>' can be const. [functionConst] tophat-2.1.1/src/gff.h:922:9: style:inconclusive: Technically the member function 'GSeqStat::operator<' can be const. [functionConst] tophat-2.1.1/src/gff.h:925:9: style:inconclusive: Technically the member function 'GSeqStat::operator==' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:184:10: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::isEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:185:10: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::notEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:186:9: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::Capacity' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:187:9: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::Count' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:199:9: style:inconclusive: Technically the member function 'GPVec < GSeqStat >::IndexOf' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:757:38: note: Technically the member function 'GPVec < GSeqStat >::IndexOf' can be const. tophat-2.1.1/src/GVec.hh:199:9: note: Technically the member function 'GPVec < GSeqStat >::IndexOf' can be const. tophat-2.1.1/src/gff.h:994:6: warning: Class 'CNonExon' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] tophat-2.1.1/src/gff.h:994:6: warning: Class 'CNonExon' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] tophat-2.1.1/src/gff.h:1071:7: warning: Class 'GffReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] tophat-2.1.1/src/gff.h:1071:7: warning: Class 'GffReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] tophat-2.1.1/src/GTFToFasta.cpp:34:5: warning: Class 'GTFToFasta' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] tophat-2.1.1/src/GTFToFasta.cpp:34:5: warning: Class 'GTFToFasta' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] tophat-2.1.1/src/gff.h:120:5: style: Class 'GffLine' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:178:4: style: Class 'GffAttr' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:230:4: style: Class 'GffNameInfo' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:260:3: style: Class 'GffNameList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:388:3: style: Class 'GffExon' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:565:3: style: Class 'GffObj' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:910:4: style: Class 'GSeqStat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:937:4: style: Class 'GfList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:1045:3: style: Class 'GffReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:1065:3: style: Class 'GffReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GHash.hh:58:3: style: Class 'GHash < GffNameInfo >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GHash.hh:59:3: style: Class 'GHash < GffNameInfo >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GHash.hh:58:3: style: Class 'GHash < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GHash.hh:59:3: style: Class 'GHash < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GHash.hh:58:3: style: Class 'GHash < GPVec < GffObj > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GHash.hh:59:3: style: Class 'GHash < GPVec < GffObj > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GHash.hh:58:3: style: Class 'GHash < CNonExon >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GHash.hh:59:3: style: Class 'GHash < CNonExon >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:95:5: style: Class 'GList < GffExon >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:98:5: style: Class 'GList < GffExon >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:95:5: style: Class 'GList < GSeg >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:98:5: style: Class 'GList < GSeg >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:32:5: style: Class 'GArray < GffCDSeg >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GList.hh:33:5: style: Class 'GArray < GffCDSeg >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:159:5: style: Class 'GPVec < GSeqStat >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:160:5: style: Class 'GPVec < GSeqStat >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:162:5: style: Class 'GPVec < GSeqStat >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.h:114:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:128:13: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:129:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:131:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:140:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:143:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:164:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:165:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:166:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:167:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:168:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:169:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:170:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:184:6: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:188:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:235:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:600:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:601:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:602:8: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:851:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:855:9: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:946:24: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:1054:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:1074:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:1087:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.h:1088:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:144:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:155:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:179:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:193:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:218:22: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:234:17: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:259:22: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:272:15: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:275:17: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:344:31: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:346:26: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:499:29: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:504:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:505:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:556:29: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GHash.hh:560:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/GTFToFasta.cpp:16:12: style: The scope of the variable 'length' can be reduced. [variableScope] tophat-2.1.1/src/GTFToFasta.cpp:148:13: style: The scope of the variable 'p_gffObj' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:168:16: style: The scope of the variable 'i' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:168:20: style: The scope of the variable 'p' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:168:22: style: The scope of the variable 'x' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:168:24: style: The scope of the variable 'h' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:327:16: style: The scope of the variable 'p' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:327:18: style: The scope of the variable 'x' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:327:20: style: The scope of the variable 'h' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:327:22: style: The scope of the variable 'n' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:364:16: style: The scope of the variable 'p' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:364:18: style: The scope of the variable 'x' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:364:20: style: The scope of the variable 'h' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:364:22: style: The scope of the variable 'n' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:387:16: style: The scope of the variable 'p' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:387:18: style: The scope of the variable 'x' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:387:20: style: The scope of the variable 'h' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:387:22: style: The scope of the variable 'n' can be reduced. [variableScope] tophat-2.1.1/src/GHash.hh:201:34: style:inconclusive: Function 'Add' argument 2 names different: declaration 'ptr' definition 'pdata'. [funcArgNamesDifferent] tophat-2.1.1/src/GHash.hh:67:45: note: Function 'Add' argument 2 names different: declaration 'ptr' definition 'pdata'. tophat-2.1.1/src/GHash.hh:201:34: note: Function 'Add' argument 2 names different: declaration 'ptr' definition 'pdata'. tophat-2.1.1/src/GHash.hh:242:34: style:inconclusive: Function 'shkAdd' argument 2 names different: declaration 'ptr' definition 'pdata'. [funcArgNamesDifferent] tophat-2.1.1/src/GHash.hh:70:48: note: Function 'shkAdd' argument 2 names different: declaration 'ptr' definition 'pdata'. tophat-2.1.1/src/GHash.hh:242:34: note: Function 'shkAdd' argument 2 names different: declaration 'ptr' definition 'pdata'. tophat-2.1.1/src/GHash.hh:284:74: style:inconclusive: Function 'Replace' argument 2 names different: declaration 'ptr' definition 'pdata'. [funcArgNamesDifferent] tophat-2.1.1/src/GHash.hh:75:43: note: Function 'Replace' argument 2 names different: declaration 'ptr' definition 'pdata'. tophat-2.1.1/src/GHash.hh:284:74: note: Function 'Replace' argument 2 names different: declaration 'ptr' definition 'pdata'. tophat-2.1.1/src/GList.hh:347:52: style:inconclusive: Function 'GList < GffExon >' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent] tophat-2.1.1/src/GList.hh:98:23: note: Function 'GList < GffExon >' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/GList.hh:347:52: note: Function 'GList < GffExon >' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/GList.hh:347:52: style:inconclusive: Function 'GList < GSeg >' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent] tophat-2.1.1/src/GList.hh:98:23: note: Function 'GList < GSeg >' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/GList.hh:347:52: note: Function 'GList < GSeg >' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/GVec.hh:577:47: style:inconclusive: Function 'GPVec < GSeqStat >' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent] tophat-2.1.1/src/GVec.hh:162:23: note: Function 'GPVec < GSeqStat >' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/GVec.hh:577:47: note: Function 'GPVec < GSeqStat >' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/GTFToFasta.cpp:30:36: performance: Function parameter 'gtf_fname' should be passed by const reference. [passedByValue] tophat-2.1.1/src/GTFToFasta.cpp:30:59: performance: Function parameter 'genome_fname' should be passed by const reference. [passedByValue] tophat-2.1.1/src/GTFToFasta.cpp:61:49: performance: Function parameter 'out_fname' should be passed by const reference. [passedByValue] tophat-2.1.1/src/gff.h:210:28: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:213:27: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:216:27: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:238:33: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:241:32: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:826:28: style: Parameter 'd' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:919:29: style: Parameter 'g' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:922:29: style: Parameter 'g' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:925:30: style: Parameter 'g' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/GTFToFasta.cpp:20:16: style: Variable 'cur_exon' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/GVec.hh:565:47: style: Parameter 'list' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/GVec.hh:589:69: style: Parameter 'list' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gff.h:298:18: style: Variable 'f' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/gff.h:565:16: style: Parameter 'anid' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/gff.h:875:46: style: Parameter 'tlabel' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/deletions.cpp:55:48: style:inconclusive: Function 'deletions_from_alignment' argument 1 names different: declaration 'spliced_alignment' definition 'bh'. [funcArgNamesDifferent] tophat-2.1.1/src/deletions.h:50:48: note: Function 'deletions_from_alignment' argument 1 names different: declaration 'spliced_alignment' definition 'bh'. tophat-2.1.1/src/deletions.cpp:55:48: note: Function 'deletions_from_alignment' argument 1 names different: declaration 'spliced_alignment' definition 'bh'. tophat-2.1.1/src/deletions.cpp:55:65: style:inconclusive: Function 'deletions_from_alignment' argument 2 names different: declaration 'junctions' definition 'deletions'. [funcArgNamesDifferent] tophat-2.1.1/src/deletions.h:50:80: note: Function 'deletions_from_alignment' argument 2 names different: declaration 'junctions' definition 'deletions'. tophat-2.1.1/src/deletions.cpp:55:65: note: Function 'deletions_from_alignment' argument 2 names different: declaration 'junctions' definition 'deletions'. tophat-2.1.1/src/deletions.cpp:36:91: style: Parameter 'ref_sequences' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/fix_map_ordering.cpp:68:7: style:inconclusive: Technically the member function 'MapOrdering::operator()' can be const. [functionConst] tophat-2.1.1/src/fix_map_ordering.cpp:92:8: style:inconclusive: Technically the member function 'BamMapOrdering::operator()' can be const. [functionConst] tophat-2.1.1/src/fix_map_ordering.cpp:36:5: warning: Struct 'TabSplitLine' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] tophat-2.1.1/src/fix_map_ordering.cpp:36:5: warning: Struct 'TabSplitLine' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] tophat-2.1.1/src/fix_map_ordering.cpp:30:3: style: Struct 'TabSplitLine' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/fix_map_ordering.cpp:368:41: warning: Either the condition '(f_in=std::fopen(map_file_name.c_str(),"r"))==NULL' is redundant or there is possible null pointer dereference: map_file. [nullPointerRedundantCheck] tophat-2.1.1/src/fix_map_ordering.cpp:445:52: note: Assuming that condition '(f_in=std::fopen(map_file_name.c_str(),"r"))==NULL' is not redundant tophat-2.1.1/src/fix_map_ordering.cpp:449:27: note: Calling function 'driver_headerless', 1st argument 'f_in' value is 0 tophat-2.1.1/src/fix_map_ordering.cpp:368:41: note: Null pointer dereference tophat-2.1.1/src/fix_map_ordering.cpp:40:7: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/fix_map_ordering.cpp:47:16: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/fix_map_ordering.cpp:233:22: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/fix_map_ordering.cpp:314:39: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/fix_map_ordering.cpp:340:44: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/fix_map_ordering.cpp:68:49: style: Parameter 'lhs' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/fix_map_ordering.cpp:68:85: style: Parameter 'rhs' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/fix_map_ordering.cpp:134:33: style: Parameter 'l' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/fix_map_ordering.cpp:148:33: style: Parameter 'l' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/fix_map_ordering.cpp:191:9: style: Variable 'qname' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/fix_map_ordering.cpp:240:15: style: Variable 'source_seq' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/fix_map_ordering.cpp:291:15: style: Variable 'mq' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/fragments.h:22:5: performance: Variable 'status' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] tophat-2.1.1/src/fragments.h:33:5: performance: Variable 'status' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] tophat-2.1.1/src/fragments.h:54:8: style:inconclusive: Technically the member function 'FragmentAlignmentGrade::operator<' can be const. [functionConst] tophat-2.1.1/src/fragments.cpp:20:17: style:inconclusive: Function 'best_fragment_mappings' argument 3 names different: declaration 'hits1_in_ref' definition 'hits_in_ref'. [funcArgNamesDifferent] tophat-2.1.1/src/fragments.h:67:17: note: Function 'best_fragment_mappings' argument 3 names different: declaration 'hits1_in_ref' definition 'hits_in_ref'. tophat-2.1.1/src/fragments.cpp:20:17: note: Function 'best_fragment_mappings' argument 3 names different: declaration 'hits1_in_ref' definition 'hits_in_ref'. tophat-2.1.1/src/fragments.cpp:20:17: style: Parameter 'hits_in_ref' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/fragments.cpp:21:19: style: Parameter 'it' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/fragments.cpp:22:36: style: Parameter 'best_status_for_fragments' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gdna.cpp:56:18: style: The scope of the variable 'c' can be reduced. [variableScope] tophat-2.1.1/src/fusions.cpp:428:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ldist [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/fusions.cpp:504:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gtf_juncs.cpp:31:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gtf_juncs.cpp:84:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gtf_juncs.cpp:101:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.cpp:126:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dest [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.cpp:146:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable skipLine [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.cpp:1269:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.cpp:1880:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.cpp:2069:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/bwt_map.h:1003:10: performance:inconclusive: Technically the member function 'BAMHitFactory::inspect_header' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/bwt_map.cpp:1454:21: note: Technically the member function 'BAMHitFactory::inspect_header' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/bwt_map.h:1003:10: note: Technically the member function 'BAMHitFactory::inspect_header' can be static (but you may consider moving to unnamed namespace). tophat-2.1.1/src/bwt_map.cpp:1802:2: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/bwt_map.cpp:1951:7: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/bwt_map.cpp:1993:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/bwt_map.cpp:2106:3: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/bwt_map.cpp:2209:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/bwt_map.cpp:2239:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/bwt_map.cpp:2269:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/bwt_map.cpp:2299:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/bwt_map.cpp:181:10: warning: Either the condition 'sam_file==NULL' is redundant or there is possible null pointer dereference: sam_file. [nullPointerRedundantCheck] tophat-2.1.1/src/bwt_map.cpp:179:19: note: Assuming that condition 'sam_file==NULL' is not redundant tophat-2.1.1/src/bwt_map.cpp:181:10: note: Null pointer dereference tophat-2.1.1/src/bwt_map.cpp:126:39: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:140:14: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:160:12: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:177:26: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:208:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:211:18: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:233:16: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:238:25: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:239:30: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:252:18: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:259:28: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:264:10: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:483:29: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:579:25: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:580:33: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:581:30: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:582:36: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:583:39: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:584:30: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:585:40: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:586:40: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:587:50: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:589:35: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:592:36: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:903:25: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:904:33: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:905:30: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:906:36: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:907:39: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:908:30: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:909:40: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:910:40: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:911:50: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:915:35: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:919:36: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:1107:28: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:1159:18: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:1167:17: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:1456:29: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:1477:28: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:1489:18: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:1497:17: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/bwt_map.cpp:483:17: style: Redundant initialization for 'tag_buf'. The initialized value is overwritten before it is read. [redundantInitialization] tophat-2.1.1/src/bwt_map.cpp:480:23: note: tag_buf is initialized tophat-2.1.1/src/bwt_map.cpp:483:17: note: tag_buf is overwritten tophat-2.1.1/src/bwt_map.cpp:700:7: style: The scope of the variable 'ref_ofs' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:701:7: style: The scope of the variable 'read_ofs' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:702:8: style: The scope of the variable 'xfound' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:705:9: style: The scope of the variable 'prev_opcode' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:706:9: style: The scope of the variable 'prev_oplen' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:939:6: style: The scope of the variable 'sam_flag' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:1118:7: style: The scope of the variable 'num_hits' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:1176:17: style: The scope of the variable 'num_splice_anchor_mismatches' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:1408:10: style: The scope of the variable 'mrnm' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:1486:8: style: The scope of the variable 'spliced_alignment' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:1561:10: style: The scope of the variable 'mrnm' can be reduced. [variableScope] tophat-2.1.1/src/bwt_map.cpp:674:15: style: Checking if unsigned expression 'op.length' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/bwt_map.cpp:562:50: style:inconclusive: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. [funcArgNamesDifferent] tophat-2.1.1/src/bwt_map.h:956:36: note: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. tophat-2.1.1/src/bwt_map.cpp:562:50: note: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. tophat-2.1.1/src/bwt_map.cpp:885:57: style:inconclusive: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. [funcArgNamesDifferent] tophat-2.1.1/src/bwt_map.h:936:36: note: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. tophat-2.1.1/src/bwt_map.cpp:885:57: note: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. tophat-2.1.1/src/bwt_map.cpp:1101:50: style:inconclusive: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. [funcArgNamesDifferent] tophat-2.1.1/src/bwt_map.h:988:39: note: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. tophat-2.1.1/src/bwt_map.cpp:1101:50: note: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. tophat-2.1.1/src/bwt_map.cpp:1469:57: style:inconclusive: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. [funcArgNamesDifferent] tophat-2.1.1/src/bwt_map.h:1018:39: note: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. tophat-2.1.1/src/bwt_map.cpp:1469:57: note: Function 'get_hit_from_buf' argument 1 names different: declaration 'bwt_buf' definition 'orig_bwt_buf'. tophat-2.1.1/src/bwt_map.cpp:1899:10: style: Local variable 'quals' shadows outer variable [shadowVariable] tophat-2.1.1/src/common.h:122:13: note: Shadowed declaration tophat-2.1.1/src/bwt_map.cpp:1899:10: note: Shadow variable tophat-2.1.1/src/bwt_map.cpp:2372:15: style: Local variable 'cigar' shadows outer function [shadowFunction] tophat-2.1.1/src/bwt_map.h:494:26: note: Shadowed declaration tophat-2.1.1/src/bwt_map.cpp:2372:15: note: Shadow variable tophat-2.1.1/src/bwt_map.cpp:681:88: performance: Function parameter 'mismatches' should be passed by const reference. [passedByValue] tophat-2.1.1/src/bwt_map.cpp:410:58: style: Parameter 'cigar' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/bwt_map.cpp:477:51: style: Parameter 'cigar' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/bwt_map.cpp:1454:47: style: Parameter 'hs' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/bwt_map.cpp:329:29: style: Parameter 'name' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/bwt_map.cpp:338:9: style: Variable 'tag_buf' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:580:8: style: Variable 'sam_flag_str' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:582:8: style: Variable 'text_offset_str' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:584:8: style: Variable 'cigar_str' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:904:8: style: Variable 'sam_flag_str' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:906:8: style: Variable 'text_offset_str' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:908:8: style: Variable 'cigar_str' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:1132:13: style: Variable 'tag_buf' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:1167:11: style: Variable 'bq' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:1456:19: style: Variable 'header' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:1497:11: style: Variable 'bq' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/bwt_map.cpp:1586:3: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam] tophat-2.1.1/src/bwt_map.cpp:2013:2: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm] tophat-2.1.1/src/bwt_map.cpp:1411:12: style: Variable 'mrnm' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/bwt_map.cpp:1418:19: style: Variable 'text_mate_pos' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/bwt_map.cpp:1564:12: style: Variable 'mrnm' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/bwt_map.cpp:1571:19: style: Variable 'text_mate_pos' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/inserts.h:35:1: warning: Member variable 'InsertAlignmentGrade::num_alignments' is not initialized in the constructor. [uninitMemberVar] tophat-2.1.1/src/inserts.h:226:7: style:inconclusive: Technically the member function 'InsertAlignmentGrade::align_score' can be const. [functionConst] tophat-2.1.1/src/inserts.h:49:1: style: Struct 'InsertAlignmentGrade' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/insertions.cpp:87:95: style: Parameter 'ref_sequences' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/gtf_juncs.cpp:85:9: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gtf_juncs.cpp:85:9: portability: %d in format string (no. 3) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gtf_juncs.cpp:82:16: style: Variable 'ex' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/gtf_juncs.cpp:83:16: style: Variable 'prex' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/inserts.cpp:182:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left_alignment [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/juncs_db.cpp:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/juncs_db.cpp:100:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/juncs_db.cpp:144:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/juncs_db.cpp:222:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/juncs_db.cpp:241:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/juncs_db.cpp:285:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/juncs_db.cpp:334:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/juncs_db.cpp:529:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/inserts.h:216:8: style:inconclusive: Technically the member function 'InsertAlignmentGrade::operator<' can be const. [functionConst] tophat-2.1.1/src/inserts.cpp:22:28: note: Technically the member function 'InsertAlignmentGrade::operator<' can be const. tophat-2.1.1/src/inserts.h:216:8: note: Technically the member function 'InsertAlignmentGrade::operator<' can be const. tophat-2.1.1/src/inserts.cpp:81:22: style: Expression is always false because 'else if' condition matches previous condition at line 35. [multiCondition] tophat-2.1.1/src/inserts.cpp:83:22: style: Return value 'num_mapped::Capacity' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:124:10: style:inconclusive: Technically the member function 'GVec < int >::Count' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:134:10: style:inconclusive: Technically the member function 'GVec < int >::isEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:135:10: style:inconclusive: Technically the member function 'GVec < int >::notEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:121:10: style:inconclusive: Technically the member function 'GVec < GPVec < GffObj > * >::Capacity' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:124:10: style:inconclusive: Technically the member function 'GVec < GPVec < GffObj > * >::Count' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:134:10: style:inconclusive: Technically the member function 'GVec < GPVec < GffObj > * >::isEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:135:10: style:inconclusive: Technically the member function 'GVec < GPVec < GffObj > * >::notEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:75:5: style: Class 'GVec < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:75:5: style: Class 'GVec < GPVec < GffObj > * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/gff.cpp:1304:16: style: Condition 'mergeCloseExons' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:1303:7: note: Assuming that condition 'mergeCloseExons' is not redundant tophat-2.1.1/src/gff.cpp:1304:16: note: Condition 'mergeCloseExons' is always true tophat-2.1.1/src/gff.cpp:1593:41: style: Condition 'seqstart<=sgend' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:1592:38: note: Assuming that condition 'seqstart>sgend' is not redundant tophat-2.1.1/src/gff.cpp:1593:41: note: Condition 'seqstart<=sgend' is always true tophat-2.1.1/src/gff.cpp:1615:40: style: Condition 'seqstart<=sgend' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:1614:37: note: Assuming that condition 'seqstart>sgend' is not redundant tophat-2.1.1/src/gff.cpp:1615:40: note: Condition 'seqstart<=sgend' is always true tophat-2.1.1/src/gff.cpp:1743:41: style: Condition 'seqstart<=sgend' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:1742:38: note: Assuming that condition 'seqstart>sgend' is not redundant tophat-2.1.1/src/gff.cpp:1743:41: note: Condition 'seqstart<=sgend' is always true tophat-2.1.1/src/gff.cpp:1773:40: style: Condition 'seqstart<=sgend' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:1772:37: note: Assuming that condition 'seqstart>sgend' is not redundant tophat-2.1.1/src/gff.cpp:1773:40: note: Condition 'seqstart<=sgend' is always true tophat-2.1.1/src/gff.cpp:1838:41: style: Condition 'seqstart<=sgend' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:1837:38: note: Assuming that condition 'seqstart>sgend' is not redundant tophat-2.1.1/src/gff.cpp:1838:41: note: Condition 'seqstart<=sgend' is always true tophat-2.1.1/src/gff.cpp:1859:40: style: Condition 'seqstart<=sgend' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:1858:37: note: Assuming that condition 'seqstart>sgend' is not redundant tophat-2.1.1/src/gff.cpp:1859:40: note: Condition 'seqstart<=sgend' is always true tophat-2.1.1/src/gff.cpp:2107:40: style: Condition 'CDstart<=sgend' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:2106:37: note: Assuming that condition 'CDstart>sgend' is not redundant tophat-2.1.1/src/gff.cpp:2107:40: note: Condition 'CDstart<=sgend' is always true tophat-2.1.1/src/gff.cpp:2125:39: style: Condition 'CDstart<=sgend' is always true [knownConditionTrueFalse] tophat-2.1.1/src/gff.cpp:2124:36: note: Assuming that condition 'CDstart>sgend' is not redundant tophat-2.1.1/src/gff.cpp:2125:39: note: Condition 'CDstart<=sgend' is always true tophat-2.1.1/src/gff.cpp:1881:2: portability: %d in format string (no. 3) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:1881:2: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:1928:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:1928:5: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:1947:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:1947:5: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:2020:4: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:2020:4: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:2023:45: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:2023:45: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] tophat-2.1.1/src/gff.cpp:776:7: warning: Either the condition 'gfrd==NULL' is redundant or there is possible null pointer dereference: gfrd. [nullPointerRedundantCheck] tophat-2.1.1/src/gff.cpp:773:11: note: Assuming that condition 'gfrd==NULL' is not redundant tophat-2.1.1/src/gff.cpp:776:7: note: Null pointer dereference tophat-2.1.1/src/gff.cpp:1295:6: warning: Either the condition 'gfr!=NULL' is redundant or there is possible null pointer dereference: gfr. [nullPointerRedundantCheck] tophat-2.1.1/src/gff.cpp:1311:13: note: Assuming that condition 'gfr!=NULL' is not redundant tophat-2.1.1/src/gff.cpp:1295:6: note: Null pointer dereference tophat-2.1.1/src/gff.cpp:46:15: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:47:15: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:142:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:144:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:244:4: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:297:4: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:380:4: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:900:2: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:1063:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:1073:4: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:1245:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:1287:22: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:1662:5: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:1721:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:1814:3: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:2000:10: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/gff.cpp:39:21: style: The scope of the variable 'extbl' can be reduced. [variableScope] tophat-2.1.1/src/gff.cpp:299:8: style: The scope of the variable 'i' can be reduced. [variableScope] tophat-2.1.1/src/gff.cpp:1997:7: style: The scope of the variable 'dbuf' can be reduced. [variableScope] tophat-2.1.1/src/GVec.hh:334:7: style: The scope of the variable 'c' can be reduced. [variableScope] tophat-2.1.1/src/map2gtf.cpp:11:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:16:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:50:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:72:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:110:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:173:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:264:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:378:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:404:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/map2gtf.cpp:438:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/gff.cpp:62:40: style:inconclusive: Function 'extractAttr' argument 1 names different: declaration 'pre' definition 'attr'. [funcArgNamesDifferent] tophat-2.1.1/src/gff.h:119:35: note: Function 'extractAttr' argument 1 names different: declaration 'pre' definition 'attr'. tophat-2.1.1/src/gff.cpp:62:40: note: Function 'extractAttr' argument 1 names different: declaration 'pre' definition 'attr'. tophat-2.1.1/src/gff.cpp:660:29: style:inconclusive: Function 'expandExon' argument 1 names different: declaration 'xovl' definition 'oi'. [funcArgNamesDifferent] tophat-2.1.1/src/gff.h:436:23: note: Function 'expandExon' argument 1 names different: declaration 'xovl' definition 'oi'. tophat-2.1.1/src/gff.cpp:660:29: note: Function 'expandExon' argument 1 names different: declaration 'xovl' definition 'oi'. tophat-2.1.1/src/gff.cpp:749:56: style:inconclusive: Function 'GffObj' argument 3 names different: declaration 'keepAttrs' definition 'keepAttr'. [funcArgNamesDifferent] tophat-2.1.1/src/gff.h:554:50: note: Function 'GffObj' argument 3 names different: declaration 'keepAttrs' definition 'keepAttr'. tophat-2.1.1/src/gff.cpp:749:56: note: Function 'GffObj' argument 3 names different: declaration 'keepAttrs' definition 'keepAttr'. tophat-2.1.1/src/gff.cpp:977:41: style:inconclusive: Function 'updateParent' argument 1 names different: declaration 'newgfh' definition 'newgfo'. [funcArgNamesDifferent] tophat-2.1.1/src/gff.h:1042:32: note: Function 'updateParent' argument 1 names different: declaration 'newgfh' definition 'newgfo'. tophat-2.1.1/src/gff.cpp:977:41: note: Function 'updateParent' argument 1 names different: declaration 'newgfh' definition 'newgfo'. tophat-2.1.1/src/gff.cpp:1570:36: style:inconclusive: Function 'mRNA_CDS_coords' argument 1 names different: declaration 'cds_start' definition 'cds_mstart'. [funcArgNamesDifferent] tophat-2.1.1/src/gff.h:882:31: note: Function 'mRNA_CDS_coords' argument 1 names different: declaration 'cds_start' definition 'cds_mstart'. tophat-2.1.1/src/gff.cpp:1570:36: note: Function 'mRNA_CDS_coords' argument 1 names different: declaration 'cds_start' definition 'cds_mstart'. tophat-2.1.1/src/gff.cpp:1570:54: style:inconclusive: Function 'mRNA_CDS_coords' argument 2 names different: declaration 'cds_end' definition 'cds_mend'. [funcArgNamesDifferent] tophat-2.1.1/src/gff.h:882:48: note: Function 'mRNA_CDS_coords' argument 2 names different: declaration 'cds_end' definition 'cds_mend'. tophat-2.1.1/src/gff.cpp:1570:54: note: Function 'mRNA_CDS_coords' argument 2 names different: declaration 'cds_end' definition 'cds_mend'. tophat-2.1.1/src/gff.cpp:299:8: style: Local variable 'i' shadows outer variable [shadowVariable] tophat-2.1.1/src/gff.cpp:148:6: note: Shadowed declaration tophat-2.1.1/src/gff.cpp:299:8: note: Shadow variable tophat-2.1.1/src/gff.cpp:453:32: style: Parameter 'reader' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/gff.cpp:729:34: style: Parameter 'p' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/gff.cpp:867:11: style: Variable 'l' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/gff.cpp:1053:45: style: Parameter 'gffline' can be declared as pointer to const [constParameterPointer] tophat-2.1.1/src/gff.cpp:1077:58: style: Parameter 'subp_name' can be declared as pointer to const [constParameterReference] tophat-2.1.1/src/gff.cpp:1363:10: style: Variable 'attr_name' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/gff.cpp:1364:10: style: Variable 'attr_val' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/gff.cpp:1367:11: style: Variable 'ov' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/gff.cpp:1449:8: style: Variable 'prod' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/gff.cpp:1395:12: style: Variable 'pch' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/long_spanning_reads.cpp:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/long_spanning_reads.cpp:76:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/long_spanning_reads.cpp:434:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/long_spanning_reads.cpp:875:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/long_spanning_reads.cpp:2295:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/long_spanning_reads.cpp:2885:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/long_spanning_reads.cpp:3153:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/qual.h:31:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/qual.h:92:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/qual.h:149:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/prep_reads.cpp:128:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/prep_reads.cpp:198:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/prep_reads.cpp:380:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/prep_reads.cpp:600:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/prep_reads.cpp:612:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/prep_reads.cpp:622:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/GVec.hh:184:10: style:inconclusive: Technically the member function 'GPVec < GffTranscript >::isEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:185:10: style:inconclusive: Technically the member function 'GPVec < GffTranscript >::notEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:186:9: style:inconclusive: Technically the member function 'GPVec < GffTranscript >::Capacity' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:187:9: style:inconclusive: Technically the member function 'GPVec < GffTranscript >::Count' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:199:9: style:inconclusive: Technically the member function 'GPVec < GffTranscript >::IndexOf' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:757:38: note: Technically the member function 'GPVec < GffTranscript >::IndexOf' can be const. tophat-2.1.1/src/GVec.hh:199:9: note: Technically the member function 'GPVec < GffTranscript >::IndexOf' can be const. tophat-2.1.1/src/GVec.hh:121:10: style:inconclusive: Technically the member function 'GVec < GSeg >::Capacity' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:124:10: style:inconclusive: Technically the member function 'GVec < GSeg >::Count' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:134:10: style:inconclusive: Technically the member function 'GVec < GSeg >::isEmpty' can be const. [functionConst] tophat-2.1.1/src/GVec.hh:135:10: style:inconclusive: Technically the member function 'GVec < GSeg >::notEmpty' can be const. [functionConst] tophat-2.1.1/src/map2gtf.h:53:2: style: Struct 'GffTranscript' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/map2gtf.h:99:3: style: Class 'TranscriptomeHit' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:159:5: style: Class 'GPVec < GffTranscript >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:160:5: style: Class 'GPVec < GffTranscript >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:162:5: style: Class 'GPVec < GffTranscript >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/GVec.hh:75:5: style: Class 'GVec < GSeg >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/map2gtf.cpp:175:21: warning: Either the condition 'out_sam_header_file==NULL' is redundant or there is possible null pointer dereference: out_sam_header_file. [nullPointerRedundantCheck] tophat-2.1.1/src/map2gtf.cpp:172:27: note: Assuming that condition 'out_sam_header_file==NULL' is not redundant tophat-2.1.1/src/map2gtf.cpp:175:21: note: Null pointer dereference tophat-2.1.1/src/map2gtf.cpp:344:18: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/map2gtf.cpp:346:18: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/map2gtf.cpp:369:40: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/map2gtf.cpp:377:11: style: The scope of the variable 'p_exon' can be reduced. [variableScope] tophat-2.1.1/src/map2gtf.cpp:401:16: style: The scope of the variable 'cur_exon' can be reduced. [variableScope] tophat-2.1.1/src/map2gtf.cpp:405:9: style: The scope of the variable 'trans_offset' can be reduced. [variableScope] tophat-2.1.1/src/map2gtf.cpp:69:67: style:inconclusive: Function 'Map2GTF' argument 2 names different: declaration 'sam_fname' definition 'in_fname'. [funcArgNamesDifferent] tophat-2.1.1/src/map2gtf.h:66:62: note: Function 'Map2GTF' argument 2 names different: declaration 'sam_fname' definition 'in_fname'. tophat-2.1.1/src/map2gtf.cpp:69:67: note: Function 'Map2GTF' argument 2 names different: declaration 'sam_fname' definition 'in_fname'. tophat-2.1.1/src/GVec.hh:577:47: style:inconclusive: Function 'GPVec < GffTranscript >' argument 1 names different: declaration 'list' definition 'plist'. [funcArgNamesDifferent] tophat-2.1.1/src/GVec.hh:162:23: note: Function 'GPVec < GffTranscript >' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/GVec.hh:577:47: note: Function 'GPVec < GffTranscript >' argument 1 names different: declaration 'list' definition 'plist'. tophat-2.1.1/src/map2gtf.cpp:15:58: performance: Function parameter 'add' should be passed by const reference. [passedByValue] tophat-2.1.1/src/map2gtf.cpp:129:13: style: Variable 'name' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/map2gtf.cpp:152:13: style: Variable 'name' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/map2gtf.cpp:171:14: style: Variable 'out_sam_header_file' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/map2gtf.cpp:377:11: style: Variable 'p_exon' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/map2gtf.cpp:189:15: style: Unused variable: hit_group [unusedVariable] tophat-2.1.1/src/map2gtf.cpp:405:22: style: Variable 'trans_offset' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/fusions.cpp:560:11: style: Same expression used in consecutive assignments of 'outer_dist' and 'max_dist'. [duplicateAssignExpression] tophat-2.1.1/src/fusions.cpp:561:11: note: Same expression used in consecutive assignments of 'outer_dist' and 'max_dist'. tophat-2.1.1/src/fusions.cpp:560:11: note: Same expression used in consecutive assignments of 'outer_dist' and 'max_dist'. tophat-2.1.1/src/fusions.cpp:150:22: style: Checking if unsigned expression 'fusion_pos' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/fusions.cpp:378:21: style: Local variable 'i' shadows outer variable [shadowVariable] tophat-2.1.1/src/fusions.cpp:358:15: note: Shadowed declaration tophat-2.1.1/src/fusions.cpp:378:21: note: Shadow variable tophat-2.1.1/src/fusions.cpp:400:21: style: Local variable 'i' shadows outer variable [shadowVariable] tophat-2.1.1/src/fusions.cpp:358:15: note: Shadowed declaration tophat-2.1.1/src/fusions.cpp:400:21: note: Shadow variable tophat-2.1.1/src/fusions.cpp:411:21: style: Local variable 'i' shadows outer variable [shadowVariable] tophat-2.1.1/src/fusions.cpp:358:15: note: Shadowed declaration tophat-2.1.1/src/fusions.cpp:411:21: note: Shadow variable tophat-2.1.1/src/fusions.cpp:418:21: style: Local variable 'i' shadows outer variable [shadowVariable] tophat-2.1.1/src/fusions.cpp:358:15: note: Shadowed declaration tophat-2.1.1/src/fusions.cpp:418:21: note: Shadow variable tophat-2.1.1/src/fusions.cpp:426:21: style: Local variable 'i' shadows outer variable [shadowVariable] tophat-2.1.1/src/fusions.cpp:358:15: note: Shadowed declaration tophat-2.1.1/src/fusions.cpp:426:21: note: Shadow variable tophat-2.1.1/src/fusions.cpp:111:26: style: Parameter 'rt' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/fusions.cpp:347:77: style: Parameter 'ref_sequences' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/reads.cpp:40:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/reads.cpp:116:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/reads.cpp:556:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FQCFAIL [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/sam_juncs.cpp:98:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/sam_juncs.cpp:111:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/sam_juncs.cpp:118:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/sam_juncs.cpp:106:2: portability: %lu in format string (no. 1) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint] tophat-2.1.1/src/assert_helpers.h:14:2: style: Class 'ReleaseAssertException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/segment_juncs.cpp:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:74:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:315:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:739:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:792:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:1258:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:1587:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:1644:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:1687:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:1762:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:2478:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:2562:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:3750:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:4194:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:4515:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:4547:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:4579:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:4726:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:5188:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/segment_juncs.cpp:2091:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/qual.h:100:10: style: Condition 'cc<33' is always false [knownConditionTrueFalse] tophat-2.1.1/src/qual.h:99:40: note: Assignment 'cc=solexaToPhred((int)c-64)+33', assigned value is greater than 32 tophat-2.1.1/src/qual.h:100:10: note: Condition 'cc<33' is always false tophat-2.1.1/src/prep_reads.cpp:470:7: style: Condition 'have_l_reads' is always true [knownConditionTrueFalse] tophat-2.1.1/src/prep_reads.cpp:468:8: note: Assuming that condition 'have_l_reads' is not redundant tophat-2.1.1/src/prep_reads.cpp:470:7: note: Condition 'have_l_reads' is always true tophat-2.1.1/src/prep_reads.cpp:470:23: style: Condition 'have_r_reads' is always true [knownConditionTrueFalse] tophat-2.1.1/src/prep_reads.cpp:468:24: note: Assuming that condition 'have_r_reads' is not redundant tophat-2.1.1/src/prep_reads.cpp:470:23: note: Condition 'have_r_reads' is always true tophat-2.1.1/src/prep_reads.cpp:326:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/prep_reads.cpp:484:4: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/prep_reads.cpp:550:2: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] tophat-2.1.1/src/prep_reads.cpp:553:4: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] tophat-2.1.1/src/prep_reads.cpp:558:2: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] tophat-2.1.1/src/prep_reads.cpp:561:4: warning: %u in format string (no. 1) requires 'unsigned int' but the argument type is 'signed int'. [invalidPrintfArgType_uint] tophat-2.1.1/src/prep_reads.cpp:575:4: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/prep_reads.cpp:576:4: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/prep_reads.cpp:581:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/prep_reads.cpp:582:5: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/prep_reads.cpp:587:6: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/prep_reads.cpp:588:6: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/prep_reads.cpp:75:42: warning: Either the condition 'fbam==NULL' is redundant or there is possible null pointer dereference: fbam. [nullPointerRedundantCheck] tophat-2.1.1/src/prep_reads.cpp:70:13: note: Assuming that condition 'fbam==NULL' is not redundant tophat-2.1.1/src/prep_reads.cpp:75:42: note: Null pointer dereference tophat-2.1.1/src/prep_reads.cpp:110:5: warning: Either the condition 'tab==NULL' is redundant or there is possible null pointer dereference: tab. [nullPointerRedundantCheck] tophat-2.1.1/src/prep_reads.cpp:107:11: note: Assuming that condition 'tab==NULL' is not redundant tophat-2.1.1/src/prep_reads.cpp:110:5: note: Null pointer dereference tophat-2.1.1/src/prep_reads.cpp:106:21: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/prep_reads.cpp:203:45: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/prep_reads.cpp:207:35: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/prep_reads.cpp:42:27: style: Parameter 'flt_fname' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/prep_reads.cpp:56:34: style: Parameter 'rmap' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/prep_reads.cpp:61:41: style: Parameter 'reads_files' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/prep_reads.cpp:177:43: style: Parameter 'read' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/prep_reads.cpp:337:36: style: Parameter 'reads_fnames' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/prep_reads.cpp:338:22: style: Parameter 'mate_fnames' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/prep_reads.cpp:604:59: style: Parameter 'quals_file_list' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/prep_reads.cpp:77:13: style: Variable 'rname' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/tokenize.cpp:18:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tokenize.cpp:34:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:74:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:523:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:588:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:808:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:1045:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:2071:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:2503:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:2694:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:3017:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/tophat_reports.cpp:3024:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/reads.cpp:75:22: style: Redundant condition: The condition 'buf[i] != 0' is redundant since 'buf[i] == ' '' is sufficient. [redundantCondition] tophat-2.1.1/src/reads.cpp:132:10: warning: Either the condition 'buf==NULL' is redundant or there is possible null pointer dereference: buf. [nullPointerRedundantCheck] tophat-2.1.1/src/reads.cpp:137:10: note: Assuming that condition 'buf==NULL' is not redundant tophat-2.1.1/src/reads.cpp:132:10: note: Null pointer dereference tophat-2.1.1/src/reads.cpp:43:13: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/reads.cpp:388:7: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization] tophat-2.1.1/src/reads.cpp:387:14: note: c is initialized tophat-2.1.1/src/reads.cpp:388:7: note: c is overwritten tophat-2.1.1/src/reads.cpp:413:7: style: Redundant initialization for 'c'. The initialized value is overwritten before it is read. [redundantInitialization] tophat-2.1.1/src/reads.cpp:412:14: note: c is initialized tophat-2.1.1/src/reads.cpp:413:7: note: c is overwritten tophat-2.1.1/src/reads.cpp:211:22: style: Checking if unsigned expression 'color.length()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/reads.cpp:546:35: style:inconclusive: Function 'get_direct' argument 1 names different: declaration 'read' definition 'r'. [funcArgNamesDifferent] tophat-2.1.1/src/reads.h:381:27: note: Function 'get_direct' argument 1 names different: declaration 'read' definition 'r'. tophat-2.1.1/src/reads.cpp:546:35: note: Function 'get_direct' argument 1 names different: declaration 'read' definition 'r'. tophat-2.1.1/src/reads.cpp:571:35: style:inconclusive: Function 'getRead' argument 1 names different: declaration 'read_id' definition 'r_id'. [funcArgNamesDifferent] tophat-2.1.1/src/reads.h:393:27: note: Function 'getRead' argument 1 names different: declaration 'read_id' definition 'r_id'. tophat-2.1.1/src/reads.cpp:571:35: note: Function 'getRead' argument 1 names different: declaration 'read_id' definition 'r_id'. tophat-2.1.1/src/reads.cpp:632:36: style:inconclusive: Function 'getQRead' argument 1 names different: declaration 'read_id' definition 'r_id'. [funcArgNamesDifferent] tophat-2.1.1/src/reads.h:408:28: note: Function 'getQRead' argument 1 names different: declaration 'read_id' definition 'r_id'. tophat-2.1.1/src/reads.cpp:632:36: note: Function 'getQRead' argument 1 names different: declaration 'read_id' definition 'r_id'. tophat-2.1.1/src/reads.cpp:633:14: style:inconclusive: Function 'getQRead' argument 2 names different: declaration 'read' definition 'qread'. [funcArgNamesDifferent] tophat-2.1.1/src/reads.h:409:18: note: Function 'getQRead' argument 2 names different: declaration 'read' definition 'qread'. tophat-2.1.1/src/reads.cpp:633:14: note: Function 'getQRead' argument 2 names different: declaration 'read' definition 'qread'. tophat-2.1.1/src/reads.cpp:379:10: style: Local variable 'color' shadows outer variable [shadowVariable] tophat-2.1.1/src/common.h:124:13: note: Shadowed declaration tophat-2.1.1/src/reads.cpp:379:10: note: Shadow variable tophat-2.1.1/src/reads.cpp:404:10: style: Local variable 'color' shadows outer variable [shadowVariable] tophat-2.1.1/src/common.h:124:13: note: Shadowed declaration tophat-2.1.1/src/reads.cpp:404:10: note: Shadow variable tophat-2.1.1/src/reads.cpp:534:17: style: Local variable 'rdata' shadows outer argument [shadowArgument] tophat-2.1.1/src/reads.cpp:528:39: note: Shadowed declaration tophat-2.1.1/src/reads.cpp:534:17: note: Shadow variable tophat-2.1.1/src/reads.cpp:69:9: style: Variable 'buf' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/utils.cpp:97:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] tophat-2.1.1/src/utils.cpp:42:8: portability: %lu in format string (no. 1) requires 'unsigned long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_uint] tophat-2.1.1/src/utils.cpp:135:36: style: Unused variable: index_list [unusedVariable] tophat-2.1.1/src/tophat_reports.cpp:1899:4: warning: Class 'MultipleBAMReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor] tophat-2.1.1/src/tophat_reports.cpp:1899:4: warning: Class 'MultipleBAMReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq] tophat-2.1.1/src/tophat_reports.cpp:265:3: style: Struct 'cmp_pair_alignment' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/tophat_reports.cpp:2198:2: style: Struct 'CReadProc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/tophat_reports.cpp:2223:2: style: Struct 'ReportWorker' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/tophat_reports.cpp:2201:15: style: The function 'process' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] tophat-2.1.1/src/reads.h:230:15: note: Virtual function in base class tophat-2.1.1/src/tophat_reports.cpp:2201:15: note: Function in derived class tophat-2.1.1/src/tophat_reports.cpp:2534:26: style: The if condition is the same as the previous if condition [duplicateCondition] tophat-2.1.1/src/tophat_reports.cpp:2507:27: note: First condition tophat-2.1.1/src/tophat_reports.cpp:2534:26: note: Second condition tophat-2.1.1/src/tophat_reports.cpp:227:19: style: Condition 'lh.ref_id()==rh.ref_id()' is always true [knownConditionTrueFalse] tophat-2.1.1/src/tophat_reports.cpp:224:19: note: Assuming that condition 'lh.ref_id()!=rh.ref_id()' is not redundant tophat-2.1.1/src/tophat_reports.cpp:227:19: note: Condition 'lh.ref_id()==rh.ref_id()' is always true tophat-2.1.1/src/tophat_reports.cpp:1360:32: style: Condition 'before_match_length>0' is always true [knownConditionTrueFalse] tophat-2.1.1/src/tophat_reports.cpp:1357:55: note: Assignment 'before_match_length=junc.left-new_left+1', assigned value is greater than 0 tophat-2.1.1/src/tophat_reports.cpp:1360:32: note: Condition 'before_match_length>0' is always true tophat-2.1.1/src/tophat_reports.cpp:1377:32: style: Condition 'before_match_length>0' is always true [knownConditionTrueFalse] tophat-2.1.1/src/tophat_reports.cpp:1374:50: note: Assignment 'before_match_length=junc.left-pos+1', assigned value is greater than 0 tophat-2.1.1/src/tophat_reports.cpp:1377:32: note: Condition 'before_match_length>0' is always true tophat-2.1.1/src/tophat_reports.cpp:1806:7: portability: %lu in format string (no. 1) requires 'unsigned long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_uint] tophat-2.1.1/src/tophat_reports.cpp:2137:3: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/tophat_reports.cpp:2156:4: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/tophat_reports.cpp:2171:6: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/tophat_reports.cpp:1937:56: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/tophat_reports.cpp:2687:32: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/tophat_reports.cpp:2688:39: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/tophat_reports.cpp:2689:40: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/tophat_reports.cpp:2690:35: style: C-style pointer casting [cstyleCast] tophat-2.1.1/src/tophat_reports.cpp:880:14: style: Redundant initialization for 'mate_pos'. The initialized value is overwritten before it is read. [redundantInitialization] tophat-2.1.1/src/tophat_reports.cpp:861:15: note: mate_pos is initialized tophat-2.1.1/src/tophat_reports.cpp:880:14: note: mate_pos is overwritten tophat-2.1.1/src/tophat_reports.cpp:130:15: style: The scope of the variable 'nhits' can be reduced. [variableScope] tophat-2.1.1/src/tophat_reports.cpp:1822:16: style: The scope of the variable 'offset' can be reduced. [variableScope] tophat-2.1.1/src/tophat_reports.cpp:1823:17: style: The scope of the variable 'read_id' can be reduced. [variableScope] tophat-2.1.1/src/tophat_reports.cpp:3095:10: style: The scope of the variable 'right_map_filename_list' can be reduced. [variableScope] tophat-2.1.1/src/tophat_reports.cpp:1922:25: style: Checking if unsigned expression 'bam_lines.size()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/tophat_reports.cpp:2489:28: style: Checking if unsigned expression 'best_hits.size()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/tophat_reports.cpp:650:14: style: Local variable 'aux' shadows outer variable [shadowVariable] tophat-2.1.1/src/tophat_reports.cpp:595:10: note: Shadowed declaration tophat-2.1.1/src/tophat_reports.cpp:650:14: note: Shadow variable tophat-2.1.1/src/tophat_reports.cpp:338:24: style: Parameter 'a' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/tophat_reports.cpp:990:22: style: Parameter 'rng' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/tophat_reports.cpp:1033:20: style: Parameter 'rng' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/tophat_reports.cpp:2119:34: style: Parameter 'alnStats' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/tophat_reports.cpp:2688:11: style: Variable 'scan_left_coord' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/tophat_reports.cpp:2689:11: style: Variable 'scan_right_coord' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/tophat_reports.cpp:2690:11: style: Variable 'orientation' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/tophat_reports.cpp:687:4: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam] tophat-2.1.1/src/tophat_reports.cpp:830:4: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam] tophat-2.1.1/src/tophat_reports.cpp:1037:10: style: Unused variable: left_read [unusedVariable] tophat-2.1.1/src/tophat_reports.cpp:1038:10: style: Unused variable: right_read [unusedVariable] tophat-2.1.1/src/tophat_reports.cpp:1877:15: style: Variable 'pushed' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/tophat_reports.cpp:3094:16: style: Variable 'unzcmd' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/tophat_reports.cpp:1214:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] tophat-2.1.1/src/segment_juncs.cpp:710:8: performance:inconclusive: Technically the member function 'IntronMotifs::unique' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/segment_juncs.cpp:734:8: performance:inconclusive: Technically the member function 'IntronMotifs::attach_upstream_mers' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/segment_juncs.cpp:787:8: performance:inconclusive: Technically the member function 'IntronMotifs::attach_downstream_mers' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/segment_juncs.cpp:1570:8: performance:inconclusive: Technically the member function 'RecordExtendableJuncs::record' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/segment_juncs.cpp:1630:8: performance:inconclusive: Technically the member function 'RecordAllJuncs::record' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/segment_juncs.cpp:1671:8: performance:inconclusive: Technically the member function 'RecordSegmentJuncs::record' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/segment_juncs.cpp:1744:8: performance:inconclusive: Technically the member function 'RecordButterflyJuncs::record' can be static (but you may consider moving to unnamed namespace). [functionStatic] tophat-2.1.1/src/segment_juncs.cpp:702:3: style: Struct 'IntronMotifs' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] tophat-2.1.1/src/segment_juncs.cpp:4851:8: style: The if condition is the same as the previous if condition [duplicateCondition] tophat-2.1.1/src/segment_juncs.cpp:4848:8: note: First condition tophat-2.1.1/src/segment_juncs.cpp:4851:8: note: Second condition tophat-2.1.1/src/segment_juncs.cpp:3283:80: style: Condition 'rightHit->antisense_align()==true' is always true [knownConditionTrueFalse] tophat-2.1.1/src/segment_juncs.cpp:3283:40: note: Assuming that condition 'leftHit->antisense_align()==false' is not redundant tophat-2.1.1/src/segment_juncs.cpp:3273:35: note: Assuming that condition 'leftHit->antisense_align()==rightHit->antisense_align()' is not redundant tophat-2.1.1/src/segment_juncs.cpp:3283:80: note: Condition 'rightHit->antisense_align()==true' is always true tophat-2.1.1/src/segment_juncs.cpp:4554:7: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:4554:7: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5041:7: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5041:7: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5063:3: portability: %lu in format string (no. 1) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint] tophat-2.1.1/src/segment_juncs.cpp:5070:7: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5070:7: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5081:3: portability: %lu in format string (no. 1) requires 'unsigned long' but the argument type is 'std::size_t {aka unsigned long}'. [invalidPrintfArgType_uint] tophat-2.1.1/src/segment_juncs.cpp:5085:7: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5085:7: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5173:4: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5173:4: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] tophat-2.1.1/src/segment_juncs.cpp:5363:3: error: Resource leak: left_reads_file_for_fusion_discovery [resourceLeak] tophat-2.1.1/src/segment_juncs.cpp:3359:16: style: The scope of the variable 'right_segment_hits' can be reduced. [variableScope] tophat-2.1.1/src/segment_juncs.cpp:4625:27: style: The scope of the variable 'last_read_id' can be reduced. [variableScope] tophat-2.1.1/src/segment_juncs.cpp:2513:36: style: Checking if unsigned expression 'bestInsertPositions.size()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/segment_juncs.cpp:3215:33: style: Checking if unsigned expression 'ignore_chromosomes.size()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/segment_juncs.cpp:3581:24: style: Checking if unsigned expression 'rrs_bhs.size()' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/segment_juncs.cpp:2174:15: style: Checking if unsigned expression 'read_len' is less than zero. [unsignedLessThanZero] tophat-2.1.1/src/segment_juncs.cpp:1533:14: style: Local variable 'color' shadows outer variable [shadowVariable] tophat-2.1.1/src/common.h:124:13: note: Shadowed declaration tophat-2.1.1/src/segment_juncs.cpp:1533:14: note: Shadow variable tophat-2.1.1/src/segment_juncs.cpp:1914:16: style: Local variable 'key' shadows outer variable [shadowVariable] tophat-2.1.1/src/segment_juncs.cpp:1896:17: note: Shadowed declaration tophat-2.1.1/src/segment_juncs.cpp:1914:16: note: Shadow variable tophat-2.1.1/src/segment_juncs.cpp:1971:16: style: Local variable 'key' shadows outer variable [shadowVariable] tophat-2.1.1/src/segment_juncs.cpp:1943:17: note: Shadowed declaration tophat-2.1.1/src/segment_juncs.cpp:1971:16: note: Shadow variable tophat-2.1.1/src/segment_juncs.cpp:3780:17: style: Local variable 'ss' shadows outer variable [shadowVariable] tophat-2.1.1/src/segment_juncs.cpp:3769:16: note: Shadowed declaration tophat-2.1.1/src/segment_juncs.cpp:3780:17: note: Shadow variable tophat-2.1.1/src/segment_juncs.cpp:5020:41: style: Local variable 'microexon_juncs' shadows outer variable [shadowVariable] tophat-2.1.1/src/segment_juncs.cpp:5016:37: note: Shadowed declaration tophat-2.1.1/src/segment_juncs.cpp:5020:41: note: Shadow variable tophat-2.1.1/src/segment_juncs.cpp:1247:18: style: Parameter 'mer_table' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:1248:28: style: Parameter 'donors' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:1309:18: style: Variable 's' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:1472:24: style: Variable 'exts' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:1491:24: style: Variable 'exts' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:1811:28: style: Variable 'fwd_exts' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:1840:28: style: Variable 'rev_exts' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:1899:25: style: Variable 'fwd_exts' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:1952:25: style: Variable 'rev_exts' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:2391:27: style: Parameter 'leftReference' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2392:27: style: Parameter 'rightReference' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2470:47: style: Parameter 'rt' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2472:19: style: Parameter 'leftHit' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2473:19: style: Parameter 'rightHit' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2554:46: style: Parameter 'rt' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2556:18: style: Parameter 'leftHit' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2557:18: style: Parameter 'rightHit' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2629:38: style: Parameter 'rt' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2631:17: style: Parameter 'leftHit' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2632:17: style: Parameter 'rightHit' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:3093:15: style: Variable 'leftHit' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:3096:19: style: Variable 'rightHit' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:3366:15: style: Variable 'leftHit' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:3369:22: style: Variable 'rightHit' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:3408:15: style: Variable 'leftHit' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:3411:19: style: Variable 'rightHit' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:3586:16: style: Variable 'd_bh' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:3746:19: style: Variable 'unaligned_segments' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:3776:19: style: Variable 'unaligned_segments' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:4200:21: style: Variable 'cov' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:4361:21: style: Variable 'cov' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:4390:21: style: Variable 'ref_cov' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:4545:36: style: Parameter 'rt' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:4545:75: style: Parameter 'juncs' can be declared as reference to const [constParameterReference] tophat-2.1.1/src/segment_juncs.cpp:2346:50: style: Variable 'fwd_donors' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:2347:50: style: Variable 'fwd_acceptors' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:2348:50: style: Variable 'rev_acceptors' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:2349:50: style: Variable 'rev_donors' can be declared as reference to const [constVariableReference] tophat-2.1.1/src/segment_juncs.cpp:5333:9: style: Variable 'left_reads_file_for_fusion_discovery' can be declared as pointer to const [constVariablePointer] tophat-2.1.1/src/segment_juncs.cpp:3906:15: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr] tophat-2.1.1/src/segment_juncs.cpp:4253:10: style: struct member 'ReadInfo::read_id' is never used. [unusedStructMember] tophat-2.1.1/src/segment_juncs.cpp:371:19: style: Variable 'left' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:412:8: style: Variable 'left' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:413:8: style: Variable 'left' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:539:26: style: Variable 'num_extensions' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:542:18: style: Variable 'num_extensions' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:606:8: style: Variable 'L' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:623:16: style: Variable 'match_chars' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:633:6: style: Variable 'L' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:3920:24: style: Unused variable: empty_seg_hits [unusedVariable] tophat-2.1.1/src/segment_juncs.cpp:4625:40: style: Variable 'last_read_id' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:4651:15: style: Variable 'last_read_id' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/segment_juncs.cpp:5316:10: style: Unused variable: left_segment_file_for_segment_search [unusedVariable] tophat-2.1.1/src/segment_juncs.cpp:5343:10: style: Unused variable: right_segment_file_for_segment_search [unusedVariable] tophat-2.1.1/src/long_spanning_reads.cpp:377:31: style: Condition 'curr_left_to_insert>0' is always true [knownConditionTrueFalse] tophat-2.1.1/src/long_spanning_reads.cpp:302:61: note: Assignment 'curr_left_to_insert=lb->left-curr_hit->left()+1', assigned value is greater than 0 tophat-2.1.1/src/long_spanning_reads.cpp:303:62: note: Assuming condition is false tophat-2.1.1/src/long_spanning_reads.cpp:377:31: note: Condition 'curr_left_to_insert>0' is always true tophat-2.1.1/src/long_spanning_reads.cpp:522:24: style: Condition 'dist_to_left>0' is always true [knownConditionTrueFalse] tophat-2.1.1/src/long_spanning_reads.cpp:505:57: note: Assignment 'dist_to_left=lb->left-prev_hit->right()+1', assigned value is greater than 0 tophat-2.1.1/src/long_spanning_reads.cpp:513:53: note: Assuming condition is false tophat-2.1.1/src/long_spanning_reads.cpp:522:24: note: Condition 'dist_to_left>0' is always true tophat-2.1.1/src/long_spanning_reads.cpp:2555:9: style: Condition 'same_contig' is always true [knownConditionTrueFalse] tophat-2.1.1/src/long_spanning_reads.cpp:2554:8: note: Assuming that condition '!same_contig' is not redundant tophat-2.1.1/src/long_spanning_reads.cpp:2555:9: note: Condition 'same_contig' is always true tophat-2.1.1/src/long_spanning_reads.cpp:2556:9: style: Condition 'same_contig' is always true [knownConditionTrueFalse] tophat-2.1.1/src/long_spanning_reads.cpp:2554:8: note: Assuming that condition '!same_contig' is not redundant tophat-2.1.1/src/long_spanning_reads.cpp:2556:9: note: Condition 'same_contig' is always true tophat-2.1.1/src/long_spanning_reads.cpp:2738:33: style: Condition 'curr_contig_obs_order==curr_spliced_obs_order' is always true [knownConditionTrueFalse] tophat-2.1.1/src/long_spanning_reads.cpp:2724:34: note: Assuming that condition 'curr_spliced_obs_order=0' is redundant, otherwise there is negative array index -1. [negativeContainerIndex] tophat-2.1.1/src/long_spanning_reads.cpp:2778:23: note: Assuming that condition 'last_non_empty>=0' is not redundant tophat-2.1.1/src/long_spanning_reads.cpp:2784:7: note: Negative array index tophat-2.1.1/src/long_spanning_reads.cpp:2851:18: style: struct member 'JoinSegmentsWorker::segmap_fnames' is never used. [unusedStructMember] tophat-2.1.1/src/long_spanning_reads.cpp:2852:18: style: struct member 'JoinSegmentsWorker::spliced_segmap_fnames' is never used. [unusedStructMember] tophat-2.1.1/src/long_spanning_reads.cpp:1681:12: style: Unused variable: new_patch_str [unusedVariable] tophat-2.1.1/src/long_spanning_reads.cpp:2058:30: style: Variable 'currCig' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/long_spanning_reads.cpp:2528:13: style: Variable 'bh_l' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/long_spanning_reads.cpp:2528:29: style: Variable 'back_right' is assigned a value that is never used. [unreadVariable] tophat-2.1.1/src/long_spanning_reads.cpp:3296:18: style: Unused variable: spliced_segmap_files [unusedVariable] tophat-2.1.1/src/long_spanning_reads.cpp:3297:10: style: Unused variable: unzcmd [unusedVariable] diff: head tophat-2.1.1/src/FastaTools.cpp:128:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/FastaTools.cpp:155:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/FastaTools.cpp:29:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/FastaTools.cpp:65:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GBase.cpp:105:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GBase.cpp:210:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GBase.cpp:220:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GBase.cpp:266:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GBase.cpp:453:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GBase.cpp:482:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GBase.cpp:81:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GFaSeqGet.cpp:70:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] 2.13.0 tophat-2.1.1/src/GHash.hh:175:3: style: Condition 'm<=(n>>1)' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:174:15: note: Assuming that condition '(n>>1)>1)' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:187:9: style: Condition '1<=x' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:186:11: note: Assignment 'x=1|(((unsigned int)(h)*17)%(n-1))', assigned value is greater than 0 tophat-2.1.1/src/GHash.hh:187:9: note: Condition '1<=x' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:189:9: style: Condition 'k[p].hash<0' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:188:24: note: Assuming that condition 'k[p].hash!=-1' is not redundant tophat-2.1.1/src/GHash.hh:189:9: note: Condition 'k[p].hash<0' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:210:3: style: Condition '1<=x' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:209:5: note: Assignment 'x=1|(((unsigned int)(h)*17)%(fCapacity-1))', assigned value is greater than 0 tophat-2.1.1/src/GHash.hh:210:3: note: Condition '1<=x' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:251:3: style: Condition '1<=x' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:250:5: note: Assignment 'x=1|(((unsigned int)(h)*17)%(fCapacity-1))', assigned value is greater than 0 tophat-2.1.1/src/GHash.hh:251:3: note: Condition '1<=x' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:293:3: style: Condition '1<=x' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:292:5: note: Assignment 'x=1|(((unsigned int)(h)*17)%(fCapacity-1))', assigned value is greater than 0 tophat-2.1.1/src/GHash.hh:293:3: note: Condition '1<=x' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:336:5: style: Condition '1<=x' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:335:7: note: Assignment 'x=1|(((unsigned int)(h)*17)%(fCapacity-1))', assigned value is greater than 0 tophat-2.1.1/src/GHash.hh:336:5: note: Condition '1<=x' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:372:5: style: Condition '1<=x' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:371:7: note: Assignment 'x=1|(((unsigned int)(h)*17)%(fCapacity-1))', assigned value is greater than 0 tophat-2.1.1/src/GHash.hh:372:5: note: Condition '1<=x' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:395:5: style: Condition '1<=x' is always true [knownConditionTrueFalse] tophat-2.1.1/src/GHash.hh:394:7: note: Assignment 'x=1|(((unsigned int)(h)*17)%(fCapacity-1))', assigned value is greater than 0 tophat-2.1.1/src/GHash.hh:395:5: note: Condition '1<=x' is always true 2.13.0 tophat-2.1.1/src/GHash.hh:55:14: style: C-style pointer casting [cstyleCast] head tophat-2.1.1/src/GList.hh:155:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:171:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:172:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:231:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:235:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:250:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:265:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:312:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:318:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:328:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:335:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:343:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fUnique [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:348:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:363:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:367:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:376:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:377:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:382:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:383:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:391:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:392:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:419:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:430:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:431:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:432:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:441:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:468:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:476:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:491:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:517:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:544:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:593:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:608:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:609:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:613:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:614:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:620:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:628:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:633:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCompareProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GList.hh:634:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GStr.cpp:1270:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GStr.cpp:697:49: warning: Either the condition 'len<0' is redundant or ::memcpy() argument nr 3 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg] tophat-2.1.1/src/GStr.cpp:690:40: note: Assuming that condition 'len<0' is not redundant tophat-2.1.1/src/GStr.cpp:697:49: note: Invalid argument 2.13.0 tophat-2.1.1/src/GStr.cpp:697:49: warning: Either the condition 'len<0' is redundant or memcpy() argument nr 3 can have invalid value. The value is -1 but the valid values are '0:'. [invalidFunctionArg] tophat-2.1.1/src/GStr.cpp:690:40: note: Assuming that condition 'len<0' is not redundant tophat-2.1.1/src/GStr.cpp:697:49: note: Invalid argument head tophat-2.1.1/src/GTFToFasta.cpp:104:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GTFToFasta.cpp:154:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GTFToFasta.cpp:162:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GTFToFasta.cpp:171:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GTFToFasta.cpp:37:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GTFToFasta.cpp:61:49: performance: Function parameter 'out_fname' should be passed by const reference. [passedByValue] 2.13.0 tophat-2.1.1/src/GVec.hh:109:10: warning: Invalid test for overflow 'fCount-1>=fCount'; signed integer overflow is undefined behavior. Some mainstream compilers remove such overflow tests when optimising the code and assume it's always false. [invalidTestForOverflow] 2.13.0 tophat-2.1.1/src/GVec.hh:113:10: style: Same expression on both sides of '<'. [duplicateExpression] 2.13.0 tophat-2.1.1/src/GVec.hh:156:14: style: C-style pointer casting [cstyleCast] head tophat-2.1.1/src/GVec.hh:207:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:216:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:226:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:238:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:258:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:261:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:282:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:288:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:315:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:316:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:327:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:333:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:343:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:356:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:388:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:398:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:399:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:411:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:421:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:425:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:434:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:442:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:466:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:471:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:480:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:482:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OBJ [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:499:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:506:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:517:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:531:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:552:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fArray [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:566:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:578:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:592:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:609:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:616:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:626:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:635:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:646:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:662:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:673:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fFreeProc [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:684:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:692:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:697:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:711:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:725:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:758:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:767:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:776:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:789:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:803:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:808:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:813:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:822:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:834:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:843:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:855:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:864:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:871:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCapacity [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:884:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/GVec.hh:908:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/align_status.cpp:127:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bam2fastx.cpp:184:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FQCFAIL [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bam2fastx.cpp:323:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bam2fastx.cpp:330:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bam2fastx.cpp:345:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bam2fastx.cpp:370:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bam2fastx.cpp:424:10: error: Resource leak: fout2 [resourceLeak] head tophat-2.1.1/src/bam_merge.cpp:28:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bam_merge.cpp:7:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bam_merge.h:47:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.cpp:1162:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_rev_table [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.cpp:1459:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.cpp:1492:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_rev_table [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.cpp:1802:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.cpp:2359:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.cpp:368:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.cpp:993:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.h:618:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/bwt_map.h:778:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable observation_order [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:1060:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CMATCH [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:1096:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_table [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:1148:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:1234:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bam_nt16_rev_table [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:1257:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:193:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:215:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:430:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:455:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:492:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optarg [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:728:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:815:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:831:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:839:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:848:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:941:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.cpp:980:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.h:468:48: style: Parameter 'idxfile' can be declared as reference to const [constParameterReference] head tophat-2.1.1/src/common.h:542:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/common.h:599:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CORE_SIZE [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/coverage.cpp:219:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/coverage.cpp:250:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/coverage.cpp:51:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fix_map_ordering.cpp:130:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FSECONDARY [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fix_map_ordering.cpp:140:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fix_map_ordering.cpp:155:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FUNMAP [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fix_map_ordering.cpp:191:9: style: Variable 'qname' can be declared as pointer to const [constVariablePointer] head tophat-2.1.1/src/fix_map_ordering.cpp:209:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fix_map_ordering.cpp:405:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fix_map_ordering.cpp:417:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fix_map_ordering.cpp:81:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREVERSE [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fragments.cpp:20:17: style: Parameter 'hits_in_ref' can be declared as reference to const [constParameterReference] head tophat-2.1.1/src/fragments.cpp:21:19: style: Parameter 'it' can be declared as reference to const [constParameterReference] head tophat-2.1.1/src/fragments.cpp:22:36: style: Parameter 'best_status_for_fragments' can be declared as reference to const [constParameterReference] head tophat-2.1.1/src/fusions.cpp:428:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ldist [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/fusions.cpp:504:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.cpp:1269:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fList [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.cpp:126:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dest [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.cpp:146:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable skipLine [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.cpp:1880:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.cpp:1881:2: portability: %d in format string (no. 3) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:1881:2: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:1881:2: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:1881:2: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:1928:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:1928:5: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:1928:5: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:1928:5: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:1947:5: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:1947:5: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:1947:5: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:1947:5: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:2020:4: portability: %d in format string (no. 4) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:2020:4: portability: %d in format string (no. 5) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:2020:4: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:2020:4: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:2023:45: portability: %d in format string (no. 1) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:2023:45: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:2023:45: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gff.cpp:2023:45: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gff.cpp:2069:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] 2.13.0 tophat-2.1.1/src/gff.h:264:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.h:267:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.h:945:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.h:953:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gff.h:960:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fCount [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gtf_juncs.cpp:101:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gtf_juncs.cpp:31:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gtf_juncs.cpp:84:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/gtf_juncs.cpp:85:9: portability: %d in format string (no. 2) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/gtf_juncs.cpp:85:9: portability: %d in format string (no. 3) requires 'int' but the argument type is 'uint {aka unsigned int}'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gtf_juncs.cpp:85:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/gtf_juncs.cpp:85:9: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/inserts.cpp:182:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left_alignment [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/juncs_db.cpp:100:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/juncs_db.cpp:144:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/juncs_db.cpp:222:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/juncs_db.cpp:241:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/juncs_db.cpp:285:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/juncs_db.cpp:334:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/juncs_db.cpp:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/juncs_db.cpp:529:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/junctions.cpp:155:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/junctions.cpp:323:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/long_spanning_reads.cpp:2033:7: portability: %d in format string (no. 1) requires 'int' but the argument type is 'ReadID {aka unsigned int}'. [invalidPrintfArgType_sint] 2.13.0 tophat-2.1.1/src/long_spanning_reads.cpp:2033:7: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint] head tophat-2.1.1/src/long_spanning_reads.cpp:2295:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] 2.13.0 tophat-2.1.1/src/long_spanning_reads.cpp:2784:24: warning: Either the condition 'seg_hits_for_read.empty()' is redundant or expression 'seg_hits_for_read[last_non_empty]' cause access out of bounds. [containerOutOfBounds] tophat-2.1.1/src/long_spanning_reads.cpp:2787:30: note: Assuming that condition 'seg_hits_for_read.empty()' is not redundant tophat-2.1.1/src/long_spanning_reads.cpp:2784:24: note: Access out of bounds head tophat-2.1.1/src/long_spanning_reads.cpp:2784:24: warning: Either the condition 'seg_hits_for_read.empty()' is redundant or expression 'seg_hits_for_read[last_non_empty]' causes access out of bounds. [containerOutOfBounds] tophat-2.1.1/src/long_spanning_reads.cpp:2787:30: note: Assuming that condition 'seg_hits_for_read.empty()' is not redundant tophat-2.1.1/src/long_spanning_reads.cpp:2784:24: note: Access out of bounds head tophat-2.1.1/src/long_spanning_reads.cpp:2885:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/long_spanning_reads.cpp:3153:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/long_spanning_reads.cpp:434:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/long_spanning_reads.cpp:56:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/long_spanning_reads.cpp:76:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/long_spanning_reads.cpp:875:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:110:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:11:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:16:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:173:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:264:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_CIGAR_MASK [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:378:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:404:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable start [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:438:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable optind [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:50:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/map2gtf.cpp:72:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/prep_reads.cpp:128:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/prep_reads.cpp:177:43: style: Parameter 'read' can be declared as reference to const [constParameterReference] head tophat-2.1.1/src/prep_reads.cpp:198:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar] 2.13.0 tophat-2.1.1/src/prep_reads.cpp:360:10: style: The scope of the variable 'outfname' can be reduced. [variableScope] 2.13.0 tophat-2.1.1/src/prep_reads.cpp:361:10: style: The scope of the variable 'mate_outfname' can be reduced. [variableScope] head tophat-2.1.1/src/prep_reads.cpp:380:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/prep_reads.cpp:600:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/prep_reads.cpp:612:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/prep_reads.cpp:622:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/qual.h:149:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/qual.h:31:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/qual.h:92:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/reads.cpp:116:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/reads.cpp:40:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable EOF [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/reads.cpp:556:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FQCFAIL [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/reads.h:169:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FREAD1 [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/reads.h:244:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/reads.h:331:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/reads.h:358:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/reads.h:42:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/sam_juncs.cpp:111:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/sam_juncs.cpp:118:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/sam_juncs.cpp:98:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:1258:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:1587:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:1644:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:1687:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:1762:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:2091:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:2478:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:2562:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:315:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:3750:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:4194:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:4515:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:4547:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:4579:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:4726:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:5188:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:5363:3: error: Resource leak: left_reads_file_for_fusion_discovery [resourceLeak] head tophat-2.1.1/src/segment_juncs.cpp:739:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:74:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/segment_juncs.cpp:792:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tokenize.cpp:34:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:1045:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:2071:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:2503:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:2694:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:3017:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:3024:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:523:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:588:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:74:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/tophat_reports.cpp:808:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BAM_FPAIRED [valueFlowBailoutIncompleteVar] head tophat-2.1.1/src/utils.cpp:97:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] DONE