2022-06-28 17:04
ftp://ftp.de.debian.org/debian/pool/main/h/hisat2/hisat2_2.2.1.orig.tar.gz
cppcheck-options: --library=posix --library=gnu  --showtime=top5 --check-library --inconclusive --enable=style,information --inline-suppr --template=daca2 -D__GNUC__ --platform=unix64 -rp=temp -j4
platform: Linux-5.10.0-15-amd64-x86_64-with-glibc2.31
python: 3.9.2
client-version: 1.3.25
compiler: g++ (Debian 10.2.1-6) 10.2.1 20210110
cppcheck: head 2.8
head-info: 2223cd2 (2022-06-28 14:02:02 +0200)
count: 2247 2164
elapsed-time: 675.8 651.6
head-timing-info:
 Overall time: 0s

old-timing-info:
 Overall time: 0s

head results:
hisat2-2.2.1/ds.h:3122:18: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4101:11: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4123:13: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4149:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4150:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4162:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4163:14: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:4169:10: warning: Assert statement calls a function which may have desired side effects: 'redBlackRepOk'. [assertWithSideEffect]
hisat2-2.2.1/aligner_cache.h:481:31: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/aligner_cache.h:983:18: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/alphabet.h:150:16: warning: Either the condition '(c)<=4' is redundant or the array 'dnacomp[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/alphabet.h:149:2: note: Assuming that condition '(c)<=4' is not redundant
hisat2-2.2.1/alphabet.h:150:16: note: Array index out of bounds
hisat2-2.2.1/tinythread.h:704:5: style: Obsolescent function 'usleep' called. It is recommended to use 'nanosleep' or 'setitimer' instead. [prohibitedusleepCalled]
hisat2-2.2.1/filebuf.h:351:18: warning: Either the condition 'c==-1' is redundant or isspace() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:255'. [invalidFunctionArg]
hisat2-2.2.1/filebuf.h:353:21: note: Assuming that condition 'c==-1' is not redundant
hisat2-2.2.1/filebuf.h:351:18: note: Invalid argument
hisat2-2.2.1/filebuf.h:390:18: warning: Either the condition 'c==-1' is redundant or isspace() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:255'. [invalidFunctionArg]
hisat2-2.2.1/filebuf.h:392:21: note: Assuming that condition 'c==-1' is not redundant
hisat2-2.2.1/filebuf.h:390:18: note: Invalid argument
hisat2-2.2.1/random_source.h:39:2: warning: Member variable 'RandomSource::last' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_source.h:39:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_source.h:41:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_source.h:43:2: warning: Member variable 'RandomSource::last' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_source.h:43:2: warning: Member variable 'RandomSource::lastOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2148:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2160:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2167:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2174:11: warning: Member variable 'SStringFixed::printcs_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:2246:21: warning: Member variable 'SStringFixed::printcs_' is not assigned a value in 'SStringFixed::operator='. [operatorEqVarError]
hisat2-2.2.1/filebuf.h:59:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:59:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:63:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:63:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:69:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:69:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:75:2: warning: Member variable 'FileBuf::_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:75:2: warning: Member variable 'FileBuf::_lastn_buf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:531:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:546:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/filebuf.h:560:2: warning: Member variable 'OutFileBuf::buf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:49:2: warning: Member variable 'Read::mate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:49:2: warning: Member variable 'Read::hitset' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:51:2: warning: Member variable 'Read::mate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:51:2: warning: Member variable 'Read::hitset' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/read.h:434:2: warning: Member variable 'PerReadMetrics::tz_beg' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable < char , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/ds.h:4232:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4232:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4257:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4257:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4257:35: performance: Variable 'c' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4282:19: performance: Variable 'a' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4282:27: performance: Variable 'b' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4282:35: performance: Variable 'c' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/ds.h:4282:43: performance: Variable 'd' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/tinythread.h:539:31: style:inconclusive: Technically the member function 'tthread::thread::native_handle' can be const. [functionConst]
hisat2-2.2.1/fast_mutex.h:154:17: style:inconclusive: Technically the member function 'tthread::fast_mutex::lock' can be const. [functionConst]
hisat2-2.2.1/fast_mutex.h:183:17: style:inconclusive: Technically the member function 'tthread::fast_mutex::try_lock' can be const. [functionConst]
hisat2-2.2.1/fast_mutex.h:237:17: style:inconclusive: Technically the member function 'tthread::fast_mutex::unlock' can be const. [functionConst]
hisat2-2.2.1/ds.h:61:11: style:inconclusive: Technically the member function 'MemoryTally::total' can be const. [functionConst]
hisat2-2.2.1/ds.h:67:11: style:inconclusive: Technically the member function 'MemoryTally::total' can be const. [functionConst]
hisat2-2.2.1/ds.h:72:11: style:inconclusive: Technically the member function 'MemoryTally::peak' can be const. [functionConst]
hisat2-2.2.1/ds.h:78:11: style:inconclusive: Technically the member function 'MemoryTally::peak' can be const. [functionConst]
hisat2-2.2.1/ds.h:3147:10: style:inconclusive: Technically the member function 'Pool::full' can be const. [functionConst]
hisat2-2.2.1/ds.h:3160:7: performance:inconclusive: Technically the member function 'Pool::free' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/filebuf.h:84:7: style:inconclusive: Technically the member function 'FileBuf::isOpen' can be const. [functionConst]
hisat2-2.2.1/filebuf.h:117:7: style:inconclusive: Technically the member function 'FileBuf::eof' can be const. [functionConst]
hisat2-2.2.1/filebuf.h:703:14: style:inconclusive: Technically the member function 'OutFileBuf::name' can be const. [functionConst]
hisat2-2.2.1/aligner_cache.h:290:7: style:inconclusive: Technically the member function 'SAVal::valid' can be const. [functionConst]
hisat2-2.2.1/aligner_cache.h:898:33: style:inconclusive: Technically the member function 'AlignmentCacheIface::current' can be const. [functionConst]
hisat2-2.2.1/fast_mutex.h:118:3: warning: Class 'fast_mutex' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/filebuf.h:463:3: warning: Class 'BitpairOutFileBuf' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/filebuf.h:463:3: warning: Class 'BitpairOutFileBuf' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/filebuf.h:463:3: warning: Class 'BitpairOutFileBuf' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
hisat2-2.2.1/filebuf.h:550:3: warning: Class 'OutFileBuf' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/filebuf.h:550:3: warning: Class 'OutFileBuf' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString(const std::basic_string<T>&str)' at line 541. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:541:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString(const T*b,long sz)' at line 552. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:552:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString(const T*b)' at line 563. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:563:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2304:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const std::basic_string<T>&str)' at line 2161. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2161:3: note: Calling install
hisat2-2.2.1/sstring.h:2304:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2304:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const T*b,long sz)' at line 2168. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2168:3: note: Calling install
hisat2-2.2.1/sstring.h:2304:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2304:15: style: Virtual function 'install' is called from constructor 'SStringFixed(const T*b)' at line 2175. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2175:3: note: Calling install
hisat2-2.2.1/sstring.h:2304:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2702:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2608. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2608:5: note: Calling installColors
hisat2-2.2.1/sstring.h:2702:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:2687:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2610. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2610:5: note: Calling installChars
hisat2-2.2.1/sstring.h:2687:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:2671:15: style: Virtual function 'install' is called from constructor 'SDnaStringFixed(const char*b,bool chars=false,bool colors=false)' at line 2613. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2613:4: note: Calling install
hisat2-2.2.1/sstring.h:2671:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:3264:15: style: Virtual function 'installChars' is called from constructor 'SDnaMaskString(const char*b,bool chars=false)' at line 3184. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:3184:4: note: Calling installChars
hisat2-2.2.1/sstring.h:3264:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:3248:15: style: Virtual function 'install' is called from constructor 'SDnaMaskString(const char*b,bool chars=false)' at line 3186. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:3186:4: note: Calling install
hisat2-2.2.1/sstring.h:3248:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:3034:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2868. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2868:5: note: Calling installColors
hisat2-2.2.1/sstring.h:3034:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:3026:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2870. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2870:5: note: Calling installChars
hisat2-2.2.1/sstring.h:3026:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:3012:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2889. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2889:5: note: Calling installColors
hisat2-2.2.1/sstring.h:3012:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:2998:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2891. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2891:5: note: Calling installChars
hisat2-2.2.1/sstring.h:2998:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:2983:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,long sz,bool chars=false,bool colors=false)' at line 2894. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2894:4: note: Calling install
hisat2-2.2.1/sstring.h:2983:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2964:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable < 1024 , 2 >(const char*b,bool chars=false,bool colors=false)' at line 2907. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2907:3: note: Calling install
hisat2-2.2.1/sstring.h:2964:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 >(const std::basic_string<char>&str)' at line 1680. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1680:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 >(const char*b,long sz)' at line 1692. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1692:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < char , 1024 , 2 >(const char*b)' at line 1704. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1704:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/assert_helpers.h:33:2: style: Class 'ReleaseAssertException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/tinythread.h:579:5: style: Class 'id' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/threading.h:39:5: style: Class 'ThreadSafe' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/random_source.h:41:2: style: Class 'RandomSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1747:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:2459:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:2471:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3199:2: style: Class 'PList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3806:2: style: Class 'RedBlack' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:63:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:69:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:75:2: style: Class 'FileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:461:2: style: Class 'BitpairOutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:531:2: style: Class 'OutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/filebuf.h:546:2: style: Class 'OutFileBuf' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sstring.h:1661:2: style: Class 'SStringExpandable < char , 1024 , 2 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sstring.h:2983:15: style: The function 'install' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/sstring.h:1841:15: note: Virtual function in base class
hisat2-2.2.1/sstring.h:2983:15: note: Function in derived class
hisat2-2.2.1/sstring.h:3145:22: style: The function 'toZBuf' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/sstring.h:2062:19: note: Virtual function in base class
hisat2-2.2.1/sstring.h:3145:22: note: Function in derived class
hisat2-2.2.1/filebuf.h:513:11: style: Class 'BitpairOutFileBuf' is unsafe, 'BitpairOutFileBuf::out_' can leak by wrong usage. [unsafeClassCanLeak]
hisat2-2.2.1/ds.h:3406:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/sstring.h:88:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:193:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:196:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:484:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:504:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/filebuf.h:686:15: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/read.h:211:9: style: The scope of the variable 'started' can be reduced. [variableScope]
hisat2-2.2.1/read.h:235:9: style: The scope of the variable 'started' can be reduced. [variableScope]
hisat2-2.2.1/ds.h:612:3: style: Unsigned expression 'len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/sstring.h:3419:46: warning: Either the condition '(poss)>(0)' is redundant or there is division by zero at line 3419. [zerodivcond]
hisat2-2.2.1/sstring.h:3418:3: note: Assuming that condition '(poss)>(0)' is not redundant
hisat2-2.2.1/sstring.h:3419:46: note: Division by zero
hisat2-2.2.1/filebuf.h:478:21: portability: Shifting a negative value is technically undefined behaviour [shiftNegativeLHS]
hisat2-2.2.1/ds.h:3249:14: style: Local variable 'i' shadows outer argument [shadowArgument]
hisat2-2.2.1/ds.h:3245:10: note: Shadowed declaration
hisat2-2.2.1/ds.h:3249:14: note: Shadow variable
hisat2-2.2.1/ds.h:3730:34: style: Parameter 'ol' can be declared as pointer to const [constParameter]
hisat2-2.2.1/sstring.h:1448:32: warning: Either the condition 'bpi==15' is redundant or there is signed integer overflow for expression '3<<(bpi<<1)'. [integerOverflowCond]
hisat2-2.2.1/sstring.h:1455:11: note: Assuming that condition 'bpi==15' is not redundant
hisat2-2.2.1/sstring.h:1448:32: note: Integer overflow
hisat2-2.2.1/sstring.h:1477:32: warning: Either the condition 'bpi==15' is redundant or there is signed integer overflow for expression '3<<(bpi<<1)'. [integerOverflowCond]
hisat2-2.2.1/sstring.h:1484:11: note: Assuming that condition 'bpi==15' is not redundant
hisat2-2.2.1/sstring.h:1477:32: note: Integer overflow
hisat2-2.2.1/sstring.h:1515:32: warning: Either the condition 'bp==15' is redundant or there is signed integer overflow for expression '3<<(bp<<1)'. [integerOverflowCond]
hisat2-2.2.1/sstring.h:1517:10: note: Assuming that condition 'bp==15' is not redundant
hisat2-2.2.1/sstring.h:1515:32: note: Integer overflow
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.alignment [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.pen [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.n [uninitStructMember]
hisat2-2.2.1/gfm.h:2497:11: warning: Assert statement calls a function which may have desired side effects: 'fchr'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:2504:11: warning: Assert statement calls a function which may have desired side effects: 'ftab'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:2505:11: warning: Assert statement calls a function which may have desired side effects: 'eftab'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:2506:11: warning: Assert statement calls a function which may have desired side effects: 'fchr'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:2507:11: warning: Assert statement calls a function which may have desired side effects: 'offs'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:2508:11: warning: Assert statement calls a function which may have desired side effects: 'rstarts'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6128:16: warning: Assert statement calls a function which may have desired side effects: 'rstarts'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6227:40: warning: Assert statement calls a function which may have desired side effects: 'fchr'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6299:20: warning: Assert statement calls a function which may have desired side effects: 'ftab'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6300:20: warning: Assert statement calls a function which may have desired side effects: 'eftab'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6634:16: warning: Assert statement calls a function which may have desired side effects: 'rstarts'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6635:16: warning: Assert statement calls a function which may have desired side effects: 'offs'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6636:16: warning: Assert statement calls a function which may have desired side effects: 'ftab'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6637:16: warning: Assert statement calls a function which may have desired side effects: 'eftab'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6874:30: warning: Assert statement calls a function which may have desired side effects: 'rstarts'. [assertWithSideEffect]
hisat2-2.2.1/gfm.h:6876:30: warning: Assert statement calls a function which may have desired side effects: 'rstarts'. [assertWithSideEffect]
hisat2-2.2.1/blockwise_sa.h:372:14: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/blockwise_sa.h:446:14: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/blockwise_sa.h:749:13: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/blockwise_sa.h:115:10: warning: Assert statement calls a function which may have desired side effects: 'suffixItrIsReset'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:1319:19: warning: Assert statement calls a function which may have desired side effects: 'ptr'. [assertWithSideEffect]
hisat2-2.2.1/alt.h:180:13: warning: Comparison of a boolean expression with an integer. [compareBoolExpressionWithInt]
hisat2-2.2.1/aligner_result.h:249:29: style:inconclusive: Boolean expression 'repeat_' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
hisat2-2.2.1/aligner_result.h:252:49: style:inconclusive: Boolean expression 'knownTranscripts_' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
hisat2-2.2.1/aligner_result.h:253:47: style:inconclusive: Boolean expression 'nearSpliceSites_' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
hisat2-2.2.1/multikey_qsort.h:1083:21: warning: Either the condition '(c)<=4' is redundant or the array 'bkts[4]' is accessed at index 4, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/multikey_qsort.h:1079:13: note: Assuming that condition '(c)<=4' is not redundant
hisat2-2.2.1/multikey_qsort.h:1083:21: note: Array index out of bounds
hisat2-2.2.1/multikey_qsort.h:1083:31: warning: Either the condition '(c)<=4' is redundant or the array 'cnts[5]' is accessed at index 5, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/multikey_qsort.h:1079:13: note: Assuming that condition '(c)<=4' is not redundant
hisat2-2.2.1/multikey_qsort.h:1083:31: note: Array index out of bounds
hisat2-2.2.1/timer.h:75:12: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
hisat2-2.2.1/ref_read.h:229:3: warning: Either the condition '-1!=(lastc)' is redundant or toupper() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:255'. [invalidFunctionArg]
hisat2-2.2.1/ref_read.h:182:2: note: Assuming that condition '-1!=(lastc)' is not redundant
hisat2-2.2.1/ref_read.h:194:4: note: c is assigned 'lastc' here.
hisat2-2.2.1/ref_read.h:229:3: note: Invalid argument
hisat2-2.2.1/ds.h:536:3: error: Using 'memset' on class that contains a virtual function. [memsetClass]
hisat2-2.2.1/aligner_result.h:902:2: warning: Member variable 'AlnRes::repeat_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_result.h:914:5: warning:inconclusive: Member variable 'AlnRes::drd' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
hisat2-2.2.1/aligner_result.h:914:5: warning: Member variable 'AlnRes::seedival_' is not initialized in the copy constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_result.h:966:13: warning:inconclusive: Member variable 'AlnRes::drd' is not assigned a value in 'AlnRes::operator='. [operatorEqVarError]
hisat2-2.2.1/aligner_result.h:966:13: warning: Member variable 'AlnRes::seedival_' is not assigned a value in 'AlnRes::operator='. [operatorEqVarError]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM < uint32_t >::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_gbwtLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_sz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_gbwtSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_offMask' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_eftabLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_eftabSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_ftabLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_ftabSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_offsLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_offsSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_lineSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_sideSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_sideGbwtSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_sideGbwtLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_numSides' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_numLines' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_gbwtTotLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_gbwtTotSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint32_t >::_numNodes' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:100:9: warning:inconclusive: Member variable 'Edge::from' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:100:9: warning:inconclusive: Member variable 'Edge::to' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:305:9: warning: Member variable 'CompositeNode::value' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::tid' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::toff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::joinedOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint32_t >::alleleID' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:50:5: warning: Member variable 'RepeatCoord < uint32_t >::alleleID' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/ls.h:43:1: style: The class 'LarssonSadakane < int >' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable < uint32_t , 1024 , 2 >::zeroT_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < uint32_t >::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < uint32_t >::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < uint32_t >::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/ref_read.h:48:3: performance: Variable 'msg' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_result.h:925:9: performance: Variable 'score_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_result.h:926:9: performance: Variable 'oscore_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_result.h:927:9: performance: Variable 'refcoord_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_result.h:929:9: performance: Variable 'refival_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/timer.h:50:7: style:inconclusive: Technically the member function 'Timer::write' can be const. [functionConst]
hisat2-2.2.1/repeat_kmer.h:170:10: style:inconclusive: Technically the member function 'RB_Alignment_CMPbyLen::operator()' can be const. [functionConst]
hisat2-2.2.1/splice_site.h:544:10: style:inconclusive: Technically the member function 'SpliceSiteDB::empty' can be const. [functionConst]
hisat2-2.2.1/aligner_result.h:1357:8: performance:inconclusive: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_result.cpp:1043:14: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aligner_result.h:1357:8: note: Technically the member function 'AlnRes::printQuals' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM < uint32_t >::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM < uint32_t >::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM < uint32_t >::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM < uint32_t >::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph < uint32_t >::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph < uint32_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB < uint32_t >::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index < uint32_t >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci < uint32_t >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele < uint32_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/diff_sample.h:509:7: style:inconclusive: Technically the member function 'DifferenceCoverSample < S2bDnaString >::print' can be const. [functionConst]
hisat2-2.2.1/ls.h:187:14: performance:inconclusive: Technically the member function 'LarssonSadakane < int >::bucketsort' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < tthread :: thread * >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < tthread :: thread * >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < uint32_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < uint32_t >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/splice_site.h:185:15: style: Virtual function 'reset' is called from constructor 'SpliceSitePos()' at line 87. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/splice_site.h:87:20: note: Calling reset
hisat2-2.2.1/splice_site.h:185:15: note: reset is a virtual function
hisat2-2.2.1/splice_site.h:322:15: style: Virtual function 'reset' is called from constructor 'SpliceSite()' at line 256. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/splice_site.h:256:17: note: Calling reset
hisat2-2.2.1/splice_site.h:322:15: note: reset is a virtual function
hisat2-2.2.1/blockwise_sa.h:352:15: style: Virtual function 'reset' is called from constructor 'KarkkainenBlockwiseSA < S2bDnaString >(const S2bDnaString&__text,uint32_t __bucketSz,int __nthreads,uint32_t __dcV,uint32_t __seed=0,bool __sanityCheck=false,bool __passMemExc=false,bool __verbose=false,std::string base_fname="",std::ostream&__logger=std::cout)' at line 206. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/blockwise_sa.h:206:29: note: Calling reset
hisat2-2.2.1/blockwise_sa.h:352:15: note: reset is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 >(const std::basic_string<uint32_t>&str)' at line 1680. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1680:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 >(const uint32_t*b,long sz)' at line 1692. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1692:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable < uint32_t , 1024 , 2 >(const uint32_t*b)' at line 1704. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1704:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString < char >(const std::basic_string<char>&str)' at line 541. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:541:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString < char >(const char*b,long sz)' at line 552. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:552:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:685:15: style: Virtual function 'install' is called from constructor 'SString < char >(const char*b)' at line 563. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:563:3: note: Calling install
hisat2-2.2.1/sstring.h:685:15: note: install is a virtual function
hisat2-2.2.1/timer.h:37:2: style: Class 'Timer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/gfm.h:306:2: style: Class 'GFMFileOpenException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_result.h:2028:2: style: Class 'RedundantAlns' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/gbwt_graph.h:347:9: style: Struct 'TempNodeLabelCmp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sstring.h:1661:2: style: Class 'SStringExpandable < uint32_t , 1024 , 2 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3806:2: style: Class 'RedBlack < SpliceSitePos , uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet < RedundantCell >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1747:2: style: Class 'ESet < RedundantCell >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray < tthread :: thread * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray < uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/splice_site.h:322:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/splice_site.h:185:15: note: Virtual function in base class
hisat2-2.2.1/splice_site.h:322:15: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:269:24: style: The function 'nextSuffix' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:90:21: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:269:24: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:331:18: style: The function 'nextBlock' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:146:15: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:331:18: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:337:15: style: The function 'hasMoreBlocks' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:148:15: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:337:15: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:352:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:138:15: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:352:15: note: Function in derived class
hisat2-2.2.1/blockwise_sa.h:361:15: style: The function 'isReset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/blockwise_sa.h:140:15: note: Virtual function in base class
hisat2-2.2.1/blockwise_sa.h:361:15: note: Function in derived class
hisat2-2.2.1/diff_sample.h:228:13: style: Condition 'keepGoing' is always false [knownConditionTrueFalse]
hisat2-2.2.1/diff_sample.h:199:22: note: Assignment 'keepGoing=false', assigned value is 0
hisat2-2.2.1/diff_sample.h:228:13: note: Condition 'keepGoing' is always false
hisat2-2.2.1/aligner_result.h:1613:8: style: Condition 'sameChr' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_result.h:1612:19: note: Assignment 'sameChr=true', assigned value is 1
hisat2-2.2.1/aligner_result.h:1613:8: note: Condition 'sameChr' is always true
hisat2-2.2.1/gfm.h:2974:44: style: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:2973:44: note: Assuming that condition 'l._sideByteOff+l._by>zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:2969:83: note: Assuming that condition 'l._sideByteOff+l._by>=zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:2974:44: note: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true
hisat2-2.2.1/gfm.h:3034:44: style: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:3033:44: note: Assuming that condition 'l._sideByteOff+l._by>zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:3029:73: note: Assuming that condition 'l._sideByteOff+l._by>=zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:3034:44: note: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true
hisat2-2.2.1/gfm.h:3113:44: style: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:3112:44: note: Assuming that condition 'l._sideByteOff+l._by>zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:3108:73: note: Assuming that condition 'l._sideByteOff+l._by>=zGbwtByteOff' is not redundant
hisat2-2.2.1/gfm.h:3113:44: note: Condition 'l._sideByteOff+l._by==zGbwtByteOff' is always true
hisat2-2.2.1/gfm.h:3214:12: style: Condition '!usePOPCNT' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:3170:26: note: Assignment 'usePOPCNT=false', assigned value is 0
hisat2-2.2.1/gfm.h:3214:12: note: Condition '!usePOPCNT' is always true
hisat2-2.2.1/gfm.h:3436:12: style: Condition '!usePOPCNT' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:3388:26: note: Assignment 'usePOPCNT=false', assigned value is 0
hisat2-2.2.1/gfm.h:3436:12: note: Condition '!usePOPCNT' is always true
hisat2-2.2.1/gfm.h:6263:20: style: Condition 'loadFtab' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:6241:12: note: Assuming that condition 'loadFtab' is not redundant
hisat2-2.2.1/gfm.h:6263:20: note: Condition 'loadFtab' is always true
hisat2-2.2.1/gfm.h:6938:16: style: Condition 'mirror' is always false [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:6929:8: note: Assuming that condition 'mirror' is not redundant
hisat2-2.2.1/gfm.h:6938:16: note: Condition 'mirror' is always false
hisat2-2.2.1/gfm.h:6942:20: style: Condition '!mirror' is always true [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:6929:8: note: Assuming that condition 'mirror' is not redundant
hisat2-2.2.1/gfm.h:6942:20: note: Condition '!mirror' is always true
hisat2-2.2.1/util.h:46:27: style: Condition 'value!=0' is always false [knownConditionTrueFalse]
hisat2-2.2.1/util.h:46:13: note: Assuming that condition 'value<=0' is not redundant
hisat2-2.2.1/util.h:46:27: note: Condition 'value!=0' is always false
hisat2-2.2.1/gfm.h:6866:9: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/alt.h:180:13: style: Comparing expression of type 'bool' against value 1. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/diff_sample.h:614:3: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/gfm.h:4595:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:4757:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:4779:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:5076:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:5201:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:5221:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:5448:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:2217:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:6070:13: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:6848:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:570:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:623:21: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:957:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:978:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:1022:17: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/blockwise_sa.h:1072:29: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:2807:9: warning: sscanf() without field width limits can crash with huge input data. [invalidscanf]
hisat2-2.2.1/endian_swap.h:31:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4946:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4949:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:5381:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:3151:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:3792:27: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:3794:27: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:3813:31: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:3815:31: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:3984:23: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:3986:23: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4058:23: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4060:23: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6061:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6119:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6169:27: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6171:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6254:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6284:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6379:36: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6387:50: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6407:38: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6410:40: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:6656:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2012:36: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2041:36: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2310:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:2337:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gbwt_graph.h:867:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:174:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/radix_sort.h:160:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/blockwise_sa.h:445:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:757:37: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:760:42: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:867:23: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/diff_sample.h:868:23: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/ds.h:4176:14: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/blockwise_sa.h:501:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/gfm.h:4010:17: style: Redundant initialization for 'bot'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/gfm.h:3975:21: note: bot is initialized
hisat2-2.2.1/gfm.h:4010:17: note: bot is overwritten
hisat2-2.2.1/gfm.h:4083:17: style: Redundant initialization for 'bot'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/gfm.h:4049:21: note: bot is initialized
hisat2-2.2.1/gfm.h:4083:17: note: bot is overwritten
hisat2-2.2.1/gfm.h:1736:46: style: The comparison 'seqlen <= 16' is always true. [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:1736:42: note: 'seqlen' is assigned value '16' here.
hisat2-2.2.1/gfm.h:1736:46: note: The comparison 'seqlen <= 16' is always true.
hisat2-2.2.1/gfm.h:1768:46: style: The comparison 'seqlen <= 16' is always true. [knownConditionTrueFalse]
hisat2-2.2.1/gfm.h:1768:42: note: 'seqlen' is assigned value '16' here.
hisat2-2.2.1/gfm.h:1768:46: note: The comparison 'seqlen <= 16' is always true.
hisat2-2.2.1/gfm.h:2857:9: style: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode]
hisat2-2.2.1/gbwt_graph.h:2622:5: style:inconclusive: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode]
hisat2-2.2.1/aligner_result.cpp:1061:31: style: The scope of the variable 'right' can be reduced. [variableScope]
hisat2-2.2.1/aligner_result.cpp:1111:31: style: The scope of the variable 'right' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:2254:7: style: The scope of the variable 'iter' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:2255:8: style: The scope of the variable 'first' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:4816:21: style: The scope of the variable 'pos' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:6091:10: style: The scope of the variable 'shmemLeader' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:6935:13: style: The scope of the variable 'lastorig' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:938:16: style: The scope of the variable 'lo' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1038:17: style: The scope of the variable 'kHi' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1038:27: style: The scope of the variable 'kLo' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1039:17: style: The scope of the variable 'jHi' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1039:27: style: The scope of the variable 'jLo' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1040:14: style: The scope of the variable 'kHiSoft' can be reduced. [variableScope]
hisat2-2.2.1/blockwise_sa.h:1040:31: style: The scope of the variable 'kLoSoft' can be reduced. [variableScope]
hisat2-2.2.1/diff_sample.h:742:16: style: The scope of the variable 'nextRank' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:101:8: style: The scope of the variable 'pl' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:101:18: style: The scope of the variable 'pn' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:102:7: style: The scope of the variable 's' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:128:7: style: The scope of the variable 'f' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:189:18: style: The scope of the variable 'd' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:189:21: style: The scope of the variable 'g' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:288:8: style: The scope of the variable 'pi' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:289:10: style: The scope of the variable 'j' can be reduced. [variableScope]
hisat2-2.2.1/ls.h:289:16: style: The scope of the variable 'sl' can be reduced. [variableScope]
hisat2-2.2.1/multikey_qsort.h:932:2: style: Unsigned expression 'lim' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_result.cpp:249:2: style: Unsigned expression 'rd_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_result.cpp:250:2: style: Unsigned expression 'rf_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_result.cpp:276:2: style: Unsigned expression 'rd_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_result.cpp:277:2: style: Unsigned expression 'rf_amt' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/gfm.h:6866:9: style: Unsigned expression 'this->plen()[i]' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/gbwt_graph.h:1715:14: style: Checking if unsigned expression 'p' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/gbwt_graph.h:2721:46: style: Checking if unsigned expression 'top' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/gbwt_graph.h:915:21: style: Checking if unsigned expression 'curr_len' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/alt.h:165:20: style: Checking if unsigned expression 'len' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/alt.h:174:20: style: Checking if unsigned expression 'len' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/diff_sample.h:614:3: style: Unsigned expression 'sz' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/util.h:35:15: style: Checking if unsigned expression 'quotient' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/util.h:46:13: style: Checking if unsigned expression 'value' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/aligner_result.cpp:900:8: style:inconclusive: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_result.h:820:37: note: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'.
hisat2-2.2.1/aligner_result.cpp:900:8: note: Function 'writeCigar' argument 2 names different: declaration 'oc' definition 'occ'.
hisat2-2.2.1/aligner_result.cpp:935:46: style:inconclusive: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_result.h:826:35: note: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'.
hisat2-2.2.1/aligner_result.cpp:935:46: note: Function 'writeMdz' argument 2 names different: declaration 'oc' definition 'occ'.
hisat2-2.2.1/gfm.h:5605:45: style:inconclusive: Function 'textOffToJoined' argument 2 names different: declaration 'tlen' definition 'textoff'. [funcArgNamesDifferent]
hisat2-2.2.1/gfm.h:2928:47: note: Function 'textOffToJoined' argument 2 names different: declaration 'tlen' definition 'textoff'.
hisat2-2.2.1/gfm.h:5605:45: note: Function 'textOffToJoined' argument 2 names different: declaration 'tlen' definition 'textoff'.
hisat2-2.2.1/gfm.h:5748:38: style:inconclusive: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'. [funcArgNamesDifferent]
hisat2-2.2.1/gfm.h:2472:12: note: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'.
hisat2-2.2.1/gfm.h:5748:38: note: Function 'contains' argument 2 names different: declaration 'top' definition 'otop'.
hisat2-2.2.1/gfm.h:5749:38: style:inconclusive: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'. [funcArgNamesDifferent]
hisat2-2.2.1/gfm.h:2473:12: note: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'.
hisat2-2.2.1/gfm.h:5749:38: note: Function 'contains' argument 3 names different: declaration 'bot' definition 'obot'.
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph < uint32_t >' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph < uint32_t >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph < uint32_t >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:2363:59: style:inconclusive: Function 'generateEdges' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1598:43: note: Function 'generateEdges' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:2363:59: note: Function 'generateEdges' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/diff_sample.h:154:16: style: Local variable 'ds' shadows outer variable [shadowVariable]
hisat2-2.2.1/diff_sample.h:150:5: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:154:16: note: Shadow variable
hisat2-2.2.1/diff_sample.h:241:8: style: Local variable 'i' shadows outer argument [shadowArgument]
hisat2-2.2.1/diff_sample.h:141:25: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:241:8: note: Shadow variable
hisat2-2.2.1/diff_sample.h:291:10: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/diff_sample.h:262:5: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:291:10: note: Shadow variable
hisat2-2.2.1/diff_sample.h:302:10: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/diff_sample.h:262:5: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:302:10: note: Shadow variable
hisat2-2.2.1/repeat_kmer.h:88:36: style: Local variable 'minimizer' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_kmer.h:70:32: note: Shadowed declaration
hisat2-2.2.1/repeat_kmer.h:88:36: note: Shadow variable
hisat2-2.2.1/aligner_result.h:325:18: style: Local variable 'score' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:311:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.h:325:18: note: Shadow variable
hisat2-2.2.1/aligner_result.h:339:18: style: Local variable 'splicescore' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:317:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.h:339:18: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:490:7: style: Local variable 'fw' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:1273:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:490:7: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:497:13: style: Local variable 'reflen' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:1330:10: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:497:13: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:498:13: style: Local variable 'refoff' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:1123:17: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:498:13: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1182:11: style: Local variable 'best' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2255:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1182:11: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1182:20: style: Local variable 'secbest' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2279:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1182:20: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1182:32: style: Local variable 'bestPaired' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2233:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1182:32: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1182:44: style: Local variable 'secbestPaired' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2234:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1182:44: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1187:7: style: Local variable 'paired' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2237:11: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1187:7: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1189:14: style: Local variable 'numAlns1' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2244:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1189:14: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1189:28: style: Local variable 'numAlns2' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2245:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1189:28: note: Shadow variable
hisat2-2.2.1/aligner_result.cpp:1189:42: style: Local variable 'numAlnsPaired' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_result.h:2246:14: note: Shadowed declaration
hisat2-2.2.1/aligner_result.cpp:1189:42: note: Shadow variable
hisat2-2.2.1/gfm.h:716:31: style: Local variable 'alts' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2451:40: note: Shadowed declaration
hisat2-2.2.1/gfm.h:716:31: note: Shadow variable
hisat2-2.2.1/gfm.h:718:24: style: Local variable 'altnames' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2452:33: note: Shadowed declaration
hisat2-2.2.1/gfm.h:718:24: note: Shadow variable
hisat2-2.2.1/gfm.h:1629:39: style: Local variable 'alts' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2451:40: note: Shadowed declaration
hisat2-2.2.1/gfm.h:1629:39: note: Shadow variable
hisat2-2.2.1/gfm.h:1886:44: style: Local variable 'alts' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2451:40: note: Shadowed declaration
hisat2-2.2.1/gfm.h:1886:44: note: Shadow variable
hisat2-2.2.1/gfm.h:1939:29: style: Local variable 'tmp_len' shadows outer variable [shadowVariable]
hisat2-2.2.1/gfm.h:1365:25: note: Shadowed declaration
hisat2-2.2.1/gfm.h:1939:29: note: Shadow variable
hisat2-2.2.1/gfm.h:2165:48: style: Local variable 'repeat' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2458:17: note: Shadowed declaration
hisat2-2.2.1/gfm.h:2165:48: note: Shadow variable
hisat2-2.2.1/gfm.h:2312:48: style: Local variable 'ftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2438:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:2312:48: note: Shadow variable
hisat2-2.2.1/gfm.h:2968:21: style: Local variable 'zGbwtByteOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2433:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:2968:21: note: Shadow variable
hisat2-2.2.1/gfm.h:2972:21: style: Local variable 'zGbwtBpOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2434:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:2972:21: note: Shadow variable
hisat2-2.2.1/gfm.h:3028:21: style: Local variable 'zGbwtByteOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2433:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:3028:21: note: Shadow variable
hisat2-2.2.1/gfm.h:3032:21: style: Local variable 'zGbwtBpOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2434:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:3032:21: note: Shadow variable
hisat2-2.2.1/gfm.h:3107:21: style: Local variable 'zGbwtByteOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2433:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:3107:21: note: Shadow variable
hisat2-2.2.1/gfm.h:3111:21: style: Local variable 'zGbwtBpOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2434:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:3111:21: note: Shadow variable
hisat2-2.2.1/gfm.h:4716:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4716:31: note: Shadow variable
hisat2-2.2.1/gfm.h:4736:11: style: Local variable 'fchr' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2437:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4736:11: note: Shadow variable
hisat2-2.2.1/gfm.h:4737:17: style: Local variable 'ftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2438:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4737:17: note: Shadow variable
hisat2-2.2.1/gfm.h:4787:10: style: Local variable 'fw' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2457:17: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4787:10: note: Shadow variable
hisat2-2.2.1/gfm.h:5068:20: style: Local variable 'eftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2439:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5068:20: note: Shadow variable
hisat2-2.2.1/gfm.h:5155:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5155:31: note: Shadow variable
hisat2-2.2.1/gfm.h:5178:14: style: Local variable 'fchr' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2437:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5178:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5179:20: style: Local variable 'ftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2438:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5179:20: note: Shadow variable
hisat2-2.2.1/gfm.h:5229:10: style: Local variable 'fw' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2457:17: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5229:10: note: Shadow variable
hisat2-2.2.1/gfm.h:5440:20: style: Local variable 'eftab' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2439:20: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5440:20: note: Shadow variable
hisat2-2.2.1/gfm.h:6003:25: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6003:25: note: Shadow variable
hisat2-2.2.1/gfm.h:6146:14: style: Local variable 'shmemLeader' shadows outer variable [shadowVariable]
hisat2-2.2.1/gfm.h:6091:10: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6146:14: note: Shadow variable
hisat2-2.2.1/gfm.h:6206:17: style: Local variable 'zOff' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2432:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6206:17: note: Shadow variable
hisat2-2.2.1/gfm.h:6407:31: style: Local variable 'offs' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2440:23: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6407:31: note: Shadow variable
hisat2-2.2.1/gfm.h:6608:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6608:31: note: Shadow variable
hisat2-2.2.1/gfm.h:6692:5: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6692:5: note: Shadow variable
hisat2-2.2.1/gfm.h:6791:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6791:31: note: Shadow variable
hisat2-2.2.1/gfm.h:6792:10: style: Local variable 'fw' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2457:17: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6792:10: note: Shadow variable
hisat2-2.2.1/gfm.h:6831:31: style: Local variable 'gh' shadows outer function [shadowFunction]
hisat2-2.2.1/gfm.h:2430:35: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6831:31: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:2506:21: style: Local variable 'past_nodes' shadows outer variable [shadowVariable]
hisat2-2.2.1/gbwt_graph.h:1684:21: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:2506:21: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:2739:25: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/gbwt_graph.h:2712:17: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:2739:25: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:639:25: style: Local variable 's' shadows outer argument [shadowArgument]
hisat2-2.2.1/gbwt_graph.h:363:50: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:639:25: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:955:25: style: Local variable 's' shadows outer variable [shadowVariable]
hisat2-2.2.1/gbwt_graph.h:870:26: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:955:25: note: Shadow variable
hisat2-2.2.1/radix_sort.h:270:13: style: Local variable 'st' shadows outer variable [shadowVariable]
hisat2-2.2.1/radix_sort.h:200:8: note: Shadowed declaration
hisat2-2.2.1/radix_sort.h:270:13: note: Shadow variable
hisat2-2.2.1/repeat.h:284:45: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:284:45: note: Shadow variable
hisat2-2.2.1/repeat.h:335:21: style: Local variable 'r' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat.h:311:24: note: Shadowed declaration
hisat2-2.2.1/repeat.h:335:21: note: Shadow variable
hisat2-2.2.1/repeat.h:364:47: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:364:47: note: Shadow variable
hisat2-2.2.1/repeat.h:386:47: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:386:47: note: Shadow variable
hisat2-2.2.1/repeat.h:446:47: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:446:47: note: Shadow variable
hisat2-2.2.1/repeat.h:518:47: style: Local variable 'repeatMap' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat.h:201:44: note: Shadowed declaration
hisat2-2.2.1/repeat.h:518:47: note: Shadow variable
hisat2-2.2.1/diff_sample.h:477:19: style: Local variable 'ds' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:495:25: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:477:19: note: Shadow variable
hisat2-2.2.1/diff_sample.h:560:11: style: Local variable 'v' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:486:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:560:11: note: Shadow variable
hisat2-2.2.1/diff_sample.h:568:12: style: Local variable 'd' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:491:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:568:12: note: Shadow variable
hisat2-2.2.1/diff_sample.h:599:25: style: Local variable 'ds' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:495:25: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:599:25: note: Shadow variable
hisat2-2.2.1/diff_sample.h:601:11: style: Local variable 'v' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:486:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:601:11: note: Shadow variable
hisat2-2.2.1/diff_sample.h:602:11: style: Local variable 'd' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:491:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:602:11: note: Shadow variable
hisat2-2.2.1/diff_sample.h:729:14: style: Local variable 'v' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:486:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:729:14: note: Shadow variable
hisat2-2.2.1/diff_sample.h:963:25: style: Local variable 'dmap' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:496:25: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:963:25: note: Shadow variable
hisat2-2.2.1/diff_sample.h:969:11: style: Local variable 'v' shadows outer function [shadowFunction]
hisat2-2.2.1/diff_sample.h:486:11: note: Shadowed declaration
hisat2-2.2.1/diff_sample.h:969:11: note: Shadow variable
hisat2-2.2.1/aligner_result.h:1216:25: performance: Function parameter 'score' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2096:12: performance: Function parameter 'best1' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2097:12: performance: Function parameter 'secbest1' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2098:12: performance: Function parameter 'best2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2099:12: performance: Function parameter 'secbest2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2100:12: performance: Function parameter 'bestPaired' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2101:12: performance: Function parameter 'secbestPaired' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2170:12: performance: Function parameter 'best1' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2171:12: performance: Function parameter 'secbest1' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2172:12: performance: Function parameter 'best2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2173:12: performance: Function parameter 'secbest2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2174:12: performance: Function parameter 'bestPaired' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.h:2175:12: performance: Function parameter 'secbestPaired' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.cpp:140:21: performance: Function parameter 'score' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_result.cpp:147:21: performance: Function parameter 'refcoord' should be passed by const reference. [passedByValue]
hisat2-2.2.1/blockwise_sa.h:202:34: performance: Function parameter 'base_fname' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat_kmer.h:355:35: style: Variable 'position' can be declared as reference to const [constVariable]
hisat2-2.2.1/repeat_kmer.h:384:35: style: Variable 'position' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:4592:21: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:4753:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:4775:21: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:5072:21: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:5197:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:5217:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:5444:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:3740:61: style: Parameter 'tloc' can be declared as reference to const [constParameter]
hisat2-2.2.1/gfm.h:3740:87: style: Parameter 'bloc' can be declared as reference to const [constParameter]
hisat2-2.2.1/gfm.h:6067:28: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:6160:32: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:6309:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:6349:36: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gfm.h:6846:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/gbwt_graph.h:1519:51: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathNodeFrom' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hisat2-2.2.1/gbwt_graph.h:1970:14: note: You might need to cast the function pointer here
hisat2-2.2.1/gbwt_graph.h:1519:51: note: Parameter 'a' can be declared as reference to const
hisat2-2.2.1/gbwt_graph.h:1523:50: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathNodeKey' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hisat2-2.2.1/gbwt_graph.h:2507:104: note: You might need to cast the function pointer here
hisat2-2.2.1/gbwt_graph.h:1523:50: note: Parameter 'a' can be declared as reference to const
hisat2-2.2.1/gbwt_graph.h:1569:49: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathEdgeTo' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
hisat2-2.2.1/gbwt_graph.h:2610:102: note: You might need to cast the function pointer here
hisat2-2.2.1/gbwt_graph.h:1569:49: note: Parameter 'a' can be declared as reference to const
hisat2-2.2.1/gbwt_graph.h:2314:46: style: Variable 'ref_nodes' can be declared as reference to const [constVariable]
hisat2-2.2.1/gbwt_graph.h:2341:46: style: Variable 'ref_nodes' can be declared as reference to const [constVariable]
hisat2-2.2.1/gbwt_graph.h:2343:46: style: Variable 'nodes' can be declared as reference to const [constVariable]
hisat2-2.2.1/gbwt_graph.h:109:29: style: Parameter 'f_in' can be declared as reference to const [constParameter]
hisat2-2.2.1/gbwt_graph.h:121:34: style: Parameter 'a' can be declared as reference to const [constParameter]
hisat2-2.2.1/gbwt_graph.h:1418:28: style: Variable 'predecessor_cnode' can be declared as reference to const [constVariable]
hisat2-2.2.1/repeat.h:343:40: style: Variable 'allele' can be declared as reference to const [constVariable]
hisat2-2.2.1/alt.h:239:25: style: Parameter 'f_in' can be declared as reference to const [constParameter]
hisat2-2.2.1/blockwise_sa.h:568:28: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/blockwise_sa.h:621:32: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/blockwise_sa.h:955:28: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/blockwise_sa.h:1020:28: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/multikey_qsort.h:252:14: style: Parameter 's' can be declared as pointer to const [constParameter]
hisat2-2.2.1/multikey_qsort.h:291:14: style: Parameter 's' can be declared as pointer to const [constParameter]
hisat2-2.2.1/multikey_qsort.h:323:53: style: Parameter 's' can be declared as pointer to const [constParameter]
hisat2-2.2.1/multikey_qsort.h:877:14: style: Parameter 's' can be declared as pointer to const [constParameter]
hisat2-2.2.1/diff_sample.h:109:27: style: Parameter 'ts' can be declared as pointer to const [constParameter]
hisat2-2.2.1/diff_sample.h:121:37: style: Parameter 'ds' can be declared as pointer to const [constParameter]
hisat2-2.2.1/bitpack.h:45:18: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 44. [shiftTooManyBits]
hisat2-2.2.1/bitpack.h:44:2: note: Assuming that condition 'off<16' is not redundant
hisat2-2.2.1/bitpack.h:45:18: note: Shift
hisat2-2.2.1/bitpack.h:50:19: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 49. [shiftTooManyBits]
hisat2-2.2.1/bitpack.h:49:2: note: Assuming that condition 'off<16' is not redundant
hisat2-2.2.1/bitpack.h:50:19: note: Shift
hisat2-2.2.1/bitpack.h:72:21: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 71. [shiftTooManyBits]
hisat2-2.2.1/bitpack.h:71:5: note: Assuming that condition 'off<32' is not redundant
hisat2-2.2.1/bitpack.h:72:21: note: Shift
hisat2-2.2.1/bitpack.h:77:22: warning: Shifting 32-bit value by 32 bits is undefined behaviour. See condition at line 76. [shiftTooManyBits]
hisat2-2.2.1/bitpack.h:76:5: note: Assuming that condition 'off<32' is not redundant
hisat2-2.2.1/bitpack.h:77:22: note: Shift
hisat2-2.2.1/radix_sort.h:193:16: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
hisat2-2.2.1/radix_sort.h:192:33: note: Assignment 'log_size=sizeof(maxv)*8', assigned value is 32
hisat2-2.2.1/radix_sort.h:193:16: note: Shift
hisat2-2.2.1/endian_swap.h:52:28: error: Signed integer overflow for expression '0xff<<24'. [integerOverflow]
hisat2-2.2.1/endian_swap.h:126:28: error: Signed integer overflow for expression '0xff<<24'. [integerOverflow]
hisat2-2.2.1/repeat_kmer.h:218:25: style: Variable 'curr_in' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_kmer.h:219:26: style: Variable 'est_count' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:4626:11: style: Unused variable: name [unusedVariable]
hisat2-2.2.1/gfm.h:4622:18: style: Variable 'patoff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:4656:25: style: Variable 'patoff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:4657:11: style: Variable 'patoff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:4669:11: style: Variable 'patoff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:6935:22: style: Variable 'lastorig' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gfm.h:6951:22: style: Variable 'lastorig' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gbwt_graph.h:1945:11: style: Variable 'start' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/gbwt_graph.h:2148:11: style: Variable 'indiv' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_seed.h:1672:25: warning: Assert statement calls a function which may have desired side effects: 'current'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:1749:25: warning: Assert statement calls a function which may have desired side effects: 'current'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:1762:27: warning: Assert statement calls a function which may have desired side effects: 'current'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2121:11: warning: Assert statement calls a function which may have desired side effects: 'sanityPartial'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2156:12: warning: Assert statement calls a function which may have desired side effects: 'sanityPartial'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2349:14: warning: Assert statement calls a function which may have desired side effects: 'sanityPartial'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2677:13: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2678:13: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2679:13: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2740:14: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2741:14: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2742:14: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2909:14: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2910:14: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2911:14: warning: Assert statement calls a function which may have desired side effects: 'acceptable'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed.h:2831:9: error: Address of local auto-variable assigned to a function parameter. [autoVariables]
hisat2-2.2.1/scoring.h:305:26: warning: Either the condition '(q)>=0' is redundant or the array 'mmpens[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
hisat2-2.2.1/scoring.h:304:3: note: Assuming that condition '(q)>=0' is not redundant
hisat2-2.2.1/scoring.h:305:26: note: Negative array index
hisat2-2.2.1/scoring.h:334:43: warning: Either the condition '(q)>=0' is redundant or the array 'matchBonuses[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
hisat2-2.2.1/scoring.h:333:3: note: Assuming that condition '(q)>=0' is not redundant
hisat2-2.2.1/scoring.h:334:43: note: Negative array index
hisat2-2.2.1/scoring.h:361:25: warning: Either the condition '(q)>=0' is redundant or the array 'npens[256]' is accessed at index -1, which is out of bounds. [negativeIndex]
hisat2-2.2.1/scoring.h:360:3: note: Assuming that condition '(q)>=0' is not redundant
hisat2-2.2.1/scoring.h:361:25: note: Negative array index
hisat2-2.2.1/ds.h:536:3: portability: Using memset() on class which contains a floating point number. [memsetClassFloat]
hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::matchBonuses' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::mmpens' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::npens' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::seq' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::qual' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::maxjump' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::seedoff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::seedoffidx' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::seedtypeidx' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:412:2: warning: Member variable 'InstantiatedSeed::nfiltered' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:616:2: warning: Member variable 'SeedResults::sorted_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::ebwtFw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::ebwtBw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::sc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::s_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::read_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::seq_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::qual_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::fw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::ca_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::bwops_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:1400:2: warning: Member variable 'SeedAligner::bwedits_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/scoring.h:170:3: performance: Variable 'scoreMin' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/scoring.h:171:3: performance: Variable 'nCeil' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_seed.h:471:7: performance:inconclusive: Technically the member function 'InstantiatedSeed::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed.h:1407:7: performance:inconclusive: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed.h:1611:28: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aligner_seed.h:1407:7: note: Technically the member function 'SeedAligner::instantiateSeq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/qual.h:117:10: style: Condition 'cc<33' is always false [knownConditionTrueFalse]
hisat2-2.2.1/qual.h:116:40: note: Assignment 'cc=solexaToPhred((int)c-64)+33', assigned value is greater than 32
hisat2-2.2.1/qual.h:117:10: note: Condition 'cc<33' is always false
hisat2-2.2.1/aligner_seed.h:2332:15: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_seed.h:2327:10: note: Assuming that condition 'ebwtfw' is not redundant
hisat2-2.2.1/aligner_seed.h:2332:15: note: Condition 'ebwtfw' is always true
hisat2-2.2.1/aligner_seed.h:2333:15: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_seed.h:2327:10: note: Assuming that condition 'ebwtfw' is not redundant
hisat2-2.2.1/aligner_seed.h:2333:15: note: Condition 'ebwtfw' is always true
hisat2-2.2.1/aligner_seed.h:2340:15: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_seed.h:2327:10: note: Assuming that condition 'ebwtfw' is not redundant
hisat2-2.2.1/aligner_seed.h:2340:15: note: Condition 'ebwtfw' is always true
hisat2-2.2.1/aligner_seed.h:2341:15: style: Condition 'ebwtfw' is always true [knownConditionTrueFalse]
hisat2-2.2.1/aligner_seed.h:2327:10: note: Assuming that condition 'ebwtfw' is not redundant
hisat2-2.2.1/aligner_seed.h:2341:15: note: Condition 'ebwtfw' is always true
hisat2-2.2.1/aligner_seed.h:2042:9: style: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_seed.h:2043:9: note: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'.
hisat2-2.2.1/aligner_seed.h:2042:9: note: Same expression used in consecutive assignments of 'halfFw' and 'halfBw'.
hisat2-2.2.1/aligner_seed.h:2866:6: style: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode]
hisat2-2.2.1/aligner_seed.h:2794:15: style: The scope of the variable 'insCons' can be reduced. [variableScope]
hisat2-2.2.1/aligner_seed.cpp:207:15: style: The scope of the variable 'cons' can be reduced. [variableScope]
hisat2-2.2.1/aligner_seed.h:1742:35: style:inconclusive: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_seed.h:1442:25: note: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'.
hisat2-2.2.1/aligner_seed.h:1742:35: note: Function 'searchAllSeeds' argument 7 names different: declaration 'hits' definition 'sr'.
hisat2-2.2.1/aligner_seed.cpp:50:59: style:inconclusive: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_seed.h:276:55: note: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'.
hisat2-2.2.1/aligner_seed.cpp:50:59: note: Function 'penaltyFuncBased' argument 1 names different: declaration 'func' definition 'f'.
hisat2-2.2.1/aligner_seed.cpp:97:20: style:inconclusive: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_seed.h:381:21: note: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'.
hisat2-2.2.1/aligner_seed.cpp:97:20: note: Function 'instantiate' argument 9 names different: declaration 'si' definition 'is'.
hisat2-2.2.1/aligner_seed.h:544:7: style: Local variable 'ns' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed.h:529:6: note: Shadowed declaration
hisat2-2.2.1/aligner_seed.h:544:7: note: Shadow variable
hisat2-2.2.1/aligner_seed.h:2477:22: style: Local variable 'tloc' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_seed.h:2465:21: note: Shadowed declaration
hisat2-2.2.1/aligner_seed.h:2477:22: note: Shadow variable
hisat2-2.2.1/aligner_seed.h:2477:28: style: Local variable 'bloc' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_seed.h:2465:27: note: Shadowed declaration
hisat2-2.2.1/aligner_seed.h:2477:28: note: Shadow variable
hisat2-2.2.1/aligner_seed.h:1621:43: style: Variable 'seedlen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_seed.h:2259:16: style: Variable 'offstr' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_seed.h:2825:22: style: Variable 'loff' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/group_walk.h:332:10: warning: Assert statement calls a function which may have desired side effects: 'repOkBasic'. [assertWithSideEffect]
hisat2-2.2.1/group_walk.h:453:19: warning: Assert statement calls a function which may have desired side effects: 'repOkBasic'. [assertWithSideEffect]
hisat2-2.2.1/aligner_seed2.h:546:15: warning: Assert statement calls a function which may have desired side effects: 'containsEx'. [assertWithSideEffect]
hisat2-2.2.1/sam.h:1242:9: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
hisat2-2.2.1/ds.h:536:3: portability: Using memset() on struct which contains a floating point number. [memsetClassFloat]
hisat2-2.2.1/random_util.h:50:2: warning: Member variable 'Random1toN::swaplist_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_util.h:50:2: warning: Member variable 'Random1toN::converted_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_util.h:55:2: warning: Member variable 'Random1toN::swaplist_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/random_util.h:55:2: warning: Member variable 'Random1toN::converted_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs::len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::pen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::depth' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:178:2: warning: Member variable 'DescentPriority::rootpri' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:630:2: warning: Member variable 'DescentRoot::l2r' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:630:2: warning: Member variable 'DescentRoot::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:630:2: warning: Member variable 'DescentRoot::pri' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::posFlag' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::d' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::topf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::botf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::topb' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::botb' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:835:2: warning: Member variable 'DescentEdge::off5p' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::rid_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::al5pi_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::al5pf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::l2r_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::gapadd_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::off5p_i_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::topf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::botf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::topb_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::botb_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::parent_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::pen_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::posid_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1060:2: warning: Member variable 'Descent::len_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1911:2: warning: Member variable 'DescentDriver::minsc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed2.h:1911:2: warning: Member variable 'DescentDriver::maxpen_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aln_sink.h:669:11: warning: Member variable 'AlnSink::numWrappers_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_driver.h:144:2: warning: Member variable 'AlignerDriver::paired_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_driver.h:98:3: performance: Variable 'rootIval_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_driver.h:156:3: performance: Variable 'totsz_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/aligner_driver.h:157:3: performance: Variable 'totfmops_' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/group_walk.h:400:7: performance:inconclusive: Technically the member function 'GWHit::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/group_walk.h:1480:7: style:inconclusive: Technically the member function 'GroupWalk2S::resolveAll' can be const. [functionConst]
hisat2-2.2.1/aligner_seed2.h:759:7: style:inconclusive: Technically the member function 'DescentPosFlags::rfgExplore' can be const. [functionConst]
hisat2-2.2.1/aligner_seed2.h:1204:7: performance:inconclusive: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed2.h:3354:24: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aligner_seed2.h:1204:7: note: Technically the member function 'Descent::print' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aligner_seed2.h:1219:7: style:inconclusive: Technically the member function 'Descent::collectEdits' can be const. [functionConst]
hisat2-2.2.1/aligner_seed2.h:2027:7: performance:inconclusive: Technically the member function 'DescentDriver::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_seed2.h:2379:7: performance:inconclusive: Technically the member function 'DescentPartialAlignmentSelector::compileBatch' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:177:7: performance:inconclusive: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:417:26: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:177:7: note: Technically the member function 'SamConfig::printRefName' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:187:7: performance:inconclusive: Technically the member function 'SamConfig::printOptFieldEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:210:7: performance:inconclusive: Technically the member function 'SamConfig::printOptFieldNewlineEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:282:7: performance:inconclusive: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:469:26: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:282:7: note: Technically the member function 'SamConfig::printHdLine' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:843:7: performance:inconclusive: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:1637:24: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:843:7: note: Technically the member function 'AlnSink::printAlSumm' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:881:7: performance:inconclusive: Technically the member function 'AlnSink::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:1220:28: style:inconclusive: Technically the member function 'AlnSinkWrap::reportingParams' can be const. [functionConst]
hisat2-2.2.1/random_util.h:50:2: style: Class 'Random1toN' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/random_util.h:55:2: style: Class 'Random1toN' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/group_walk.h:166:2: style: Struct 'GroupWalkState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_seed2.h:1911:2: style: Class 'DescentDriver' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aln_sink.h:411:2: style: Class 'ReportingState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:2459:2: style: Class 'EMap < DescentRedundancyKey , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:2471:2: style: Class 'EMap < DescentRedundancyKey , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/unique.h:111:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:77:16: note: Virtual function in base class
hisat2-2.2.1/unique.h:111:16: note: Function in derived class
hisat2-2.2.1/unique.h:186:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:77:16: note: Virtual function in base class
hisat2-2.2.1/unique.h:186:16: note: Function in derived class
hisat2-2.2.1/unique.h:446:16: style: The function 'mapq' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/unique.h:77:16: note: Virtual function in base class
hisat2-2.2.1/unique.h:446:16: note: Function in derived class
hisat2-2.2.1/aln_sink.h:1547:15: style: The function 'append' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/aln_sink.h:701:15: note: Virtual function in base class
hisat2-2.2.1/aln_sink.h:1547:15: note: Function in derived class
hisat2-2.2.1/aligner_driver.h:104:15: style: The function 'select' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/aligner_seed2.h:1830:15: note: Virtual function in base class
hisat2-2.2.1/aligner_driver.h:104:15: note: Function in derived class
hisat2-2.2.1/aligner_seed2.h:687:11: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_seed2.h:531:3: style:inconclusive: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode]
hisat2-2.2.1/aligner_seed2.h:573:3: style:inconclusive: Statements following return, break, continue, goto or throw will never be executed. [unreachableCode]
hisat2-2.2.1/aligner_seed2.h:3824:9: style: The scope of the variable 'nobranchDepth' can be reduced. [variableScope]
hisat2-2.2.1/unique.h:132:4: style: Unsigned expression 'best_bin' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/unique.h:138:5: style: Unsigned expression 'diff_bin' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aln_sink.h:3037:23: style:inconclusive: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'. [funcArgNamesDifferent]
hisat2-2.2.1/aln_sink.h:1605:15: note: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'.
hisat2-2.2.1/aln_sink.h:3037:23: note: Function 'appendMate' argument 13 names different: declaration 'mapq' definition 'mapqCalc'.
hisat2-2.2.1/group_walk.h:685:21: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:532:33: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:685:21: note: Shadow variable
hisat2-2.2.1/group_walk.h:716:21: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:532:33: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:716:21: note: Shadow variable
hisat2-2.2.1/group_walk.h:765:28: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:532:33: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:765:28: note: Shadow variable
hisat2-2.2.1/group_walk.h:811:29: style: Local variable 'n' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:765:21: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:811:29: note: Shadow variable
hisat2-2.2.1/group_walk.h:856:25: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/group_walk.h:765:28: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:856:25: note: Shadow variable
hisat2-2.2.1/group_walk.h:1118:52: style: Local variable 'range' shadows outer argument [shadowArgument]
hisat2-2.2.1/group_walk.h:1040:11: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:1118:52: note: Shadow variable
hisat2-2.2.1/group_walk.h:1199:52: style: Local variable 'range' shadows outer argument [shadowArgument]
hisat2-2.2.1/group_walk.h:1040:11: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:1199:52: note: Shadow variable
hisat2-2.2.1/group_walk.h:1306:27: style: Local variable 'range' shadows outer argument [shadowArgument]
hisat2-2.2.1/group_walk.h:1040:11: note: Shadowed declaration
hisat2-2.2.1/group_walk.h:1306:27: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3118:11: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3118:11: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3182:13: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3182:13: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3212:14: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3212:14: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3263:12: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3263:12: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:3290:13: style: Local variable 'edit' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_seed2.h:1145:14: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:3290:13: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:4132:11: style: Local variable 'nopts' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_seed2.h:4106:10: note: Shadowed declaration
hisat2-2.2.1/aligner_seed2.h:4132:11: note: Shadow variable
hisat2-2.2.1/aligner_seed2.h:838:8: performance: Function parameter 'e_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:840:19: performance: Function parameter 'pri_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:874:8: performance: Function parameter 'e_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:876:19: performance: Function parameter 'pri_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:977:26: performance: Function parameter 'e' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_seed2.h:580:39: style: Variable 'map' can be declared as reference to const [constVariable]
hisat2-2.2.1/aligner_seed2.h:4136:27: style: Variable 'nopts' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/unique.h:229:20: style: Variable 'secbest' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/unique.h:461:20: style: Variable 'secbest' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/sam.h:1242:9: style: Variable 'first' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aln_sink.h:3013:2: style: Variable 'firstfield' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_bt.cpp:1463:20: warning: Assert statement calls a function which may have desired side effects: 'ned'. [assertWithSideEffect]
hisat2-2.2.1/aligner_bt.cpp:1587:20: warning: Assert statement calls a function which may have desired side effects: 'ned'. [assertWithSideEffect]
hisat2-2.2.1/aligner_bt.cpp:1593:20: warning: Assert statement calls a function which may have desired side effects: 'ned'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:2380:19: warning: Assert statement calls a function which may have desired side effects: 'ptr'. [assertWithSideEffect]
hisat2-2.2.1/mask.h:64:31: warning: Either the condition 'mask<32' is redundant or the array 'alts5[32]' is accessed at index 32, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/mask.h:63:2: note: Assuming that condition 'mask<32' is not redundant
hisat2-2.2.1/mask.h:64:31: note: Array index out of bounds
hisat2-2.2.1/aligner_sw_common.h:42:2: warning: Member variable 'SwResult::nup' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw_common.h:42:2: warning: Member variable 'SwResult::ndn' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/dp_framer.h:61:2: warning: Member variable 'DPRect::refl_pretrim' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/dp_framer.h:61:2: warning: Member variable 'DPRect::refr_pretrim' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/dp_framer.h:61:2: warning: Member variable 'DPRect::maxgap' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::sortedSel_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::cur_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nmm_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nnmm_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdop_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfop_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdex_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfex_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nmmPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nnmmPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdopPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfopPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrdexPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::nrfexPrune_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::row_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_bt.h:548:11: warning: Member variable 'BtBranchTracer::col_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/dp_framer.h:241:7: performance:inconclusive: Technically the member function 'DynProgFramer::trimToRef' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/dp_framer.h:61:2: style: Struct 'DPRect' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/dp_framer.h:126:2: style: Class 'DynProgFramer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet < unsigned long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:1747:2: style: Class 'ESet < unsigned long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/sse_util.h:386:6: style: Condition 'debug_' is always true [knownConditionTrueFalse]
hisat2-2.2.1/sse_util.h:370:12: note: Assignment 'debug_=true', assigned value is 1
hisat2-2.2.1/sse_util.h:386:6: note: Condition 'debug_' is always true
hisat2-2.2.1/aligner_bt.cpp:551:12: style: Condition 'rowc<0' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_bt.cpp:521:23: note: Assuming that condition 'rowc<0' is not redundant
hisat2-2.2.1/aligner_bt.cpp:551:12: note: Condition 'rowc<0' is always false
hisat2-2.2.1/aligner_bt.cpp:551:24: style: Condition 'colc<0' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_bt.cpp:521:11: note: Assuming that condition 'colc<0' is not redundant
hisat2-2.2.1/aligner_bt.cpp:551:24: note: Condition 'colc<0' is always false
hisat2-2.2.1/aligner_bt.cpp:1098:12: style: Condition 'rowc<0' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_bt.cpp:1066:23: note: Assuming that condition 'rowc<0' is not redundant
hisat2-2.2.1/aligner_bt.cpp:1098:12: note: Condition 'rowc<0' is always false
hisat2-2.2.1/aligner_bt.cpp:1098:24: style: Condition 'colc<0' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_bt.cpp:1066:11: note: Assuming that condition 'colc<0' is not redundant
hisat2-2.2.1/aligner_bt.cpp:1098:24: note: Condition 'colc<0' is always false
hisat2-2.2.1/aligner_bt.cpp:1332:7: style: Condition 'prune' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_bt.cpp:1322:17: note: Assignment 'prune=false', assigned value is 0
hisat2-2.2.1/aligner_bt.cpp:1332:7: note: Condition 'prune' is always false
hisat2-2.2.1/aligner_bt.cpp:1528:17: style: Condition 'hi-lo<hi_sm-lo_sm' is always false [knownConditionTrueFalse]
hisat2-2.2.1/aligner_bt.cpp:1515:13: note: Assuming that condition 'newhi>newlo' is not redundant
hisat2-2.2.1/aligner_bt.cpp:1527:19: note: lo_sm is assigned 'newlo' here.
hisat2-2.2.1/aligner_bt.cpp:1527:36: note: Assignment 'hi_sm=newhi', assigned value is less than symbolic=lo_sm
hisat2-2.2.1/aligner_bt.cpp:1528:17: note: Condition 'hi-lo<hi_sm-lo_sm' is always false
hisat2-2.2.1/sse_util.h:410:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/sse_util.h:487:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_bt.cpp:704:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_bt.cpp:705:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_bt.cpp:716:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_bt.cpp:717:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/mask.h:76:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/aligner_bt.cpp:1170:9: style: The scope of the variable 'iters' can be reduced. [variableScope]
hisat2-2.2.1/aligner_bt.cpp:696:25: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:696:25: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:726:5: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:726:5: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:727:5: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:727:5: style: Unsigned expression 'xi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:755:7: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:755:7: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:760:7: style: Unsigned expression 'yi-1' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:760:7: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:852:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:852:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:853:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:853:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:854:4: style: Unsigned expression 'yi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_bt.cpp:854:4: style: Unsigned expression 'xi' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/sse_util.h:218:12: style: Local variable 'last_alloc_' shadows outer variable [shadowVariable]
hisat2-2.2.1/sse_util.h:314:11: note: Shadowed declaration
hisat2-2.2.1/sse_util.h:218:12: note: Shadow variable
hisat2-2.2.1/aligner_bt.h:736:12: style: Local variable 'row' shadows outer argument [shadowArgument]
hisat2-2.2.1/aligner_bt.h:687:18: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.h:736:12: note: Shadow variable
hisat2-2.2.1/aligner_bt.h:736:24: style: Local variable 'col' shadows outer argument [shadowArgument]
hisat2-2.2.1/aligner_bt.h:688:18: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.h:736:24: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:356:10: style: Local variable 'mod' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_bt.cpp:68:9: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:356:10: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:420:10: style: Local variable 'empty' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_bt.h:602:7: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:420:10: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:531:11: style: Local variable 'cur' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_bt.cpp:358:12: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:531:11: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:963:10: style: Local variable 'empty' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_bt.h:602:7: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:963:10: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:1076:11: style: Local variable 'cur' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_bt.cpp:903:12: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:1076:11: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:1177:9: style: Local variable 'matches' shadows outer function [shadowFunction]
hisat2-2.2.1/mask.h:48:20: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:1177:9: note: Shadow variable
hisat2-2.2.1/aligner_bt.cpp:1487:11: style: Local variable 'diag' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_bt.cpp:1476:10: note: Shadowed declaration
hisat2-2.2.1/aligner_bt.cpp:1487:11: note: Shadow variable
hisat2-2.2.1/aligner_bt.h:337:8: performance: Function parameter 'e' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_bt.cpp:1143:7: performance: Function parameter 'e' should be passed by const reference. [passedByValue]
hisat2-2.2.1/aligner_bt.cpp:647:12: style: Variable 'xi' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_bt.cpp:670:20: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_bt.cpp:670:39: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::inited_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::nrow_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::ncol_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::nvecrow_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::nveccol_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::wperv_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::vecshift_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::nvecPerCol_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::colstride_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: warning: Member variable 'SSEMatrix::rowstride_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::qprofStride_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::gbarStride_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::maxPen_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::maxBonus_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::lastIter_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::lastWord_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:409:2: warning: Member variable 'SSEData::bias_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_swsse.h:108:2: style: Struct 'SSEMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_swsse.h:409:2: style: Struct 'SSEData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_swsse.cpp:48:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/aligner_swsse.h:233:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse.h:236:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse.cpp:83:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse.cpp:86:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse.h:125:10: style: Local variable 'elt' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_swsse.h:222:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse.h:125:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse.h:137:10: style: Local variable 'elt' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_swsse.h:222:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse.h:137:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse.h:149:10: style: Local variable 'elt' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_swsse.h:222:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse.h:149:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse.h:161:10: style: Local variable 'elt' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_swsse.h:222:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse.h:161:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse.h:173:10: style: Local variable 'elt' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_swsse.h:222:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse.h:173:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse.h:185:10: style: Local variable 'elt' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_swsse.h:222:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse.h:185:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse.cpp:43:21: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rd_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qu_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdfw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdrc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qufw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::qurc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdi_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::fw_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::refidx_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::reflen_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rect_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rfi_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rff_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rdgap_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::rfgap_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::enable8_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::extend_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::minsc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nceil_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sse8succ_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sse16succ_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseU8fwBuilt_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseU8rcBuilt_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseI16fwBuilt_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::sseI16rcBuilt_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltst_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltsc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw.h:207:11: warning: Member variable 'SwAligner::nbtfiltdo_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_sw_nuc.h:119:14: style:inconclusive: Technically the member function 'DpBtCandidate::dominatedBy' can be const. [functionConst]
hisat2-2.2.1/aligner_sw.cpp:199:8: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_sw.cpp:332:8: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_sw.h:565:10: style: The scope of the variable 'nrej' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw.cpp:84:2: style: Unsigned expression 'readGaps' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_sw.cpp:85:2: style: Unsigned expression 'refGaps' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_sw.cpp:923:18: style: Local variable 'col' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw.cpp:741:10: note: Shadowed declaration
hisat2-2.2.1/aligner_sw.cpp:923:18: note: Shadow variable
hisat2-2.2.1/aligner_sw.cpp:924:18: style: Local variable 'row' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw.cpp:740:10: note: Shadowed declaration
hisat2-2.2.1/aligner_sw.cpp:924:18: note: Shadow variable
hisat2-2.2.1/aligner_sw_nuc.h:54:12: performance: Function parameter 'score_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.nedsz [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.aedsz [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.celsz [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.row [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.col [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.gaps [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.readGaps [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.refGaps [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.ct [uninitStructMember]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:943:29: warning: Assert statement calls a function which may have desired side effects: 'fvec'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:944:29: warning: Assert statement calls a function which may have desired side effects: 'hvec'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1672:32: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1701:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1726:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1750:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1774:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1836:29: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:785:5: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:779:5: note: First condition
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:785:5: note: Second condition
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:607:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:660:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:661:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:662:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:710:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:711:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:712:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1137:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1233:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1392:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1400:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1405:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1451:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1452:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1453:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1508:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1509:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1510:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1511:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1512:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1513:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:416:9: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:365:19: note: vhilsw is initialized
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:416:9: note: vhilsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:412:9: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:366:19: note: vlolsw is initialized
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:412:9: note: vlolsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:884:9: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:831:19: note: vhilsw is initialized
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:884:9: note: vhilsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:880:9: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:832:19: note: vlolsw is initialized
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:880:9: note: vlolsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:690:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:691:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:690:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:425:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:893:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1794:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1331:17: style:inconclusive: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw.h:542:18: note: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1331:17: note: Function 'backtraceNucleotidesEnd2EndSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:77:8: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:77:8: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:605:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:372:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:605:12: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:644:10: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:644:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:648:17: style: Local variable 'j' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:491:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:648:17: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:708:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:461:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:708:16: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1135:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:840:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:1135:12: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:187:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:188:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:189:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:190:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:430:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:431:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_i16.cpp:432:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:936:29: warning: Assert statement calls a function which may have desired side effects: 'fvec'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:937:29: warning: Assert statement calls a function which may have desired side effects: 'hvec'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1659:32: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1688:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1713:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1737:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1761:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1827:29: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:783:5: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:777:5: note: First condition
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:783:5: note: Second condition
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:599:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:652:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:653:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:654:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:705:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:707:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1122:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1218:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1377:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1385:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1390:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1436:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1437:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1438:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1493:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1494:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1495:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1496:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1497:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1498:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:414:9: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:375:19: note: vhilsw is initialized
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:414:9: note: vhilsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:879:9: style: Redundant initialization for 'vhilsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:840:19: note: vhilsw is initialized
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:879:9: note: vhilsw is overwritten
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:685:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:686:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:685:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:423:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:888:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1781:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1316:17: style:inconclusive: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw.h:533:18: note: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1316:17: note: Function 'backtraceNucleotidesEnd2EndSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:77:8: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:77:8: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:597:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:373:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:597:12: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:636:10: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:636:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:640:17: style: Local variable 'j' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:487:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:640:17: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:703:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:459:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:703:16: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1120:12: style: Local variable 'vtmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:838:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:1120:12: note: Shadow variable
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:184:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:185:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:186:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:187:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:428:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:429:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_ee_u8.cpp:430:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/banded.h:33:7: performance:inconclusive: Technically the member function 'BandedSseAligner::init' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/banded.h:44:7: performance:inconclusive: Technically the member function 'BandedSseAligner::nextAlignment' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1108:29: warning: Assert statement calls a function which may have desired side effects: 'fvec'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1109:29: warning: Assert statement calls a function which may have desired side effects: 'hvec'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:2033:32: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:2062:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:2087:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:2111:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:2135:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:2199:29: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:959:5: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:953:5: note: First condition
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:959:5: note: Second condition
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:755:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:756:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:757:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:805:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:807:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1515:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1554:33: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1743:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1751:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1756:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1806:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1807:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1808:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1863:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1864:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1865:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1866:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1867:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1868:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:425:9: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:365:19: note: vlolsw is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:425:9: note: vlolsw is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:422:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:366:19: note: vmax is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:422:7: note: vmax is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:910:7: style: Redundant initialization for 'vtmp'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:374:19: note: vtmp is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:910:7: note: vtmp is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1055:9: style: Redundant initialization for 'vlolsw'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1005:19: note: vlolsw is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1055:9: note: vlolsw is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1052:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1006:19: note: vmax is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1052:7: note: vmax is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1373:7: style: Redundant initialization for 'vtmp'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1012:19: note: vtmp is initialized
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1373:7: note: vtmp is overwritten
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:785:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:786:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:785:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1064:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:2153:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1489:49: warning: Either the condition '(bonus)>(0)' is redundant or there is division by zero at line 1489. [zerodivcond]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1488:2: note: Assuming that condition '(bonus)>(0)' is not redundant
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1489:49: note: Division by zero
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1677:17: style:inconclusive: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw.h:524:18: note: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1677:17: note: Function 'backtraceNucleotidesLocalSseI16' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:77:8: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:77:8: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:694:9: style: Local variable 'cmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:634:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:694:9: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:739:10: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:739:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:743:17: style: Local variable 'j' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:563:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:743:17: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:803:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:471:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:803:16: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1510:13: style: Local variable 'max' shadows outer function [shadowFunction]
hisat2-2.2.1/splice_site.h:76:29: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:1510:13: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:185:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:186:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:187:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:188:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:439:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:441:20: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_i16.cpp:442:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/sstring.h:1642:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1649:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1674:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1686:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1698:11: warning: Member variable 'SStringExpandable::zero_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/sstring.h:1758:26: warning: Member variable 'SStringExpandable::zero_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
hisat2-2.2.1/sstring.h:1758:26: warning:inconclusive: Member variable 'SStringExpandable::zeroT_' is not assigned a value in 'SStringExpandable::operator='. [operatorEqVarError]
hisat2-2.2.1/ls.h:43:1: style: The class 'LarssonSadakane' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
hisat2-2.2.1/ls.h:187:14: performance:inconclusive: Technically the member function 'LarssonSadakane::bucketsort' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const std::basic_string<T>&str)' at line 1680. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1680:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const T*b,long sz)' at line 1692. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1692:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:1841:15: style: Virtual function 'install' is called from constructor 'SStringExpandable(const T*b)' at line 1704. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:1704:3: note: Calling install
hisat2-2.2.1/sstring.h:1841:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:3034:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2868. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2868:5: note: Calling installColors
hisat2-2.2.1/sstring.h:3034:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:3026:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2870. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2870:5: note: Calling installChars
hisat2-2.2.1/sstring.h:3026:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:3012:15: style: Virtual function 'installColors' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2889. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2889:5: note: Calling installColors
hisat2-2.2.1/sstring.h:3012:15: note: installColors is a virtual function
hisat2-2.2.1/sstring.h:2998:15: style: Virtual function 'installChars' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2891. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2891:5: note: Calling installChars
hisat2-2.2.1/sstring.h:2998:15: note: installChars is a virtual function
hisat2-2.2.1/sstring.h:2983:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const char*b,long sz,bool chars=false,bool colors=false)' at line 2894. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2894:4: note: Calling install
hisat2-2.2.1/sstring.h:2983:15: note: install is a virtual function
hisat2-2.2.1/sstring.h:2964:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const char*b,bool chars=false,bool colors=false)' at line 2907. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2907:3: note: Calling install
hisat2-2.2.1/sstring.h:2964:15: note: install is a virtual function
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1117:29: warning: Assert statement calls a function which may have desired side effects: 'fvec'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1118:29: warning: Assert statement calls a function which may have desired side effects: 'hvec'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:2027:32: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:2056:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:2081:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:2105:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:2129:31: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:2193:29: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:965:5: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:958:5: note: First condition
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:965:5: note: Second condition
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:761:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:762:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:763:24: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:810:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:812:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1517:31: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1554:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1747:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1755:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1760:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1806:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1807:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1808:26: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1863:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1864:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1865:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1866:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1867:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1868:41: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:440:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:378:19: note: vmax is initialized
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:440:7: note: vmax is overwritten
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:919:7: style: Redundant initialization for 'vtmp'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:386:19: note: vtmp is initialized
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:919:7: note: vtmp is overwritten
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1059:7: style: Redundant initialization for 'vmax'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1014:19: note: vmax is initialized
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1059:7: note: vmax is overwritten
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1378:7: style: Redundant initialization for 'vtmp'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1020:19: note: vtmp is initialized
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1378:7: note: vtmp is overwritten
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:790:13: style: Same expression used in consecutive assignments of 'cpi' and 'cpimod'. [duplicateAssignExpression]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:791:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:790:13: note: Same expression used in consecutive assignments of 'cpi' and 'cpimod'.
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1073:17: style: The scope of the variable 'pvScore' can be reduced. [variableScope]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:2147:2: style: Unsigned expression 'col' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1490:49: warning: Either the condition '(bonus)>(0)' is redundant or there is division by zero at line 1490. [zerodivcond]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1489:2: note: Assuming that condition '(bonus)>(0)' is not redundant
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1490:49: note: Division by zero
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1686:17: style:inconclusive: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw.h:515:18: note: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1686:17: note: Function 'backtraceNucleotidesLocalSseU8' argument 7 names different: declaration 'rand' definition 'rnd'.
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:77:8: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:77:8: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:701:9: style: Local variable 'cmp' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:642:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:701:9: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:745:10: style: Local variable 'done' shadows outer function [shadowFunction]
hisat2-2.2.1/aligner_sw.h:350:7: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:745:10: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:749:17: style: Local variable 'j' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:569:10: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:749:17: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:808:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:488:13: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:808:16: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1513:13: style: Local variable 'max' shadows outer function [shadowFunction]
hisat2-2.2.1/splice_site.h:76:29: note: Shadowed declaration
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:1513:13: note: Shadow variable
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:199:22: style: Variable 'sc_h_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:200:22: style: Variable 'sc_e_left' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:201:22: style: Variable 'sc_h_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:202:22: style: Variable 'sc_f_up' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:459:19: style: Variable 'pvELeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:460:57: style: Variable 'pvFRight' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_swsse_loc_u8.cpp:461:19: style: Variable 'pvHLeft' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/edit.cpp:393:9: style:inconclusive: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'. [funcArgNamesDifferent]
hisat2-2.2.1/edit.h:363:10: note: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'.
hisat2-2.2.1/edit.cpp:393:9: note: Function 'repOk' argument 4 names different: declaration 'trim5' definition 'trimBeg'.
hisat2-2.2.1/edit.cpp:394:9: style:inconclusive: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'. [funcArgNamesDifferent]
hisat2-2.2.1/edit.h:364:10: note: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'.
hisat2-2.2.1/edit.cpp:394:9: note: Function 'repOk' argument 5 names different: declaration 'trim3' definition 'trimEnd'.
hisat2-2.2.1/edit.cpp:468:32: style:inconclusive: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'. [funcArgNamesDifferent]
hisat2-2.2.1/edit.h:288:34: note: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'.
hisat2-2.2.1/edit.cpp:468:32: note: Function 'clipLo' argument 1 names different: declaration 'edits' definition 'ed'.
hisat2-2.2.1/edit.cpp:485:32: style:inconclusive: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'. [funcArgNamesDifferent]
hisat2-2.2.1/edit.h:293:34: note: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'.
hisat2-2.2.1/edit.cpp:485:32: note: Function 'clipHi' argument 1 names different: declaration 'edits' definition 'ed'.
hisat2-2.2.1/edit.cpp:487:9: style: Local variable 'max' shadows outer function [shadowFunction]
hisat2-2.2.1/splice_site.h:76:29: note: Shadowed declaration
hisat2-2.2.1/edit.cpp:487:9: note: Shadow variable
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:266:13: performance: Variable 'id' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sstring.h:2964:15: style: Virtual function 'install' is called from constructor 'SDnaStringExpandable(const std::basic_string<char>&str,bool chars=false,bool colors=false)' at line 2873. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/sstring.h:2873:4: note: Calling install
hisat2-2.2.1/sstring.h:2964:15: note: install is a virtual function
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gfm.cpp:45:37: style:inconclusive: Function 'adjustEbwtBase' argument 2 names different: declaration 'ebwtFileBase' definition 'gfmFileBase'. [funcArgNamesDifferent]
hisat2-2.2.1/gfm.h:6972:37: note: Function 'adjustEbwtBase' argument 2 names different: declaration 'ebwtFileBase' definition 'gfmFileBase'.
hisat2-2.2.1/gfm.cpp:45:37: note: Function 'adjustEbwtBase' argument 2 names different: declaration 'ebwtFileBase' definition 'gfmFileBase'.
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::item_bit_size_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::elm_bit_size_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::items_per_block_bit_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::items_per_block_bit_mask_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::items_per_block_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::cur_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::sz_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:36:5: warning: Member variable 'BitPackedArray::block_size_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/bit_packed_array.h:82:10: style: Unused private function: 'BitPackedArray::expand' [unusedPrivateFunction]
hisat2-2.2.1/bit_packed_array.h:70:21: performance:inconclusive: Technically the member function 'BitPackedArray::bitToMask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/bit_packed_array.cpp:65:19: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/bit_packed_array.cpp:126:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/bit_packed_array.cpp:31:39: style:inconclusive: Function 'get' argument 1 names different: declaration 'idx' definition 'index'. [funcArgNamesDifferent]
hisat2-2.2.1/bit_packed_array.h:46:27: note: Function 'get' argument 1 names different: declaration 'idx' definition 'index'.
hisat2-2.2.1/bit_packed_array.cpp:31:39: note: Function 'get' argument 1 names different: declaration 'idx' definition 'index'.
hisat2-2.2.1/bit_packed_array.cpp:165:46: style: Parameter 'block' can be declared as pointer to const [constParameter]
hisat2-2.2.1/hisat2_build_main.cpp:54:27: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2_main.cpp:53:27: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2_build.cpp:473:15: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_build.cpp:474:14: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_build.cpp:476:15: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_build.cpp:492:16: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_build.cpp:493:15: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_build.cpp:495:16: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/hgfm.h:1839:28: warning: Assert statement calls a function which may have desired side effects: 'suffixItrIsReset'. [assertWithSideEffect]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM::mmFile5_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM::mmFile6_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:281:2: warning: Member variable 'RFM::mmFile1_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:281:2: warning: Member variable 'RFM::mmFile2_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM < TIndexOffU >::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < TIndexOffU >::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < TIndexOffU >::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < TIndexOffU >::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < TIndexOffU >::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < TIndexOffU >::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < TIndexOffU >::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < TIndexOffU >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < TIndexOffU >::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < TIndexOffU >::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < TIndexOffU >::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/hgfm.h:1606:9: performance: Variable '_in5Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/hgfm.h:1607:9: performance: Variable '_in6Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/rfm.h:328:9: performance: Variable '_in1Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/rfm.h:329:9: performance: Variable '_in2Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM < TIndexOffU >::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM < TIndexOffU >::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM < TIndexOffU >::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM < TIndexOffU >::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph < TIndexOffU >::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph < TIndexOffU >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB < TIndexOffU >::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index < TIndexOffU >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci < TIndexOffU >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele < TIndexOffU >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/diff_sample.h:509:7: style:inconclusive: Technically the member function 'DifferenceCoverSample < SString < char > >::print' can be const. [functionConst]
hisat2-2.2.1/blockwise_sa.h:352:15: style: Virtual function 'reset' is called from constructor 'KarkkainenBlockwiseSA < SString < char > >(const SString < char >&__text,uint32_t __bucketSz,int __nthreads,uint32_t __dcV,uint32_t __seed=0,bool __sanityCheck=false,bool __passMemExc=false,bool __verbose=false,std::string base_fname="",std::ostream&__logger=std::cout)' at line 206. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/blockwise_sa.h:206:29: note: Calling reset
hisat2-2.2.1/blockwise_sa.h:352:15: note: reset is a virtual function
hisat2-2.2.1/hgfm.h:1388:8: style: Condition 'loadFtab' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hgfm.h:1366:6: note: Assuming that condition 'loadFtab' is not redundant
hisat2-2.2.1/hgfm.h:1388:8: note: Condition 'loadFtab' is always true
hisat2-2.2.1/hgfm.h:395:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:417:3: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:705:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:823:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:843:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:1064:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hisat2_build.cpp:826:21: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:1205:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/hgfm.h:582:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:585:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1002:25: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/rfm.h:533:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1805:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1196:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1243:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1293:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1296:16: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1379:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1409:17: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1482:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1490:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1513:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1515:20: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hgfm.h:1524:19: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2_build.cpp:281:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hgfm.h:2023:13: style: The scope of the variable 'cumlen' can be reduced. [variableScope]
hisat2-2.2.1/hgfm.h:1209:7: style: The scope of the variable 'shmemLeader' can be reduced. [variableScope]
hisat2-2.2.1/hgfm.h:1145:9: style: Checking if unsigned expression 'len' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/hgfm.h:1352:14: style: Checking if unsigned expression 'i' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph < TIndexOffU >' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph < TIndexOffU >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph < TIndexOffU >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/hgfm.h:1117:58: style:inconclusive: Function 'readIntoMemory' argument 11 names different: declaration 'needEntireRev' definition 'entireRev'. [funcArgNamesDifferent]
hisat2-2.2.1/hgfm.h:297:11: note: Function 'readIntoMemory' argument 11 names different: declaration 'needEntireRev' definition 'entireRev'.
hisat2-2.2.1/hgfm.h:1117:58: note: Function 'readIntoMemory' argument 11 names different: declaration 'needEntireRev' definition 'entireRev'.
hisat2-2.2.1/gfm.h:4367:13: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:63:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4367:13: note: Shadow variable
hisat2-2.2.1/gfm.h:4369:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:66:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4369:13: note: Shadow variable
hisat2-2.2.1/gfm.h:4370:13: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:67:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4370:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6479:13: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:63:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6479:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6481:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:66:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6481:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6482:13: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:67:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6482:13: note: Shadow variable
hisat2-2.2.1/gfm.h:5975:14: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:63:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5975:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5979:14: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:66:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5979:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5984:14: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:67:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5984:14: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:1775:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:70:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:1775:16: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:372:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:70:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:372:16: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:880:13: style: Local variable 'nthreads' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:77:12: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:880:13: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:893:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:70:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:893:16: note: Shadow variable
hisat2-2.2.1/hgfm.h:2269:45: style: Local variable 'alt' shadows outer variable [shadowVariable]
hisat2-2.2.1/hgfm.h:2265:34: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2269:45: note: Shadow variable
hisat2-2.2.1/hgfm.h:2303:51: style: Local variable 'haplotype' shadows outer variable [shadowVariable]
hisat2-2.2.1/hgfm.h:2299:40: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2303:51: note: Shadow variable
hisat2-2.2.1/hgfm.h:2310:41: style: Local variable 'alt_i' shadows outer variable [shadowVariable]
hisat2-2.2.1/hgfm.h:2267:29: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2310:41: note: Shadow variable
hisat2-2.2.1/hgfm.h:2583:10: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:63:16: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2583:10: note: Shadow variable
hisat2-2.2.1/hgfm.h:2585:10: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:66:16: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2585:10: note: Shadow variable
hisat2-2.2.1/hgfm.h:2589:10: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_build.cpp:67:16: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2589:10: note: Shadow variable
hisat2-2.2.1/hgfm.h:1270:8: style: Local variable 'shmemLeader' shadows outer variable [shadowVariable]
hisat2-2.2.1/hgfm.h:1209:7: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:1270:8: note: Shadow variable
hisat2-2.2.1/hgfm.h:391:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:413:21: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:701:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:819:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:839:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:1060:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/rfm.h:459:21: style: Variable 'ref' can be declared as reference to const [constVariable]
hisat2-2.2.1/hisat2_build.cpp:821:32: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:1202:22: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:1284:23: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:1433:21: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hgfm.h:1452:24: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/rfm.h:843:9: style: Instance of 'LocalRFM < uint32_t >' object is destroyed immediately. [unusedScopedObject]
hisat2-2.2.1/hgfm.h:2349:21: style: Instance of 'LocalGFM < uint16_t , uint32_t >' object is destroyed immediately. [unusedScopedObject]
hisat2-2.2.1/hgfm.h:1252:16: warning: Assert statement calls a function which may have desired side effects: 'rstarts'. [assertWithSideEffect]
hisat2-2.2.1/hgfm.h:1352:28: warning: Assert statement calls a function which may have desired side effects: 'fchr'. [assertWithSideEffect]
hisat2-2.2.1/hgfm.h:1424:17: warning: Assert statement calls a function which may have desired side effects: 'ftab'. [assertWithSideEffect]
hisat2-2.2.1/hgfm.h:1425:17: warning: Assert statement calls a function which may have desired side effects: 'eftab'. [assertWithSideEffect]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM < uint32_t , uint16_t >::_nrefs' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM < uint32_t , uint16_t >::_nlocalGFMs' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM < uint32_t , uint16_t >::mmFile5_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hgfm.h:1559:2: warning: Member variable 'HGFM < uint32_t , uint16_t >::mmFile6_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM < uint16_t >::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_gbwtLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_sz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_gbwtSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_offMask' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_eftabLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_eftabSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_ftabLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_ftabSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_offsLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_offsSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_lineSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_sideSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_sideGbwtSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_sideGbwtLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_numSides' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_numLines' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_gbwtTotLen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_gbwtTotSz' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < uint16_t >::_numNodes' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::tid' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::toff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::joinedOff' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < uint16_t >::alleleID' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:50:5: warning: Member variable 'RepeatCoord < uint16_t >::alleleID' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < uint16_t >::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < uint16_t >::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < uint16_t >::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM < uint16_t >::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM < uint16_t >::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM < uint16_t >::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM < uint16_t >::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph < uint16_t >::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph < uint16_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB < uint16_t >::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index < uint16_t >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci < uint16_t >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele < uint16_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hisat2_inspect.cpp:617:39: style: Condition 'entireReverse' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hisat2_inspect.cpp:585:23: note: Assignment 'entireReverse=false', assigned value is 0
hisat2-2.2.1/hisat2_inspect.cpp:617:39: note: Condition 'entireReverse' is always false
hisat2-2.2.1/hgfm.h:1815:26: style: Condition 'tParam.last' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hgfm.h:1806:11: note: Assuming that condition '!tParam.last' is not redundant
hisat2-2.2.1/hgfm.h:1815:26: note: Condition 'tParam.last' is always false
hisat2-2.2.1/gfm.h:6866:9: style: Comparing expression of type 'unsigned short' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/gbwt_graph.h:383:38: style: Comparing expression of type 'unsigned short' against value 65536. Condition is always false. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hisat2_inspect.cpp:220:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2_inspect.cpp:135:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat2_inspect.cpp:730:10: style: The scope of the variable 'outfile' can be reduced. [variableScope]
hisat2-2.2.1/hisat2_inspect.cpp:283:13: style: The scope of the variable 'tlen' can be reduced. [variableScope]
hisat2-2.2.1/hgfm.h:1809:34: style: Checking if unsigned expression 'tParam.s.length()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/hgfm.h:1823:34: style: Checking if unsigned expression 'tParam.s.length()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph < uint16_t >' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph < uint16_t >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph < uint16_t >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/hisat2_inspect.cpp:419:25: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_inspect.cpp:387:16: note: Shadowed declaration
hisat2-2.2.1/hisat2_inspect.cpp:419:25: note: Shadow variable
hisat2-2.2.1/hisat2_repeat_main.cpp:54:27: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:33:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:49:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:64:21: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_index.cpp:67:52: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_init.cpp:184:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_init.cpp:208:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:32:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:58:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2lib/ht2_repeat.cpp:88:48: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat2_inspect.cpp:283:18: style: Variable 'tlen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/li_hla/alignments.hpp:46:2: warning: Member variable 'Alignments::fpSam' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/li_hla/alignments.hpp:46:2: warning: Member variable 'Alignments::fileName' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/li_hla/alignments.hpp:46:2: warning: Member variable 'Alignments::segments' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/li_hla/alignments.hpp:46:2: warning: Member variable 'Alignments::segCnt' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/li_hla/alignments.hpp:67:7: style:inconclusive: Technically the member function 'Alignments::IsOpened' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:160:6: style:inconclusive: Technically the member function 'Alignments::GetChromId' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:181:6: style:inconclusive: Technically the member function 'Alignments::GetChromLength' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:186:7: style:inconclusive: Technically the member function 'Alignments::GetMatePosition' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:208:7: style:inconclusive: Technically the member function 'Alignments::IsReverse' can be const. [functionConst]
hisat2-2.2.1/li_hla/alignments.hpp:215:7: style:inconclusive: Technically the member function 'Alignments::IsMateReverse' can be const. [functionConst]
hisat2-2.2.1/li_hla/main.cpp:443:6: style: The scope of the variable 'maxk' can be reduced. [variableScope]
hisat2-2.2.1/li_hla/main.cpp:303:8: style: Local variable 'size' shadows outer variable [shadowVariable]
hisat2-2.2.1/li_hla/main.cpp:292:7: note: Shadowed declaration
hisat2-2.2.1/li_hla/main.cpp:303:8: note: Shadow variable
hisat2-2.2.1/li_hla/main.cpp:149:42: performance: Searching before insertion is not necessary. Instead of 'positionToSnp[info.position+p]=tmpList' consider using 'positionToSnp.try_emplace(info.position+p, tmpList);'. [stlFindInsert]
hisat2-2.2.1/li_hla/main.cpp:225:35: performance: Searching before insertion is not necessary. Instead of 'alleleNameToId[fields[i]]=k' consider using 'alleleNameToId.try_emplace(fields[i], k);'. [stlFindInsert]
hisat2-2.2.1/li_hla/main.cpp:140:22: error: Uninitialized variable: info.nucleotide [uninitvar]
hisat2-2.2.1/li_hla/main.cpp:124:18: note: Assuming condition is true
hisat2-2.2.1/li_hla/main.cpp:140:22: note: Uninitialized variable: info.nucleotide
hisat2-2.2.1/li_hla/main.cpp:140:22: error: Uninitialized struct member: info.nucleotide [uninitStructMember]
hisat2-2.2.1/li_hla/main.cpp:14:6: style: struct member '_compatible::weight' is never used. [unusedStructMember]
hisat2-2.2.1/li_hla/main.cpp:28:7: style: struct member '_mdComponent::type' is never used. [unusedStructMember]
hisat2-2.2.1/li_hla/main.cpp:29:6: style: struct member '_mdComponent::length' is never used. [unusedStructMember]
hisat2-2.2.1/li_hla/main.cpp:30:6: style: struct member '_mdComponent::num' is never used. [unusedStructMember]
hisat2-2.2.1/li_hla/alignments.hpp:117:11: style: Variable 'num' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/li_hla/alignments.hpp:139:8: style: Variable 'mChrId' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/li_hla/main.cpp:443:11: style: Variable 'maxk' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/li_hla/main.cpp:452:10: style: Variable 'maxk' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/msvcc/codeStubs/getopt.c:528:60: style:inconclusive: Function '_getopt_internal' argument 3 names different: declaration 'shortopts' definition 'optstring'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:134:21: note: Function '_getopt_internal' argument 3 names different: declaration 'shortopts' definition 'optstring'.
hisat2-2.2.1/msvcc/codeStubs/getopt.c:528:60: note: Function '_getopt_internal' argument 3 names different: declaration 'shortopts' definition 'optstring'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:69:57: style:inconclusive: Function 'getopt_long' argument 3 names different: declaration 'shortopts' definition 'options'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:126:66: note: Function 'getopt_long' argument 3 names different: declaration 'shortopts' definition 'options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:69:57: note: Function 'getopt_long' argument 3 names different: declaration 'shortopts' definition 'options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:70:35: style:inconclusive: Function 'getopt_long' argument 4 names different: declaration 'longopts' definition 'long_options'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:127:32: note: Function 'getopt_long' argument 4 names different: declaration 'longopts' definition 'long_options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:70:35: note: Function 'getopt_long' argument 4 names different: declaration 'longopts' definition 'long_options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:70:54: style:inconclusive: Function 'getopt_long' argument 5 names different: declaration 'longind' definition 'opt_index'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:127:47: note: Function 'getopt_long' argument 5 names different: declaration 'longind' definition 'opt_index'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:70:54: note: Function 'getopt_long' argument 5 names different: declaration 'longind' definition 'opt_index'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:81:60: style:inconclusive: Function 'getopt_long_only' argument 3 names different: declaration 'shortopts' definition 'options'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:129:21: note: Function 'getopt_long_only' argument 3 names different: declaration 'shortopts' definition 'options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:81:60: note: Function 'getopt_long_only' argument 3 names different: declaration 'shortopts' definition 'options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:82:40: style:inconclusive: Function 'getopt_long_only' argument 4 names different: declaration 'longopts' definition 'long_options'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:130:37: note: Function 'getopt_long_only' argument 4 names different: declaration 'longopts' definition 'long_options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:82:40: note: Function 'getopt_long_only' argument 4 names different: declaration 'longopts' definition 'long_options'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:82:59: style:inconclusive: Function 'getopt_long_only' argument 5 names different: declaration 'longind' definition 'opt_index'. [funcArgNamesDifferent]
hisat2-2.2.1/msvcc/codeStubs/getopt.h:130:52: note: Function 'getopt_long_only' argument 5 names different: declaration 'longind' definition 'opt_index'.
hisat2-2.2.1/msvcc/codeStubs/getopt1.c:82:59: note: Function 'getopt_long_only' argument 5 names different: declaration 'longind' definition 'opt_index'.
hisat2-2.2.1/msvcc/codeStubs/sys/time.cpp:27:14: style: The scope of the variable 'tzflag' can be reduced. [variableScope]
hisat2-2.2.1/msvcc/codeStubs/sys/time.cpp:27:14: style: Variable 'tzflag' is not assigned a value. [unassignedVariable]
hisat2-2.2.1/pat.h:637:14: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/pat.h:772:15: warning: Assert statement calls a function which may have desired side effects: 'isOpen'. [assertWithSideEffect]
hisat2-2.2.1/pat.cpp:735:13: warning: Assert statement calls a function which may have desired side effects: 'isOpen'. [assertWithSideEffect]
hisat2-2.2.1/pat.cpp:693:44: warning: Either the condition 'c!=-1' is redundant or isspace() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:255'. [invalidFunctionArg]
hisat2-2.2.1/pat.cpp:665:38: note: Assuming that condition 'c!=-1' is not redundant
hisat2-2.2.1/pat.cpp:693:44: note: Invalid argument
hisat2-2.2.1/pat.cpp:701:44: warning: Either the condition 'c!=-1' is redundant or isspace() argument nr 1 can have invalid value. The value is -1 but the valid values are '0:255'. [invalidFunctionArg]
hisat2-2.2.1/pat.cpp:698:38: note: Assuming that condition 'c!=-1' is not redundant
hisat2-2.2.1/pat.cpp:701:44: note: Invalid argument
hisat2-2.2.1/pat.h:1216:2: warning: Member variable 'FastaContinuousPatternSource::buf_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/pat.h:1330:15: style: Virtual function 'resetForNextFile' is called from constructor 'FastaContinuousPatternSource(const EList < string , 128 >&infiles,const PatternParams&p)' at line 1222. Dynamic binding is not used. [virtualCallInConstructor]
hisat2-2.2.1/pat.h:1222:3: note: Calling resetForNextFile
hisat2-2.2.1/pat.h:1330:15: note: resetForNextFile is a virtual function
hisat2-2.2.1/pat.h:995:7: warning: The class 'FastaPatternSource' defines member variable with name 'first_' also defined in its parent class 'BufferedFilePatternSource'. [duplInheritedMember]
hisat2-2.2.1/pat.h:911:7: note: Parent variable 'BufferedFilePatternSource::first_'
hisat2-2.2.1/pat.h:995:7: note: Derived variable 'FastaPatternSource::first_'
hisat2-2.2.1/pat.h:1465:7: warning: The class 'FastqPatternSource' defines member variable with name 'first_' also defined in its parent class 'BufferedFilePatternSource'. [duplInheritedMember]
hisat2-2.2.1/pat.h:911:7: note: Parent variable 'BufferedFilePatternSource::first_'
hisat2-2.2.1/pat.h:1465:7: note: Derived variable 'FastqPatternSource::first_'
hisat2-2.2.1/pat.h:1619:7: warning: The class 'RawPatternSource' defines member variable with name 'first_' also defined in its parent class 'BufferedFilePatternSource'. [duplInheritedMember]
hisat2-2.2.1/pat.h:911:7: note: Parent variable 'BufferedFilePatternSource::first_'
hisat2-2.2.1/pat.h:1619:7: note: Derived variable 'RawPatternSource::first_'
hisat2-2.2.1/pat.h:592:2: style: Class 'WrappedPatternSourcePerThread' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/pat.h:619:2: style: Class 'WrappedPatternSourcePerThreadFactory' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/pat.h:368:15: style: The function 'addWrapper' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:284:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:368:15: note: Function in derived class
hisat2-2.2.1/pat.h:378:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:285:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:378:15: note: Function in derived class
hisat2-2.2.1/pat.h:390:15: style: The function 'nextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:287:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:390:15: note: Function in derived class
hisat2-2.2.1/pat.h:403:33: style: The function 'readCnt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:297:33: note: Virtual function in base class
hisat2-2.2.1/pat.h:403:33: note: Function in derived class
hisat2-2.2.1/pat.h:454:15: style: The function 'addWrapper' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:284:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:454:15: note: Function in derived class
hisat2-2.2.1/pat.h:467:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:285:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:467:15: note: Function in derived class
hisat2-2.2.1/pat.h:482:15: style: The function 'nextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:287:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:482:15: note: Function in derived class
hisat2-2.2.1/pat.h:495:33: style: The function 'readCnt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:297:33: note: Virtual function in base class
hisat2-2.2.1/pat.h:495:33: note: Function in derived class
hisat2-2.2.1/pat.h:602:15: style: The function 'nextReadPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:523:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:602:15: note: Function in derived class
hisat2-2.2.1/pat.h:625:34: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:562:34: note: Virtual function in base class
hisat2-2.2.1/pat.h:625:34: note: Function in derived class
hisat2-2.2.1/pat.h:633:42: style: The function 'create' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:563:42: note: Virtual function in base class
hisat2-2.2.1/pat.h:633:42: note: Function in derived class
hisat2-2.2.1/pat.h:717:15: style: The function 'nextReadImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:216:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:717:15: note: Function in derived class
hisat2-2.2.1/pat.h:727:15: style: The function 'nextReadPairImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:200:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:727:15: note: Function in derived class
hisat2-2.2.1/pat.h:736:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:224:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:736:15: note: Function in derived class
hisat2-2.2.1/pat.h:786:15: style: The function 'nextReadImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:216:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:786:15: note: Function in derived class
hisat2-2.2.1/pat.h:816:15: style: The function 'nextReadPairImpl' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:200:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:816:15: note: Function in derived class
hisat2-2.2.1/pat.h:851:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:224:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:851:15: note: Function in derived class
hisat2-2.2.1/pat.h:943:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:851:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:943:15: note: Function in derived class
hisat2-2.2.1/pat.h:967:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:967:15: note: Function in derived class
hisat2-2.2.1/pat.h:975:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:975:15: note: Function in derived class
hisat2-2.2.1/pat.h:990:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:881:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:990:15: note: Function in derived class
hisat2-2.2.1/pat.h:1042:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1042:15: note: Function in derived class
hisat2-2.2.1/pat.h:1050:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1050:15: note: Function in derived class
hisat2-2.2.1/pat.h:1179:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1179:15: note: Function in derived class
hisat2-2.2.1/pat.h:1189:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1189:15: note: Function in derived class
hisat2-2.2.1/pat.h:1225:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:851:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1225:15: note: Function in derived class
hisat2-2.2.1/pat.h:1233:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1233:15: note: Function in derived class
hisat2-2.2.1/pat.h:1313:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1313:15: note: Function in derived class
hisat2-2.2.1/pat.h:1330:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:881:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1330:15: note: Function in derived class
hisat2-2.2.1/pat.h:1373:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:851:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1373:15: note: Function in derived class
hisat2-2.2.1/pat.h:1426:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1426:15: note: Function in derived class
hisat2-2.2.1/pat.h:1434:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1434:15: note: Function in derived class
hisat2-2.2.1/pat.h:1449:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:881:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1449:15: note: Function in derived class
hisat2-2.2.1/pat.h:1485:15: style: The function 'reset' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:851:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1485:15: note: Function in derived class
hisat2-2.2.1/pat.h:1493:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:862:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1493:15: note: Function in derived class
hisat2-2.2.1/pat.h:1588:15: style: The function 'readPair' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:871:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1588:15: note: Function in derived class
hisat2-2.2.1/pat.h:1603:15: style: The function 'resetForNextFile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/pat.h:881:15: note: Virtual function in base class
hisat2-2.2.1/pat.h:1603:15: note: Function in derived class
hisat2-2.2.1/pat.cpp:746:5: style: Variable 'c' is reassigned a value before the old one has been used. [redundantAssignment]
hisat2-2.2.1/pat.cpp:744:5: note: c is assigned
hisat2-2.2.1/pat.cpp:746:5: note: c is overwritten
hisat2-2.2.1/pat.cpp:1141:4: style: Variable 'c' is reassigned a value before the old one has been used. [redundantAssignment]
hisat2-2.2.1/pat.cpp:1133:6: note: c is assigned
hisat2-2.2.1/pat.cpp:1141:4: note: c is overwritten
hisat2-2.2.1/pat.cpp:1141:4: style: Variable 'c' is reassigned a value before the old one has been used. [redundantAssignment]
hisat2-2.2.1/pat.cpp:1135:6: note: c is assigned
hisat2-2.2.1/pat.cpp:1141:4: note: c is overwritten
hisat2-2.2.1/pat.cpp:765:18: style: The comparison 'qc < 0' is always false. [knownConditionTrueFalse]
hisat2-2.2.1/pat.cpp:732:14: note: 'qc' is assigned value '0' here.
hisat2-2.2.1/pat.cpp:765:18: note: The comparison 'qc < 0' is always false.
hisat2-2.2.1/pat.cpp:776:20: style: The comparison 'qc < 0' is always false. [knownConditionTrueFalse]
hisat2-2.2.1/pat.cpp:732:14: note: 'qc' is assigned value '0' here.
hisat2-2.2.1/pat.cpp:776:20: note: The comparison 'qc < 0' is always false.
hisat2-2.2.1/pat.h:987:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.h:1201:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.h:1324:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.h:1446:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.h:1600:3: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/pat.cpp:1356:6: style: The scope of the variable 'c' can be reduced. [variableScope]
hisat2-2.2.1/pat.cpp:718:21: style: Checking if unsigned expression 'r.qual.length()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/pat.cpp:490:15: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/pat.cpp:466:13: note: Shadowed declaration
hisat2-2.2.1/pat.cpp:490:15: note: Shadow variable
hisat2-2.2.1/pat.cpp:1008:9: style: Local variable 'c' shadows outer variable [shadowVariable]
hisat2-2.2.1/pat.cpp:859:6: note: Shadowed declaration
hisat2-2.2.1/pat.cpp:1008:9: note: Shadow variable
hisat2-2.2.1/pat.cpp:1461:10: style: Local variable 'c' shadows outer variable [shadowVariable]
hisat2-2.2.1/pat.cpp:1454:6: note: Shadowed declaration
hisat2-2.2.1/pat.cpp:1461:10: note: Shadow variable
hisat2-2.2.1/pat.cpp:929:12: style: Variable 'trim5' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/pat.cpp:1356:8: style: Variable 'c' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/pe.cpp:182:2: style: Unsigned expression 'minfrag_' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/presets.h:59:15: style: The function 'apply' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/presets.h:41:15: note: Virtual function in base class
hisat2-2.2.1/presets.h:59:15: note: Function in derived class
hisat2-2.2.1/presets.h:64:23: style: The function 'name' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/presets.h:46:23: note: Virtual function in base class
hisat2-2.2.1/presets.h:64:23: note: Function in derived class
hisat2-2.2.1/read_qseq.cpp:156:10: style: Local variable 'c' shadows outer variable [shadowVariable]
hisat2-2.2.1/read_qseq.cpp:148:6: note: Shadowed declaration
hisat2-2.2.1/read_qseq.cpp:156:10: note: Shadow variable
hisat2-2.2.1/ref_read.cpp:47:14: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/ref_read.cpp:416:10: style: The if condition is the same as the previous if condition [duplicateCondition]
hisat2-2.2.1/ref_read.cpp:415:10: note: First condition
hisat2-2.2.1/ref_read.cpp:416:10: note: Second condition
hisat2-2.2.1/ref_read.cpp:377:2: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/ref_read.cpp:450:2: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/ref_read.cpp:376:2: style: Unsigned expression 'bothTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/ref_read.cpp:377:2: style: Unsigned expression 'unambigTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/ref_read.cpp:449:2: style: Unsigned expression 'bothTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/ref_read.cpp:450:2: style: Unsigned expression 'unambigTot' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/reference.cpp:217:5: warning: Class 'BitPairReference' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/reference.cpp:217:5: warning: Class 'BitPairReference' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/reference.cpp:475:14: style: Condition 'count>0' is always true [knownConditionTrueFalse]
hisat2-2.2.1/reference.cpp:470:12: note: Assuming that condition 'count==0' is not redundant
hisat2-2.2.1/reference.cpp:475:14: note: Condition 'count>0' is always true
hisat2-2.2.1/reference.cpp:639:14: style: Condition 'count>0' is always true [knownConditionTrueFalse]
hisat2-2.2.1/reference.cpp:633:12: note: Assuming that condition 'count==0' is not redundant
hisat2-2.2.1/reference.cpp:639:14: note: Condition 'count>0' is always true
hisat2-2.2.1/reference.cpp:66:3: error: Resource leak: f3 [resourceLeak]
hisat2-2.2.1/reference.cpp:108:4: error: Resource leak: f4 [resourceLeak]
hisat2-2.2.1/reference.cpp:119:3: error: Resource leak: f4 [resourceLeak]
hisat2-2.2.1/reference.cpp:370:22: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/reference.cpp:439:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/reference.cpp:496:18: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/reference.cpp:504:13: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/reference.cpp:254:39: style: The scope of the variable 'four_buf2' can be reduced. [variableScope]
hisat2-2.2.1/reference.cpp:500:6: style: The scope of the variable 'off2' can be reduced. [variableScope]
hisat2-2.2.1/reference.cpp:231:10: style: Local variable 'f4' shadows outer variable [shadowVariable]
hisat2-2.2.1/reference.cpp:54:13: note: Shadowed declaration
hisat2-2.2.1/reference.cpp:231:10: note: Shadow variable
hisat2-2.2.1/reference.cpp:341:31: style: Local variable 'tmp_destU32_' shadows outer variable [shadowVariable]
hisat2-2.2.1/reference.h:188:2: note: Shadowed declaration
hisat2-2.2.1/reference.cpp:341:31: note: Shadow variable
hisat2-2.2.1/reference.cpp:219:28: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/reference.cpp:254:49: style: Variable 'four_buf2' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/reference.cpp:289:29: style: Variable 'seq_pos' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/reference.cpp:519:17: style: Variable 'mid' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2_repeat.cpp:522:15: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_repeat.cpp:523:14: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_repeat.cpp:525:15: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_repeat.cpp:541:16: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_repeat.cpp:542:15: warning: Assert statement calls a function which may have desired side effects: 'get'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_repeat.cpp:544:16: warning: Assert statement calls a function which may have desired side effects: 'eof'. [assertWithSideEffect]
hisat2-2.2.1/hisat2_repeat.cpp:691:28: warning: Assert statement calls a function which may have desired side effects: 'suffixItrIsReset'. [assertWithSideEffect]
hisat2-2.2.1/ds.h:536:3: error: Using 'memset' on class that contains a 'std::pair'. [memsetClass]
hisat2-2.2.1/repeat_builder.h:156:5: warning: Member variable 'SeedSNP::type' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:156:5: warning: Member variable 'SeedSNP::pos' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:156:5: warning: Member variable 'SeedSNP::len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:156:5: warning: Member variable 'SeedSNP::id' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:505:5: warning: Member variable 'RB_Repeat::repeat_id_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:505:5: warning: Member variable 'RB_Repeat::parent_id_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:505:5: warning: Member variable 'RB_Repeat::self_repeat_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:768:5: warning: Member variable 'RB_SubSA::sa_size_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:768:5: warning: Member variable 'RB_SubSA::seed_len_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:768:5: warning: Member variable 'RB_SubSA::seed_count_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:930:2: warning: Member variable 'GFM < SString < char > >::_repeat' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_lineRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_origOffRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_offRate' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_ftabChars' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_entireReverse' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gfm.h:118:2: warning:inconclusive: Member variable 'GFMParams < SString < char > >::_linearFM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat.h:49:5: warning:inconclusive: Member variable 'RepeatCoord < SString < char > >::fw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/gbwt_graph.h:202:35: style: Unused private function: 'RefGraph < SString < char > >::findEdgesFrom' [unusedPrivateFunction]
hisat2-2.2.1/gbwt_graph.h:208:35: style: Unused private function: 'RefGraph < SString < char > >::getNextEdgeRange' [unusedPrivateFunction]
hisat2-2.2.1/repeat.h:608:28: style: Unused private function: 'RepeatDB < SString < char > >::get_alt_range' [unusedPrivateFunction]
hisat2-2.2.1/repeat_builder.h:65:7: style:inconclusive: Technically the member function 'Fragments::contain' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1266:7: style:inconclusive: Technically the member function 'GFM < SString < char > >::isPacked' can be const. [functionConst]
hisat2-2.2.1/gfm.h:1273:10: performance:inconclusive: Technically the member function 'GFM < SString < char > >::checkPosToSzs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:2402:10: performance:inconclusive: Technically the member function 'GFM < SString < char > >::joinedLen' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gfm.h:4329:11: performance:inconclusive: Technically the member function 'GFM < SString < char > >::log' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:1731:13: performance:inconclusive: Technically the member function 'PathGraph < SString < char > >::rank' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/gbwt_graph.h:146:10: performance:inconclusive: Technically the member function 'RefGraph < SString < char > >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:608:28: performance:inconclusive: Technically the member function 'RepeatDB < SString < char > >::get_alt_range' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat.h:123:10: style:inconclusive: Technically the member function 'sort_pair_loci_by_index < SString < char > >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:116:10: style:inconclusive: Technically the member function 'sort_pair_loci < SString < char > >::operator()' can be const. [functionConst]
hisat2-2.2.1/repeat.h:84:10: performance:inconclusive: Technically the member function 'RepeatAllele < SString < char > >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < uint8_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < uint8_t >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray < uint8_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/hisat2_repeat.cpp:715:20: style: Condition 'passMemExc' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hisat2_repeat.cpp:629:27: note: Assignment 'passMemExc=false', assigned value is 0
hisat2-2.2.1/hisat2_repeat.cpp:715:20: note: Condition 'passMemExc' is always false
hisat2-2.2.1/hisat2_repeat.cpp:862:21: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
hisat2-2.2.1/gfm.h:4010:17: style:inconclusive: Redundant initialization for 'bot'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/gfm.h:3975:21: note: bot is initialized
hisat2-2.2.1/gfm.h:4010:17: note: bot is overwritten
hisat2-2.2.1/gfm.h:4083:17: style:inconclusive: Redundant initialization for 'bot'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/gfm.h:4049:21: note: bot is initialized
hisat2-2.2.1/gfm.h:4083:17: note: bot is overwritten
hisat2-2.2.1/hisat2_repeat.cpp:290:5: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat2_repeat.cpp:779:12: style: The scope of the variable 'outfile' can be reduced. [variableScope]
hisat2-2.2.1/diff_sample.h:479:26: warning: Either the condition 'dcv==0' is redundant or there is division by zero at line 479. [zerodivcond]
hisat2-2.2.1/hisat2_repeat.cpp:653:24: note: Assuming that condition 'dcv==0' is not redundant
hisat2-2.2.1/hisat2_repeat.cpp:663:21: note: Compound assignment '<<=', assigned value is 0
hisat2-2.2.1/hisat2_repeat.cpp:664:101: note: Calling function 'simulateAllocs', 2nd argument 'dcv>>1' value is 0
hisat2-2.2.1/diff_sample.h:479:26: note: Division by zero
hisat2-2.2.1/gbwt_graph.h:1755:50: style:inconclusive: Function 'PathGraph < SString < char > >' argument 1 names different: declaration 'parent' definition 'base'. [funcArgNamesDifferent]
hisat2-2.2.1/gbwt_graph.h:1588:34: note: Function 'PathGraph < SString < char > >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gbwt_graph.h:1755:50: note: Function 'PathGraph < SString < char > >' argument 1 names different: declaration 'parent' definition 'base'.
hisat2-2.2.1/gfm.h:4367:13: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:68:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4367:13: note: Shadow variable
hisat2-2.2.1/gfm.h:4369:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:71:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4369:13: note: Shadow variable
hisat2-2.2.1/gfm.h:4370:13: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:72:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4370:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6479:13: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:68:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6479:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6481:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:71:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6481:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6482:13: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:72:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6482:13: note: Shadow variable
hisat2-2.2.1/gfm.h:5975:14: style: Local variable 'lineRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:68:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5975:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5979:14: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:71:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5979:14: note: Shadow variable
hisat2-2.2.1/gfm.h:5984:14: style: Local variable 'ftabChars' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:72:16: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5984:14: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:1775:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:75:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:1775:16: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:372:16: style: Local variable 'bigEndian' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2_repeat.cpp:75:13: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:372:16: note: Shadow variable
hisat2-2.2.1/repeat_builder.h:158:56: performance: Function parameter 'bs' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:940:12: performance: Function parameter 'sztot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:1316:30: performance: Function parameter 'sztot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:1323:30: performance: Function parameter 'bmaxSqrtMult' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:1324:30: performance: Function parameter 'bmaxDivN' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2571:11: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2620:11: performance: Function parameter 'gbwtLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2621:11: performance: Function parameter 'ftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2622:11: performance: Function parameter 'eftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2651:49: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2658:49: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2672:11: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2699:11: performance: Function parameter 'gbwtLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2700:11: performance: Function parameter 'ftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2701:11: performance: Function parameter 'eftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2719:28: performance: Function parameter 'elt' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2719:41: performance: Function parameter 'node' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:2743:11: performance: Function parameter 'hitlen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3547:11: performance: Function parameter 'num' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3550:11: performance: Function parameter 'maskOff' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3625:26: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3639:11: performance: Function parameter 'num' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3763:50: performance: Function parameter 'k' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3893:11: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:3958:51: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:4174:40: performance: Function parameter 'bot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:4495:33: performance: Function parameter 'sztot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:4565:10: performance: Function parameter 'sztot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5528:44: performance: Function parameter 'qlen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5529:44: performance: Function parameter 'off' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5604:45: performance: Function parameter 'tid' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5605:45: performance: Function parameter 'textoff' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5682:54: performance: Function parameter 'node' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5724:41: performance: Function parameter 'elt' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:5726:41: performance: Function parameter 'hitlen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:339:20: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:348:11: performance: Function parameter 'top' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:349:11: performance: Function parameter 'bot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:377:30: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:400:44: performance: Function parameter 'top' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:401:44: performance: Function parameter 'bot' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:429:34: performance: Function parameter 'row' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:121:11: performance: Function parameter 'len' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:122:17: performance: Function parameter 'gbwtLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:123:17: performance: Function parameter 'numNodes' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:127:17: performance: Function parameter 'eftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:139:23: performance: Function parameter 'len' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gfm.h:145:23: performance: Function parameter 'eftabLen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1555:26: performance: Function parameter 'from_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1555:41: performance: Function parameter 'ranking_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1727:55: performance: Function parameter 'p' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1731:52: performance: Function parameter 'p' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1741:53: performance: Function parameter 'p' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:69:35: performance: Function parameter 'value_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:101:22: performance: Function parameter 'from_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:101:37: performance: Function parameter 'to_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:202:83: performance: Function parameter 'node' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:205:81: performance: Function parameter 'node' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:305:44: performance: Function parameter 'node_id' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:329:31: performance: Function parameter 'from_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:329:46: performance: Function parameter 'to_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:815:87: performance: Function parameter 'node' should be passed by const reference. [passedByValue]
hisat2-2.2.1/gbwt_graph.h:1305:111: performance: Function parameter 'lastNode_add' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:275:52: performance: Function parameter 'rlen' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:359:59: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:375:42: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:379:28: performance: Function parameter 'max_positions' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:430:43: performance: Function parameter 'anchor_left' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:431:43: performance: Function parameter 'anchor_right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:434:43: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:438:29: performance: Function parameter 'max_positions' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:439:29: performance: Function parameter 'dist' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:502:49: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:506:49: performance: Function parameter 'right2' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:510:35: performance: Function parameter 'max_positions' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:511:35: performance: Function parameter 'dist' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:609:50: performance: Function parameter 'left' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:610:50: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:132:29: performance: Function parameter 'repID_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:133:29: performance: Function parameter 'repPos_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:134:29: performance: Function parameter 'repLen_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:66:23: performance: Function parameter 'allelePos_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:67:23: performance: Function parameter 'alleleLen_' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:101:29: performance: Function parameter 'left' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:101:43: performance: Function parameter 'right' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:50:25: performance: Function parameter 'l_tid' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:50:40: performance: Function parameter 'l_toff' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:50:56: performance: Function parameter 'l_joinedOff' should be passed by const reference. [passedByValue]
hisat2-2.2.1/repeat.h:50:88: performance: Function parameter 'l_alleleID' should be passed by const reference. [passedByValue]
hisat2-2.2.1/word_io.h:319:44: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
hisat2-2.2.1/hisat2_repeat.cpp:858:32: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/hisat2_repeat.cpp:714:33: style: Variable 'e' can be declared as reference to const [constVariable]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.joinedOff [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.length [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.frag_id [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.seq_id [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.seqOff [uninitStructMember]
hisat2-2.2.1/ds.h:959:10: error: Uninitialized struct member: tmp.first [uninitStructMember]
hisat2-2.2.1/gfm.h:4513:35: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4524:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:755:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:766:25: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:767:25: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:769:25: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:788:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:870:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:910:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:912:58: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1186:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1276:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1366:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1400:58: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1402:65: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1440:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1456:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1577:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1592:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1646:58: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1684:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1705:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1739:72: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1742:82: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1771:80: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1774:90: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1805:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1818:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1914:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1920:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1940:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:1978:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2024:70: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2050:70: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2073:78: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2178:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2383:60: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2721:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2786:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2858:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2967:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:2976:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3027:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3106:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3581:4: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3799:27: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3817:27: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3900:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3932:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:3991:23: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4036:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4065:23: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4192:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4195:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4207:19: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4211:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4222:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4468:35: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4581:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4582:28: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4583:44: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4599:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4647:33: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4653:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4662:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4811:36: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:4876:19: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5000:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5006:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5055:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5081:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5097:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5103:34: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5115:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5254:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5435:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5451:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5468:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5480:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5625:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5640:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5664:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5672:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5685:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5700:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:5704:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6024:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6057:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6205:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6291:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6391:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6643:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6658:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6661:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6670:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6672:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6795:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6834:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6852:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6865:41: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6871:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6900:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6911:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:6952:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gfm.h:455:3: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1624:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1641:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1716:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1719:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1734:36: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1736:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1823:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1866:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1876:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1886:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1900:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1901:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1914:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1919:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1959:5: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1977:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2051:119: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2060:115: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2068:115: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2164:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2171:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2177:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2187:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2191:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2195:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2213:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2230:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2282:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2356:89: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2392:39: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2496:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2612:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2626:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2628:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2643:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2671:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2713:35: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:2739:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:155:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:159:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:178:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:183:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:272:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:387:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:421:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:435:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:473:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:486:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:507:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:512:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:526:53: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:542:56: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:544:63: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:548:25: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:554:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:559:55: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:573:64: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:633:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:639:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:678:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:679:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:746:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:799:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:806:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:908:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:913:34: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:948:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:955:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:994:67: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:995:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1069:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1099:38: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1137:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1149:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1182:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1184:21: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1186:72: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1202:62: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1216:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1226:22: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1227:22: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1230:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1234:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1243:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1247:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1261:56: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1280:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1337:70: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1401:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1423:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1427:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1455:29: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1467:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/gbwt_graph.h:1473:43: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:209:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:225:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:229:52: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:233:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:242:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:251:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:255:59: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:264:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:279:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:295:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:298:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:323:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:329:13: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:335:49: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:338:54: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:354:17: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:403:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:467:37: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:554:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:559:59: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:146:48: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:150:50: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:164:44: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat.h:169:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/alt.h:233:45: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/alt.h:245:42: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/scoring.cpp:107:2: style: Unsigned expression 'rd.length()' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/scoring.cpp:33:10: style: Local variable 'sc' shadows outer function [shadowFunction]
hisat2-2.2.1/scoring.h:312:16: note: Shadowed declaration
hisat2-2.2.1/scoring.cpp:33:10: note: Shadow variable
hisat2-2.2.1/scoring.cpp:48:10: style: Local variable 'sc' shadows outer function [shadowFunction]
hisat2-2.2.1/scoring.h:312:16: note: Shadowed declaration
hisat2-2.2.1/scoring.cpp:48:10: note: Shadow variable
hisat2-2.2.1/scoring.cpp:79:10: style: Local variable 'sc' shadows outer function [shadowFunction]
hisat2-2.2.1/scoring.h:312:16: note: Shadowed declaration
hisat2-2.2.1/scoring.cpp:79:10: note: Shadow variable
hisat2-2.2.1/splice_site.cpp:784:17: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/splice_site.h:583:10: style:inconclusive: Technically the member function 'SpliceSiteDB::print_impl' can be const. [functionConst]
hisat2-2.2.1/splice_site.cpp:605:20: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
hisat2-2.2.1/splice_site.h:583:10: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
hisat2-2.2.1/aligner_report.h:30:7: performance:inconclusive: Technically the member function 'Reporter::report' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aligner_cache.h:898:33: style:inconclusive: Technically the member function 'AlignmentCacheIface < uint32_t >::current' can be const. [functionConst]
hisat2-2.2.1/aligner_cache.h:290:7: style:inconclusive: Technically the member function 'SAVal < uint32_t >::valid' can be const. [functionConst]
hisat2-2.2.1/ds.h:3806:2: style: Class 'RedBlack < QKey , QVal < uint32_t > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3806:2: style: Class 'RedBlack < QKey , SAVal < uint32_t > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3199:2: style: Class 'PList < QKey , 16384 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:3199:2: style: Class 'PList < uint32_t , 16384 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/splice_site.cpp:717:52: style: Condition 'fw=='+'' is always false [knownConditionTrueFalse]
hisat2-2.2.1/splice_site.cpp:663:22: note: Assignment 'fw=alt.fw', assigned value is less than 2
hisat2-2.2.1/splice_site.cpp:717:52: note: Condition 'fw=='+'' is always false
hisat2-2.2.1/splice_site.cpp:781:20: style: Checking if unsigned expression 'pool.size()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/splice_site.cpp:107:53: style:inconclusive: Function 'operator<<' argument 2 names different: declaration 'c' definition 's'. [funcArgNamesDifferent]
hisat2-2.2.1/splice_site.h:372:63: note: Function 'operator<<' argument 2 names different: declaration 'c' definition 's'.
hisat2-2.2.1/splice_site.cpp:107:53: note: Function 'operator<<' argument 2 names different: declaration 'c' definition 's'.
hisat2-2.2.1/splice_site.cpp:168:23: style: Local variable 'pool' shadows outer function [shadowFunction]
hisat2-2.2.1/splice_site.h:581:11: note: Shadowed declaration
hisat2-2.2.1/splice_site.cpp:168:23: note: Shadow variable
hisat2-2.2.1/splice_site.cpp:520:21: style: Local variable 'e' shadows outer variable [shadowVariable]
hisat2-2.2.1/splice_site.cpp:517:10: note: Shadowed declaration
hisat2-2.2.1/splice_site.cpp:520:21: note: Shadow variable
hisat2-2.2.1/splice_site.cpp:168:23: style: Variable 'pool' can be declared as reference to const [constVariable]
hisat2-2.2.1/splice_site.cpp:216:48: style: Variable 'rightAnchorLen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/splice_site.cpp:282:36: style: Variable 'rightAnchorLen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:365:14: warning: Member variable 'CoordHelper::cached_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.cpp:2856:15: warning: Member variable 'RB_SWAligner::sc_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.cpp:172:2: warning: Member variable 'RepeatRange::rg_id' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/repeat_builder.h:940:10: style:inconclusive: Member variable 'RepeatBuilder < SString < char > >::forward_only_' is in the wrong place in the initializer list. [initializerList]
hisat2-2.2.1/repeat_builder.cpp:3174:1: note: Member variable 'RepeatBuilder < SString < char > >::forward_only_' is in the wrong place in the initializer list.
hisat2-2.2.1/repeat_builder.h:940:10: note: Member variable 'RepeatBuilder < SString < char > >::forward_only_' is in the wrong place in the initializer list.
hisat2-2.2.1/repeat_builder.h:609:10: performance:inconclusive: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.cpp:1484:17: note: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:609:10: note: Technically the member function 'RB_Repeat::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:666:10: performance:inconclusive: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.cpp:1659:20: note: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:666:10: note: Technically the member function 'RB_RepeatExt::get_consensus_seq' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:693:10: performance:inconclusive: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.cpp:2523:20: note: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:693:10: note: Technically the member function 'RB_RepeatExt::isSelfRepeat' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:739:10: performance:inconclusive: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.cpp:2906:20: note: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:739:10: note: Technically the member function 'RB_SWAligner::makePadString' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:922:10: performance:inconclusive: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/repeat_builder.cpp:3685:27: note: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.h:922:10: note: Technically the member function 'RepeatBuilder < SString < char > >::writeSNPs' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/repeat_builder.cpp:1528:29: style: Condition 'min_left_ext>0' is always true [knownConditionTrueFalse]
hisat2-2.2.1/repeat_builder.cpp:1517:24: note: Assuming that condition 'min_left_ext>0' is not redundant
hisat2-2.2.1/repeat_builder.cpp:1523:69: note: Assuming condition is false
hisat2-2.2.1/repeat_builder.cpp:1528:29: note: Condition 'min_left_ext>0' is always true
hisat2-2.2.1/repeat_builder.cpp:429:10: style: Redundant initialization for 'frag'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/repeat_builder.cpp:417:21: note: frag is initialized
hisat2-2.2.1/repeat_builder.cpp:429:10: note: frag is overwritten
hisat2-2.2.1/repeat_builder.cpp:853:26: style: The scope of the variable 'seed' can be reduced. [variableScope]
hisat2-2.2.1/repeat_builder.cpp:3065:13: style: The scope of the variable 'max_match_len' can be reduced. [variableScope]
hisat2-2.2.1/repeat_builder.cpp:3351:16: style: The scope of the variable 'query2' can be reduced. [variableScope]
hisat2-2.2.1/repeat_builder.cpp:3351:24: style: The scope of the variable 'rc_query2' can be reduced. [variableScope]
hisat2-2.2.1/repeat_builder.cpp:826:23: style: Checking if unsigned expression 'extlen' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:1002:21: style: Checking if unsigned expression 'remove_count' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:1346:18: style: Checking if unsigned expression 'max_count' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:1899:23: style: Checking if unsigned expression 'extlen' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:2845:25: style: Checking if unsigned expression 'remove_count' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/repeat_builder.cpp:399:47: style:inconclusive: Function 'mapJoinedOffToSeq' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:88:38: note: Function 'mapJoinedOffToSeq' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'.
hisat2-2.2.1/repeat_builder.cpp:399:47: note: Function 'mapJoinedOffToSeq' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'.
hisat2-2.2.1/repeat_builder.cpp:447:44: style:inconclusive: Function 'getGenomeCoord' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:89:35: note: Function 'getGenomeCoord' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'.
hisat2-2.2.1/repeat_builder.cpp:447:44: note: Function 'getGenomeCoord' argument 1 names different: declaration 'joined_pos' definition 'joinedOff'.
hisat2-2.2.1/repeat_builder.cpp:1053:46: style:inconclusive: Function 'saveSeedExtension' argument 4 names different: declaration 'seed_grp_id' definition 'grp_id'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:553:39: note: Function 'saveSeedExtension' argument 4 names different: declaration 'seed_grp_id' definition 'grp_id'.
hisat2-2.2.1/repeat_builder.cpp:1053:46: note: Function 'saveSeedExtension' argument 4 names different: declaration 'seed_grp_id' definition 'grp_id'.
hisat2-2.2.1/repeat_builder.cpp:3591:63: style:inconclusive: Function 'writeHaploType' argument 1 names different: declaration 'haplo_list' definition 'haplo_lists'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:926:46: note: Function 'writeHaploType' argument 1 names different: declaration 'haplo_list' definition 'haplo_lists'.
hisat2-2.2.1/repeat_builder.cpp:3591:63: note: Function 'writeHaploType' argument 1 names different: declaration 'haplo_list' definition 'haplo_lists'.
hisat2-2.2.1/repeat_builder.cpp:3949:60: style:inconclusive: Function 'addRepeatGroup' argument 3 names different: declaration 'repeat_manger' definition 'repeat_manager'. [funcArgNamesDifferent]
hisat2-2.2.1/repeat_builder.h:880:43: note: Function 'addRepeatGroup' argument 3 names different: declaration 'repeat_manger' definition 'repeat_manager'.
hisat2-2.2.1/repeat_builder.cpp:3949:60: note: Function 'addRepeatGroup' argument 3 names different: declaration 'repeat_manger' definition 'repeat_manager'.
hisat2-2.2.1/repeat_builder.cpp:747:24: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:736:20: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:747:24: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:1060:36: style: Local variable 'reset' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat_builder.h:582:10: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:1060:36: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2122:21: style: Local variable 'seeds' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat_builder.h:523:21: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2122:21: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2370:17: style: Local variable 'left' shadows outer argument [shadowArgument]
hisat2-2.2.1/repeat_builder.cpp:2234:33: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2370:17: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2370:36: style: Local variable 'right' shadows outer argument [shadowArgument]
hisat2-2.2.1/repeat_builder.cpp:2235:33: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2370:36: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2436:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:2356:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2436:16: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2455:17: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:2356:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2455:17: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:2468:17: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:2356:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:2468:17: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:3758:36: style: Local variable 'overlap' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:3739:22: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:3758:36: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4465:24: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4445:20: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4465:24: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4469:24: style: Local variable 'saBegin' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4455:20: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4469:24: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4499:32: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4465:24: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4499:32: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4500:28: style: Local variable 'num' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4446:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4500:28: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4548:32: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4465:24: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4548:32: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4558:32: style: Local variable 'idx' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4465:24: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4558:32: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:4559:32: style: Local variable 'num' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:4446:9: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:4559:32: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:3472:20: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:3453:12: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:3472:20: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:3495:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:3453:12: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:3495:16: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:3520:20: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/repeat_builder.cpp:3453:12: note: Shadowed declaration
hisat2-2.2.1/repeat_builder.cpp:3520:20: note: Shadow variable
hisat2-2.2.1/repeat_kmer.h:50:22: style: Local variable 'next_kmer' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat_builder.cpp:1222:8: note: Shadowed declaration
hisat2-2.2.1/repeat_kmer.h:50:22: note: Shadow variable
hisat2-2.2.1/repeat_kmer.h:74:22: style: Local variable 'next_kmer' shadows outer function [shadowFunction]
hisat2-2.2.1/repeat_builder.cpp:1222:8: note: Shadowed declaration
hisat2-2.2.1/repeat_kmer.h:74:22: note: Shadow variable
hisat2-2.2.1/repeat_builder.cpp:142:35: style: Parameter 'coordHelper' can be declared as reference to const [constParameter]
hisat2-2.2.1/repeat_builder.cpp:387:17: style: Variable 'nameline' can be declared as reference to const [constVariable]
hisat2-2.2.1/repeat_builder.cpp:600:65: style: Parameter 'snp' can be declared as reference to const [constParameter]
hisat2-2.2.1/repeat_builder.cpp:932:29: style: Variable 'range2' can be declared as reference to const [constVariable]
hisat2-2.2.1/repeat_builder.cpp:2030:29: style: Variable 'range2' can be declared as reference to const [constVariable]
hisat2-2.2.1/repeat_builder.cpp:2099:39: style: Parameter 'coordHelper' can be declared as reference to const [constParameter]
hisat2-2.2.1/repeat_builder.cpp:3455:20: style: Variable 'repeat' can be declared as reference to const [constVariable]
hisat2-2.2.1/repeat_builder.cpp:3555:34: style: Variable 'seed' can be declared as reference to const [constVariable]
hisat2-2.2.1/repeat_builder.cpp:3565:34: style: Variable 'seed' can be declared as reference to const [constVariable]
hisat2-2.2.1/repeat_builder.cpp:352:22: style: Parameter 'array' can be declared as const array [constParameter]
hisat2-2.2.1/repeat_builder.cpp:3802:49: performance: Searching before insertion is not necessary. Instead of 'range_to_repeats_[range]=EList < unsigned long , 128 >()' consider using 'range_to_repeats_.try_emplace(range, EList < unsigned long , 128 >());'. [stlFindInsert]
hisat2-2.2.1/repeat_builder.cpp:2458:25: warning: Either the condition '(offsets[i+1])>=0' is redundant, otherwise there is negative array index -2. [negativeContainerIndex]
hisat2-2.2.1/repeat_builder.cpp:2456:13: note: Assuming that condition '(offsets[i+1])>=0' is not redundant
hisat2-2.2.1/repeat_builder.cpp:2458:25: note: Negative array index
hisat2-2.2.1/repeat_builder.cpp:665:27: style: Variable 'gap_str' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:677:27: style: Variable 'gap_str' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3065:27: style: Variable 'max_match_len' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3088:27: style: Variable 'max_match_len' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3131:17: style: Variable 'ref2' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3132:18: style: Variable 'read2' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3747:88: style: Variable 'num_overlap_bp' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3756:40: style: Variable 'num_overlap_bp' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3761:44: style: Variable 'num_overlap_bp' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/repeat_builder.cpp:3726:106: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3839:40: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3842:61: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3843:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3184:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3294:104: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3454:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3469:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3496:98: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:3550:102: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:4034:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:4058:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/repeat_builder.cpp:4101:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hisat2-2.2.1/sse_util.h:510:7: performance:inconclusive: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sse_util.cpp:27:20: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sse_util.h:510:7: note: Technically the member function 'Checkpointer::commitCol' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/tinythread.cpp:212:13: error: Memory leak: ti [memleak]
hisat2-2.2.1/tinythread.cpp:215:13: error: Memory leak: ti [memleak]
hisat2-2.2.1/tinythread.cpp:220:17: error: Memory leak: ti [memleak]
hisat2-2.2.1/tinythread.cpp:164:29: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/tinythread.cpp:224:70: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/tinythread.cpp:135:28: style: The scope of the variable 'idCount' can be reduced. [variableScope]
hisat2-2.2.1/tinythread.cpp:139:30: performance: Searching before insertion is not necessary. Instead of 'idMap[aHandle]=idCount++' consider using 'idMap.try_emplace(aHandle, idCount++);'. [stlFindInsert]
hisat2-2.2.1/tinythread.cpp:222:9: style: Variable 'err' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/splice_site_new.cpp:1089:17: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/splice_site.h:583:10: style:inconclusive: Technically the member function 'SpliceSiteDB::print_impl' can be const. [functionConst]
hisat2-2.2.1/splice_site_new.cpp:1001:20: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
hisat2-2.2.1/splice_site.h:583:10: note: Technically the member function 'SpliceSiteDB::print_impl' can be const.
hisat2-2.2.1/splice_site_new.cpp:1086:20: style: Checking if unsigned expression 'pool.size()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/splice_site_new.cpp:107:53: style:inconclusive: Function 'operator<<' argument 2 names different: declaration 'c' definition 's'. [funcArgNamesDifferent]
hisat2-2.2.1/splice_site.h:372:63: note: Function 'operator<<' argument 2 names different: declaration 'c' definition 's'.
hisat2-2.2.1/splice_site_new.cpp:107:53: note: Function 'operator<<' argument 2 names different: declaration 'c' definition 's'.
hisat2-2.2.1/splice_site_new.cpp:1043:44: style:inconclusive: Function 'read' argument 2 names different: declaration 'known' definition 'novel'. [funcArgNamesDifferent]
hisat2-2.2.1/splice_site.h:557:34: note: Function 'read' argument 2 names different: declaration 'known' definition 'novel'.
hisat2-2.2.1/splice_site_new.cpp:1043:44: note: Function 'read' argument 2 names different: declaration 'known' definition 'novel'.
hisat2-2.2.1/splice_site_new.cpp:656:23: style: Local variable 'pool' shadows outer function [shadowFunction]
hisat2-2.2.1/splice_site.h:581:11: note: Shadowed declaration
hisat2-2.2.1/splice_site_new.cpp:656:23: note: Shadow variable
hisat2-2.2.1/splice_site_new.cpp:656:23: style: Variable 'pool' can be declared as reference to const [constVariable]
hisat2-2.2.1/splice_site_new.cpp:697:48: style: Variable 'rightAnchorLen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/splice_site_new.cpp:761:36: style: Variable 'rightAnchorLen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_sw_driver.h:1049:22: warning: Assert statement calls a function which may have desired side effects: 'current'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:4668:25: warning: Assert statement calls a function which may have desired side effects: 'done'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:5030:20: warning: Assert statement calls a function which may have desired side effects: 'done'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:5509:16: warning: Assert statement calls a function which may have desired side effects: 'done'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:6919:13: warning: Assert statement calls a function which may have desired side effects: 'isSearched'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:1523:16: warning: Assert statement calls a function which may have desired side effects: 'repOk'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:2023:12: warning: Assert statement calls a function which may have desired side effects: 'repOk'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:2230:12: warning: Assert statement calls a function which may have desired side effects: 'repOk'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:2360:34: warning: Assert statement calls a function which may have desired side effects: 'repOk'. [assertWithSideEffect]
hisat2-2.2.1/hi_aligner.h:2472:16: warning: Assert statement calls a function which may have desired side effects: 'repOk'. [assertWithSideEffect]
hisat2-2.2.1/group_walk.h:1131:75: warning: Assert statement calls a function which may have desired side effects: 'back'. [assertWithSideEffect]
hisat2-2.2.1/rfm.h:545:27: warning: Assert statement calls a function which may have desired side effects: 'suffixItrIsReset'. [assertWithSideEffect]
hisat2-2.2.1/hisat2.cpp:3185:34: style:inconclusive: Boolean expression 'sensitive' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
hisat2-2.2.1/hi_aligner.h:5028:20: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5027:9: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5028:20: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:5029:41: warning: Either the condition 'rdi<2' is redundant or the array '_hits[2][2]' is accessed at index _hits[2][*], which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5027:9: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5029:41: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:5224:20: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5223:9: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5224:20: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:5225:25: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5223:9: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5225:25: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:5507:16: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5506:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5507:16: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:5508:37: warning: Either the condition 'rdi<2' is redundant or the array '_hits[2][2]' is accessed at index _hits[2][*], which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:5506:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:5508:37: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6081:16: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6080:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6081:16: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6082:27: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6080:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6082:27: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6317:16: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6316:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6317:16: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6318:34: warning: Either the condition 'rdi<2' is redundant or the array '_rds[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6316:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6318:34: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6903:62: warning: Either the condition 'rdi<2' is redundant or the array '_hits_searched[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6902:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6903:62: note: Array index out of bounds
hisat2-2.2.1/hi_aligner.h:6920:62: warning: Either the condition 'rdi<2' is redundant or the array '_hits_searched[2]' is accessed at index 2, which is out of bounds. [arrayIndexOutOfBoundsCond]
hisat2-2.2.1/hi_aligner.h:6918:5: note: Assuming that condition 'rdi<2' is not redundant
hisat2-2.2.1/hi_aligner.h:6920:62: note: Array index out of bounds
hisat2-2.2.1/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_oldM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_newM' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_oldS' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_metrics.h:37:2: warning: Member variable 'RunningStat::m_newS' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hisat2.cpp:2075:2: warning: Member variable 'PerfMetrics::lastElapsed' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_rds' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_paired' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_rightendonly' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_nofw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_norc' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_minsc' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::_maxpen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::max_localindexatts' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::bwops_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3970:2: warning: Member variable 'HI_Aligner < uint32_t , uint16_t >::bwedits_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_rds' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_paired' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_rightendonly' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_nofw' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_norc' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_minsc' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_maxpen' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_anchorStop' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_minK' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_minK_local' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::max_localindexatts' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::bwops_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::bwedits_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:3988:5: warning:inconclusive: Member variable 'HI_Aligner < uint32_t , uint16_t >::_thread_rids_mindist' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:432:2: warning: Member variable 'GenomeHit < uint32_t >::_splicescore' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hi_aligner.h:218:2: warning: Member variable 'ReadBWTHit < uint32_t >::_cur_local' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > , uint32_t >::botf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > , uint32_t >::node_top' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > , uint32_t >::node_bot' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint32_t , 16 > , uint32_t >::len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint16_t , 16 > , uint16_t >::botf' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint16_t , 16 > , uint16_t >::node_top' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint16_t , 16 > , uint16_t >::node_bot' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/group_walk.h:100:2: warning: Member variable 'SARangeWithOffs < EListSlice < uint16_t , 16 > , uint16_t >::len' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aln_sink.h:669:11: warning: Member variable 'AlnSink < uint32_t >::numWrappers_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:281:2: warning: Member variable 'RFM < uint32_t >::mmFile1_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:281:2: warning: Member variable 'RFM < uint32_t >::mmFile2_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:373:2: warning: Member variable 'RFM < uint32_t >::_in1' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:373:2: warning: Member variable 'RFM < uint32_t >::_in2' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:373:2: warning: Member variable 'RFM < uint32_t >::mmFile1_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:373:2: warning: Member variable 'RFM < uint32_t >::mmFile2_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/aligner_seed.h:616:2: warning: Member variable 'SeedResults < uint32_t >::sorted_' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/rfm.h:693:5: performance: Variable '_in1Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/rfm.h:694:5: performance: Variable '_in2Str' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hisat2-2.2.1/hi_aligner.h:5347:10: performance:inconclusive: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hi_aligner.h:6282:42: note: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/hi_aligner.h:5347:10: note: Technically the member function 'HI_Aligner < uint32_t , uint16_t >::redundant' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/hi_aligner.h:1192:6: performance:inconclusive: Technically the member function 'GenomeHit < uint32_t >::mms' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hi_aligner.h:1204:6: performance:inconclusive: Technically the member function 'GenomeHit < uint32_t >::ns' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hi_aligner.h:1218:9: performance:inconclusive: Technically the member function 'GenomeHit < uint32_t >::ngaps' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/hi_aligner.h:267:13: style:inconclusive: Technically the member function 'ReadBWTHit < uint32_t >::numPartialSearch' can be const. [functionConst]
hisat2-2.2.1/group_walk.h:1480:7: style:inconclusive: Technically the member function 'GroupWalk2S < uint32_t , EListSlice < uint32_t , 16 > , 16 >::resolveAll' can be const. [functionConst]
hisat2-2.2.1/group_walk.h:1480:7: style:inconclusive: Technically the member function 'GroupWalk2S < uint16_t , EListSlice < uint16_t , 16 > , 16 >::resolveAll' can be const. [functionConst]
hisat2-2.2.1/group_walk.h:400:7: performance:inconclusive: Technically the member function 'GWHit < uint32_t , EListSlice < uint32_t , 16 > >::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/group_walk.h:400:7: performance:inconclusive: Technically the member function 'GWHit < uint16_t , EListSlice < uint16_t , 16 > >::repOkBasic' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:1220:28: style:inconclusive: Technically the member function 'AlnSinkWrap < uint32_t >::reportingParams' can be const. [functionConst]
hisat2-2.2.1/aln_sink.h:843:7: performance:inconclusive: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/aln_sink.h:1637:24: note: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:843:7: note: Technically the member function 'AlnSink < uint32_t >::printAlSumm' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/aln_sink.h:881:7: performance:inconclusive: Technically the member function 'AlnSink < uint32_t >::repOk' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:177:7: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:417:26: note: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:177:7: note: Technically the member function 'SamConfig < uint32_t >::printRefName' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:187:7: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printOptFieldEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:210:7: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printOptFieldNewlineEscapedZ' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:282:7: performance:inconclusive: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hisat2-2.2.1/sam.h:469:26: note: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/sam.h:282:7: note: Technically the member function 'SamConfig < uint32_t >::printHdLine' can be static (but you may consider moving to unnamed namespace).
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < int >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hisat2-2.2.1/ds.h:116:3: warning: Class 'AutoArray < int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hisat2-2.2.1/rfm.h:494:31: warning: The class 'RFM < uint32_t >' defines member variable with name '_in1' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4261:14: note: Parent variable 'GFM < uint32_t >::_in1'
hisat2-2.2.1/rfm.h:494:31: note: Derived variable 'RFM < uint32_t >::_in1'
hisat2-2.2.1/rfm.h:495:31: warning: The class 'RFM < uint32_t >' defines member variable with name '_in2' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4262:14: note: Parent variable 'GFM < uint32_t >::_in2'
hisat2-2.2.1/rfm.h:495:31: note: Derived variable 'RFM < uint32_t >::_in2'
hisat2-2.2.1/rfm.h:496:30: warning: The class 'RFM < uint32_t >' defines member variable with name '_in1Str' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4263:13: note: Parent variable 'GFM < uint32_t >::_in1Str'
hisat2-2.2.1/rfm.h:496:30: note: Derived variable 'RFM < uint32_t >::_in1Str'
hisat2-2.2.1/rfm.h:497:30: warning: The class 'RFM < uint32_t >' defines member variable with name '_in2Str' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4264:13: note: Parent variable 'GFM < uint32_t >::_in2Str'
hisat2-2.2.1/rfm.h:497:30: note: Derived variable 'RFM < uint32_t >::_in2Str'
hisat2-2.2.1/rfm.h:499:31: warning: The class 'RFM < uint32_t >' defines member variable with name 'mmFile1_' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4291:11: note: Parent variable 'GFM < uint32_t >::mmFile1_'
hisat2-2.2.1/rfm.h:499:31: note: Derived variable 'RFM < uint32_t >::mmFile1_'
hisat2-2.2.1/rfm.h:500:31: warning: The class 'RFM < uint32_t >' defines member variable with name 'mmFile2_' also defined in its parent class 'GFM < uint32_t >'. [duplInheritedMember]
hisat2-2.2.1/gfm.h:4292:8: note: Parent variable 'GFM < uint32_t >::mmFile2_'
hisat2-2.2.1/rfm.h:500:31: note: Derived variable 'RFM < uint32_t >::mmFile2_'
hisat2-2.2.1/aligner_sw_driver.h:194:2: style: Class 'RowSampler' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/aligner_sw_driver.h:312:2: style: Class 'SwDriver' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/hi_aligner.h:3970:2: style: Class 'HI_Aligner < uint32_t , uint16_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/group_walk.h:166:2: style: Struct 'GroupWalkState < uint32_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/group_walk.h:166:2: style: Struct 'GroupWalkState < uint16_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/ds.h:114:2: style: Class 'AutoArray < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hisat2-2.2.1/spliced_aligner.h:55:10: style: The function 'hybridSearch' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/hi_aligner.h:4812:10: note: Virtual function in base class
hisat2-2.2.1/spliced_aligner.h:55:10: note: Function in derived class
hisat2-2.2.1/spliced_aligner.h:81:13: style: The function 'hybridSearch_recur' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hisat2-2.2.1/hi_aligner.h:4839:13: note: Virtual function in base class
hisat2-2.2.1/spliced_aligner.h:81:13: note: Function in derived class
hisat2-2.2.1/hisat2.cpp:1601:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat2.cpp:1644:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat2.cpp:1663:32: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat2.cpp:1557:19: style: Condition 'args.size()>=1' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat2.cpp:1552:38: note: Assuming that condition 'args.size()==0' is not redundant
hisat2-2.2.1/hisat2.cpp:1557:19: note: Condition 'args.size()>=1' is always true
hisat2-2.2.1/hisat2.cpp:1575:28: style: Condition 'args.size()>=1' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat2.cpp:1570:47: note: Assuming that condition 'args.size()==0' is not redundant
hisat2-2.2.1/hisat2.cpp:1575:28: note: Condition 'args.size()>=1' is always true
hisat2-2.2.1/hisat2.cpp:3589:28: style: Condition '!done[mate]' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat2.cpp:3587:24: note: Assuming that condition '!done[mate]' is not redundant
hisat2-2.2.1/hisat2.cpp:3589:28: note: Condition '!done[mate]' is always true
hisat2-2.2.1/hi_aligner.h:5987:40: style: Condition 'r2.repeat()' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hi_aligner.h:5987:25: note: Assuming that condition 'r1.repeat()' is not redundant
hisat2-2.2.1/hi_aligner.h:5983:28: note: Assuming that condition 'r1.repeat()!=r2.repeat()' is not redundant
hisat2-2.2.1/hi_aligner.h:5987:40: note: Condition 'r2.repeat()' is always true
hisat2-2.2.1/hi_aligner.h:1549:24: style: Condition 'this_toff+len>reflen' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hi_aligner.h:1472:24: note: Assuming that condition 'this_toff+len>reflen' is not redundant
hisat2-2.2.1/hi_aligner.h:1506:33: note: Assuming condition is false
hisat2-2.2.1/hi_aligner.h:1549:24: note: Condition 'this_toff+len>reflen' is always false
hisat2-2.2.1/hi_aligner.h:2218:8: style: Condition 'doLeftAlign' is always false [knownConditionTrueFalse]
hisat2-2.2.1/hi_aligner.h:2056:24: note: Assignment 'doLeftAlign=false', assigned value is 0
hisat2-2.2.1/hi_aligner.h:2218:8: note: Condition 'doLeftAlign' is always false
hisat2-2.2.1/hi_aligner.h:573:24: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hi_aligner.h:956:9: style: Comparing expression of type 'unsigned int &' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hi_aligner.h:1014:9: style: Comparing expression of type 'unsigned int &' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hi_aligner.h:1393:5: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hi_aligner.h:1396:5: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hi_aligner.h:1452:5: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hi_aligner.h:1461:5: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/hi_aligner.h:2940:9: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/group_walk.h:681:3: style: Comparing expression of type 'unsigned int' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/group_walk.h:681:3: style: Comparing expression of type 'unsigned short' against value 0. Condition is always true. [compareValueOutOfTypeRangeError]
hisat2-2.2.1/aligner_sw_driver.h:1316:13: warning: Either the condition 'msink!=NULL' is redundant or there is possible null pointer dereference: msink. [nullPointerRedundantCheck]
hisat2-2.2.1/aligner_sw_driver.h:1319:37: note: Assuming that condition 'msink!=NULL' is not redundant
hisat2-2.2.1/aligner_sw_driver.h:1316:13: note: Null pointer dereference
hisat2-2.2.1/aligner_sw_driver.h:1963:13: warning: Either the condition 'msink!=NULL' is redundant or there is possible null pointer dereference: msink. [nullPointerRedundantCheck]
hisat2-2.2.1/aligner_sw_driver.h:1966:37: note: Assuming that condition 'msink!=NULL' is not redundant
hisat2-2.2.1/aligner_sw_driver.h:1963:13: note: Null pointer dereference
hisat2-2.2.1/aln_sink.h:2591:19: warning: Possible null pointer dereference: rs1 [nullPointer]
hisat2-2.2.1/hi_aligner.h:6195:35: note: Calling function 'report', 2nd argument 'NULL' value is 0
hisat2-2.2.1/aln_sink.h:2591:19: note: Null pointer dereference
hisat2-2.2.1/aln_sink.h:2592:19: warning: Possible null pointer dereference: rs2 [nullPointer]
hisat2-2.2.1/hi_aligner.h:6193:40: note: Calling function 'report', 3rd argument 'NULL' value is 0
hisat2-2.2.1/aln_sink.h:2592:19: note: Null pointer dereference
hisat2-2.2.1/aln_sink.h:2596:21: warning: Possible null pointer dereference: rs1 [nullPointer]
hisat2-2.2.1/hi_aligner.h:6195:35: note: Calling function 'report', 2nd argument 'NULL' value is 0
hisat2-2.2.1/aln_sink.h:2596:21: note: Null pointer dereference
hisat2-2.2.1/aln_sink.h:2598:21: warning: Possible null pointer dereference: rs2 [nullPointer]
hisat2-2.2.1/hi_aligner.h:6193:40: note: Calling function 'report', 3rd argument 'NULL' value is 0
hisat2-2.2.1/aln_sink.h:2598:21: note: Null pointer dereference
hisat2-2.2.1/hisat2.cpp:3149:14: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hi_aligner.h:4157:30: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hi_aligner.h:4159:28: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hi_aligner.h:4161:32: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hi_aligner.h:4163:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hi_aligner.h:4288:39: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hi_aligner.h:4289:46: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/spliced_aligner.h:188:15: style: Redundant initialization for 'maxsc'. The initialized value is overwritten before it is read. [redundantInitialization]
hisat2-2.2.1/spliced_aligner.h:187:23: note: maxsc is initialized
hisat2-2.2.1/spliced_aligner.h:188:15: note: maxsc is overwritten
hisat2-2.2.1/hisat2.cpp:3568:64: style: The comparison 'mate == 0' is always true. [knownConditionTrueFalse]
hisat2-2.2.1/hisat2.cpp:3559:35: note: 'mate' is assigned value '0' here.
hisat2-2.2.1/hisat2.cpp:3568:64: note: The comparison 'mate == 0' is always true.
hisat2-2.2.1/hisat2.cpp:1028:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat2.cpp:1150:4: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/aligner_sw_driver.h:1625:12: style: The scope of the variable 'nsInLeftShift' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2323:12: style: The scope of the variable 'nsInLeftShift' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2453:11: style: The scope of the variable 'foundMate' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2670:8: style: The scope of the variable 'refid' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2671:16: style: The scope of the variable 'off1' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2671:22: style: The scope of the variable 'off2' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2672:15: style: The scope of the variable 'len1' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2672:21: style: The scope of the variable 'len2' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2673:13: style: The scope of the variable 'fw1' can be reduced. [variableScope]
hisat2-2.2.1/aligner_sw_driver.h:2673:18: style: The scope of the variable 'fw2' can be reduced. [variableScope]
hisat2-2.2.1/hisat2.cpp:3527:22: style: The scope of the variable 'done' can be reduced. [variableScope]
hisat2-2.2.1/spliced_aligner.h:408:18: style: The scope of the variable 'another_spliced' can be reduced. [variableScope]
hisat2-2.2.1/spliced_aligner.h:1553:18: style: The scope of the variable 'uniqueStop' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1247:23: style: The scope of the variable 'next_i' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1553:21: style: The scope of the variable 'temp_scores' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1554:21: style: The scope of the variable 'temp_scores2' can be reduced. [variableScope]
hisat2-2.2.1/hi_aligner.h:1570:11: style: The scope of the variable 'maxsplscore' can be reduced. [variableScope]
hisat2-2.2.1/spliced_aligner.h:485:42: style: Checking if unsigned expression 'tempHit.len()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/spliced_aligner.h:606:46: style: Checking if unsigned expression 'tempHit.len()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/spliced_aligner.h:750:38: style: Checking if unsigned expression 'tempHit.len()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/spliced_aligner.h:1433:38: style: Checking if unsigned expression 'tempHit.len()' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/hi_aligner.h:5069:38: style: Checking if unsigned expression 'remainedGenomeHitSize' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/hi_aligner.h:5542:16: style: Checking if unsigned expression 'numHits' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/hi_aligner.h:573:21: style: Unsigned expression '_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:956:9: style: Unsigned expression 'len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1014:9: style: Unsigned expression 'len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1393:5: style: Unsigned expression 'this_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1396:5: style: Unsigned expression 'other_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1452:5: style: Unsigned expression 'this_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:1461:5: style: Unsigned expression 'other_len' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:2073:18: style: Checking if unsigned expression '_toff' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/hi_aligner.h:2940:9: style: Unsigned expression 'rdoff' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/hi_aligner.h:3619:13: style: Checking if unsigned expression '_len' is less than zero. [unsignedLessThanZero]
hisat2-2.2.1/group_walk.h:681:3: style: Unsigned expression 'trimBegin' can't be negative so it is unnecessary to test it. [unsignedPositive]
hisat2-2.2.1/aligner_sw_driver.h:596:18: style:inconclusive: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:466:17: note: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'.
hisat2-2.2.1/aligner_sw_driver.h:596:18: note: Function 'eeSaTups' argument 9 names different: declaration 'maxelts' definition 'maxelt'.
hisat2-2.2.1/aligner_sw_driver.h:1014:24: style:inconclusive: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:485:15: note: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'.
hisat2-2.2.1/aligner_sw_driver.h:1014:24: note: Function 'prioritizeSATups' argument 1 names different: declaration 'rd' definition 'read'.
hisat2-2.2.1/aligner_sw_driver.h:1312:34: style:inconclusive: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:366:25: note: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'.
hisat2-2.2.1/aligner_sw_driver.h:1312:34: note: Function 'extendSeeds' argument 32 names different: declaration 'mhs' definition 'msink'.
hisat2-2.2.1/aligner_sw_driver.h:1923:23: style:inconclusive: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:391:14: note: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'.
hisat2-2.2.1/aligner_sw_driver.h:1923:23: note: Function 'extendSeedsPaired' argument 10 names different: declaration 'swao' definition 'oswa'.
hisat2-2.2.1/aligner_sw_driver.h:1950:42: style:inconclusive: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'. [funcArgNamesDifferent]
hisat2-2.2.1/aligner_sw_driver.h:418:33: note: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'.
hisat2-2.2.1/aligner_sw_driver.h:1950:42: note: Function 'extendSeedsPaired' argument 37 names different: declaration 'cs' definition 'ca'.
hisat2-2.2.1/gfm.h:4369:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:88:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4369:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6481:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:88:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6481:13: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:649:29: style: Local variable 'rn' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:627:11: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:649:29: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:671:29: style: Local variable 'width' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:643:25: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:671:29: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:687:33: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:669:25: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:687:33: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:760:21: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:727:15: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:760:21: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:762:25: style: Local variable 'width' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:734:21: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:762:25: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:777:28: style: Local variable 'i' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:760:21: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:777:28: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:870:22: style: Local variable 'tloc' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:838:21: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:870:22: note: Shadow variable
hisat2-2.2.1/aligner_sw_driver.h:870:28: style: Local variable 'bloc' shadows outer variable [shadowVariable]
hisat2-2.2.1/aligner_sw_driver.h:838:27: note: Shadowed declaration
hisat2-2.2.1/aligner_sw_driver.h:870:28: note: Shadow variable
hisat2-2.2.1/hisat2.cpp:1387:11: style: Local variable 'argstr' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:3700:15: note: Shadowed declaration
hisat2-2.2.1/hisat2.cpp:1387:11: note: Shadow variable
hisat2-2.2.1/hisat2.cpp:1399:11: style: Local variable 'argstr' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:3700:15: note: Shadowed declaration
hisat2-2.2.1/hisat2.cpp:1399:11: note: Shadow variable
hisat2-2.2.1/hisat2.cpp:3527:22: style: Local variable 'done' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:3274:25: note: Shadowed declaration
hisat2-2.2.1/hisat2.cpp:3527:22: note: Shadow variable
hisat2-2.2.1/hisat2.cpp:4083:21: style: Local variable 'gpol' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:2018:42: note: Shadowed declaration
hisat2-2.2.1/hisat2.cpp:4083:21: note: Shadow variable
hisat2-2.2.1/spliced_aligner.h:224:64: style: Local variable 'maxhalf' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:213:15: note: Shadowed declaration
hisat2-2.2.1/spliced_aligner.h:224:64: note: Shadow variable
hisat2-2.2.1/spliced_aligner.h:237:24: style: Local variable 'cminlen' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:227:15: note: Shadowed declaration
hisat2-2.2.1/spliced_aligner.h:237:24: note: Shadow variable
hisat2-2.2.1/spliced_aligner.h:237:40: style: Local variable 'cpow2' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:228:15: note: Shadowed declaration
hisat2-2.2.1/spliced_aligner.h:237:40: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4152:14: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4152:14: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4106:30: style: Local variable 'fw' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4072:14: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4106:30: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4246:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4246:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4249:26: style: Local variable 'fw' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4072:14: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4249:26: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4255:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4255:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4293:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4293:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4300:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4300:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4357:24: style: Local variable 'rdi' shadows outer variable [shadowVariable]
hisat2-2.2.1/hi_aligner.h:4071:17: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4357:24: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4669:18: style: Local variable 'pseudogeneStop' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:264:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4669:18: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:4670:18: style: Local variable 'anchorStop' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:263:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:4670:18: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:1470:13: style: Local variable 'len' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:827:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:1470:13: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:1478:10: style: Local variable 'spliced' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:1086:22: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:1478:10: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:2059:19: style: Local variable 'minIntronLen' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:253:15: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:2059:19: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:2060:19: style: Local variable 'maxIntronLen' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:254:15: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:2060:19: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:3639:13: style: Local variable 'refoff' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:895:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:3639:13: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:3722:13: style: Local variable 'score' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:910:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:3722:13: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:3723:12: style: Local variable 'splicescore' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:912:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:3723:12: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:3724:13: style: Local variable 'localscore' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:911:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:3724:13: note: Shadow variable
hisat2-2.2.1/hi_aligner.h:325:21: style: Local variable 'len' shadows outer function [shadowFunction]
hisat2-2.2.1/hi_aligner.h:262:13: note: Shadowed declaration
hisat2-2.2.1/hi_aligner.h:325:21: note: Shadow variable
hisat2-2.2.1/aln_sink.h:2207:54: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/aln_sink.h:2207:54: note: Shadow variable
hisat2-2.2.1/hgfm.h:2585:10: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:88:12: note: Shadowed declaration
hisat2-2.2.1/hgfm.h:2585:10: note: Shadow variable
hisat2-2.2.1/gfm.h:2165:48: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/gfm.h:2165:48: note: Shadow variable
hisat2-2.2.1/gfm.h:5979:14: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:88:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5979:14: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:2685:19: style: Local variable 'queries' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:233:22: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:2685:19: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:880:13: style: Local variable 'nthreads' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:92:12: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:880:13: note: Shadow variable
hisat2-2.2.1/repeat.h:296:30: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:296:30: note: Shadow variable
hisat2-2.2.1/repeat.h:336:30: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:336:30: note: Shadow variable
hisat2-2.2.1/repeat.h:365:32: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:365:32: note: Shadow variable
hisat2-2.2.1/repeat.h:387:32: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:387:32: note: Shadow variable
hisat2-2.2.1/repeat.h:447:32: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:447:32: note: Shadow variable
hisat2-2.2.1/repeat.h:520:32: style: Local variable 'repeat' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat2.cpp:298:13: note: Shadowed declaration
hisat2-2.2.1/repeat.h:520:32: note: Shadow variable
hisat2-2.2.1/spliced_aligner.h:175:33: style: Variable 'genomeHit_j' can be declared as reference to const [constVariable]
hisat2-2.2.1/spliced_aligner.h:176:33: style: Variable 'genomeHit_k' can be declared as reference to const [constVariable]
hisat2-2.2.1/spliced_aligner.h:1040:41: style: Variable 'tempHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/spliced_aligner.h:1727:41: style: Variable 'tempHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:4187:46: style: Variable 'partialHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:4199:46: style: Variable 'partialHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:4236:42: style: Variable 'partialHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:4262:42: style: Variable 'partialHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:5036:34: style: Variable 'partialHit_j' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:5044:34: style: Variable 'partialHit_j' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:5045:34: style: Variable 'partialHit_k' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:6283:77: style: Parameter 'sink' can be declared as reference to const [constParameter]
hisat2-2.2.1/hi_aligner.h:1255:27: style: Variable 'next_ed' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:1290:43: style: Variable 'ii_ed' can be declared as reference to const [constVariable]
hisat2-2.2.1/hi_aligner.h:4019:39: style: Parameter 'nofw' can be declared as const array [constParameter]
hisat2-2.2.1/hi_aligner.h:4019:53: style: Parameter 'norc' can be declared as const array [constParameter]
hisat2-2.2.1/hi_aligner.h:4019:71: style: Parameter 'minsc' can be declared as const array [constParameter]
hisat2-2.2.1/hi_aligner.h:4019:90: style: Parameter 'maxpen' can be declared as const array [constParameter]
hisat2-2.2.1/hi_aligner.h:4102:25: style: Variable 'rs_size' can be declared as const array [constVariable]
hisat2-2.2.1/hi_aligner.h:4174:25: style: Variable 'fwi' can be declared as const array [constVariable]
hisat2-2.2.1/hisat2.cpp:3962:20: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
hisat2-2.2.1/hisat2.cpp:3969:20: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
hisat2-2.2.1/hi_aligner.h:323:40: style: int result is assigned to long variable. If the variable is long to avoid loss of information, then you have loss of information. [truncLongCastAssignment]
hisat2-2.2.1/aligner_sw_driver.h:1164:16: style: Variable 'nlarge_elts' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_sw_driver.h:1166:16: style: Variable 'nlarge_elts' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/aligner_sw_driver.h:2453:21: style: Variable 'foundMate' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3456:15: style: Variable 'nceil[1]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3474:21: style: Variable 'interval[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3484:18: style: Variable 'mtStreak[0]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3484:32: style: Variable 'mtStreak[1]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3491:22: style: Variable 'mtStreak[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat2.cpp:3590:40: style: Variable 'done[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hi_aligner.h:3637:22: style: Variable 'refallen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hi_aligner.h:3654:26: style: Variable 'refallen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hi_aligner.h:3665:14: style: Variable 'refallen' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/group_walk.h:1059:13: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/group_walk.h:1276:25: style: Variable 'sum' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:1741:2: warning: Member variable 'PerfMetrics::lastElapsed' is not initialized in the constructor. [uninitMemberVar]
hisat2-2.2.1/hisat_bp.cpp:1412:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat_bp.cpp:1451:23: warning: Logical conjunction always evaluates to false: args.size() > 3 && args.size() == 0. [incorrectLogicOperator]
hisat2-2.2.1/hisat_bp.cpp:1395:19: style: Condition 'args.size()>=1' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat_bp.cpp:1390:38: note: Assuming that condition 'args.size()==0' is not redundant
hisat2-2.2.1/hisat_bp.cpp:1395:19: note: Condition 'args.size()>=1' is always true
hisat2-2.2.1/hisat_bp.cpp:3242:28: style: Condition '!done[mate]' is always true [knownConditionTrueFalse]
hisat2-2.2.1/hisat_bp.cpp:3240:24: note: Assuming that condition '!done[mate]' is not redundant
hisat2-2.2.1/hisat_bp.cpp:3242:28: note: Condition '!done[mate]' is always true
hisat2-2.2.1/hisat_bp.cpp:3525:4: warning: Either the condition 'fout!=NULL' is redundant or there is possible null pointer dereference: fout. [nullPointerRedundantCheck]
hisat2-2.2.1/hisat_bp.cpp:3736:11: note: Assuming that condition 'fout!=NULL' is not redundant
hisat2-2.2.1/hisat_bp.cpp:3525:4: note: Null pointer dereference
hisat2-2.2.1/hisat_bp.cpp:3696:5: warning: Either the condition 'ebwtBw!=NULL' is redundant or there is possible null pointer dereference: ebwtBw. [nullPointerRedundantCheck]
hisat2-2.2.1/hisat_bp.cpp:3704:13: note: Assuming that condition 'ebwtBw!=NULL' is not redundant
hisat2-2.2.1/hisat_bp.cpp:3696:5: note: Null pointer dereference
hisat2-2.2.1/hisat_bp.cpp:2815:14: style: C-style pointer casting [cstyleCast]
hisat2-2.2.1/hisat_bp.cpp:3221:64: style: The comparison 'mate == 0' is always true. [knownConditionTrueFalse]
hisat2-2.2.1/hisat_bp.cpp:3212:35: note: 'mate' is assigned value '0' here.
hisat2-2.2.1/hisat_bp.cpp:3221:64: note: The comparison 'mate == 0' is always true.
hisat2-2.2.1/hisat_bp.cpp:873:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat_bp.cpp:995:4: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
hisat2-2.2.1/hisat_bp.cpp:3201:22: style: The scope of the variable 'done' can be reduced. [variableScope]
hisat2-2.2.1/bp_aligner.h:846:18: style: The scope of the variable 'uniqueStop' can be reduced. [variableScope]
hisat2-2.2.1/gfm.h:4369:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:87:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:4369:13: note: Shadow variable
hisat2-2.2.1/gfm.h:6481:13: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:87:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:6481:13: note: Shadow variable
hisat2-2.2.1/hisat_bp.cpp:1228:11: style: Local variable 'argstr' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:3389:15: note: Shadowed declaration
hisat2-2.2.1/hisat_bp.cpp:1228:11: note: Shadow variable
hisat2-2.2.1/hisat_bp.cpp:1240:11: style: Local variable 'argstr' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:3389:15: note: Shadowed declaration
hisat2-2.2.1/hisat_bp.cpp:1240:11: note: Shadow variable
hisat2-2.2.1/hisat_bp.cpp:3201:22: style: Local variable 'done' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:2944:25: note: Shadowed declaration
hisat2-2.2.1/hisat_bp.cpp:3201:22: note: Shadow variable
hisat2-2.2.1/bp_aligner.h:559:29: style: Local variable 'minsc' shadows outer variable [shadowVariable]
hisat2-2.2.1/bp_aligner.h:554:21: note: Shadowed declaration
hisat2-2.2.1/bp_aligner.h:559:29: note: Shadow variable
hisat2-2.2.1/bp_aligner.h:1034:29: style: Local variable 'minsc' shadows outer variable [shadowVariable]
hisat2-2.2.1/bp_aligner.h:1029:21: note: Shadowed declaration
hisat2-2.2.1/bp_aligner.h:1034:29: note: Shadow variable
hisat2-2.2.1/gfm.h:5979:14: style: Local variable 'offRate' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:87:12: note: Shadowed declaration
hisat2-2.2.1/gfm.h:5979:14: note: Shadow variable
hisat2-2.2.1/gbwt_graph.h:2685:19: style: Local variable 'queries' shadows outer variable [shadowVariable]
hisat2-2.2.1/hisat_bp.cpp:229:22: note: Shadowed declaration
hisat2-2.2.1/gbwt_graph.h:2685:19: note: Shadow variable
hisat2-2.2.1/bp_aligner.h:184:33: style: Variable 'genomeHit_j' can be declared as reference to const [constVariable]
hisat2-2.2.1/bp_aligner.h:185:33: style: Variable 'genomeHit_k' can be declared as reference to const [constVariable]
hisat2-2.2.1/bp_aligner.h:194:29: style: Variable 'genomeHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/bp_aligner.h:558:41: style: Variable 'tempHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/bp_aligner.h:1033:41: style: Variable 'tempHit' can be declared as reference to const [constVariable]
hisat2-2.2.1/hisat_bp.cpp:3130:15: style: Variable 'nceil[1]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3148:21: style: Variable 'interval[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3158:18: style: Variable 'mtStreak[0]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3158:32: style: Variable 'mtStreak[1]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3165:22: style: Variable 'mtStreak[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3243:40: style: Variable 'done[mate]' is assigned a value that is never used. [unreadVariable]
hisat2-2.2.1/hisat_bp.cpp:3710:15: style: Variable 'repThresh' is assigned a value that is never used. [unreadVariable]
diff:
head hisat2-2.2.1/aligner_result.h:2028:2: style: Class 'RedundantAlns' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/aligner_seed2.h:580:39: style: Variable 'map' can be declared as reference to const [constVariable]
2.8 hisat2-2.2.1/aligner_seed2.h:580:39: style: Variable 'map' can be declared with const [constVariable]
head hisat2-2.2.1/aligner_sw_driver.h:194:2: style: Class 'RowSampler' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/aligner_swsse.cpp:43:21: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/aligner_swsse.h:108:2: style: Struct 'SSEMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/aligner_swsse.h:409:2: style: Struct 'SSEData' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/alt.h:239:25: style: Parameter 'f_in' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/alt.h:239:25: style: Parameter 'f_in' can be declared with const [constParameter]
head hisat2-2.2.1/assert_helpers.h:33:2: style: Class 'ReleaseAssertException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/bit_packed_array.cpp:165:46: style: Parameter 'block' can be declared as pointer to const [constParameter]
2.8 hisat2-2.2.1/bit_packed_array.cpp:165:46: style: Parameter 'block' can be declared with const [constParameter]
head hisat2-2.2.1/blockwise_sa.h:1020:28: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/blockwise_sa.h:568:28: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/blockwise_sa.h:621:32: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/blockwise_sa.h:955:28: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/bp_aligner.h:1033:41: style: Variable 'tempHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/bp_aligner.h:184:33: style: Variable 'genomeHit_j' can be declared as reference to const [constVariable]
head hisat2-2.2.1/bp_aligner.h:185:33: style: Variable 'genomeHit_k' can be declared as reference to const [constVariable]
head hisat2-2.2.1/bp_aligner.h:194:29: style: Variable 'genomeHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/bp_aligner.h:558:41: style: Variable 'tempHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/diff_sample.h:109:27: style: Parameter 'ts' can be declared as pointer to const [constParameter]
2.8 hisat2-2.2.1/diff_sample.h:109:27: style: Parameter 'ts' can be declared with const [constParameter]
head hisat2-2.2.1/diff_sample.h:121:37: style: Parameter 'ds' can be declared as pointer to const [constParameter]
2.8 hisat2-2.2.1/diff_sample.h:121:37: style: Parameter 'ds' can be declared with const [constParameter]
head hisat2-2.2.1/dp_framer.h:61:2: style: Struct 'DPRect' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet < RedundantCell >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet < unsigned long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:1733:2: style: Class 'ESet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:2459:2: style: Class 'EMap < DescentRedundancyKey , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:2459:2: style: Class 'EMap' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:3199:2: style: Class 'PList < QKey , 16384 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:3199:2: style: Class 'PList < uint32_t , 16384 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:3199:2: style: Class 'PList' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/ds.h:3730:34: style: Parameter 'ol' can be declared as pointer to const [constParameter]
2.8 hisat2-2.2.1/ds.h:3730:34: style: Parameter 'ol' can be declared with const [constParameter]
head hisat2-2.2.1/gbwt_graph.h:109:29: style: Parameter 'f_in' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/gbwt_graph.h:109:29: style: Parameter 'f_in' can be declared with const [constParameter]
head hisat2-2.2.1/gbwt_graph.h:121:34: style: Parameter 'a' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/gbwt_graph.h:121:34: style: Parameter 'a' can be declared with const [constParameter]
head hisat2-2.2.1/gbwt_graph.h:1418:28: style: Variable 'predecessor_cnode' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gbwt_graph.h:1519:51: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathNodeFrom' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     hisat2-2.2.1/gbwt_graph.h:1970:14: note: You might need to cast the function pointer here
     hisat2-2.2.1/gbwt_graph.h:1519:51: note: Parameter 'a' can be declared as reference to const
2.8 hisat2-2.2.1/gbwt_graph.h:1519:51: style: Parameter 'a' can be declared with const. However it seems that 'PathNodeFrom' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     hisat2-2.2.1/gbwt_graph.h:1970:14: note: You might need to cast the function pointer here
     hisat2-2.2.1/gbwt_graph.h:1519:51: note: Parameter 'a' can be declared with const
head hisat2-2.2.1/gbwt_graph.h:1523:50: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathNodeKey' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     hisat2-2.2.1/gbwt_graph.h:2507:104: note: You might need to cast the function pointer here
     hisat2-2.2.1/gbwt_graph.h:1523:50: note: Parameter 'a' can be declared as reference to const
2.8 hisat2-2.2.1/gbwt_graph.h:1523:50: style: Parameter 'a' can be declared with const. However it seems that 'PathNodeKey' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     hisat2-2.2.1/gbwt_graph.h:2507:104: note: You might need to cast the function pointer here
     hisat2-2.2.1/gbwt_graph.h:1523:50: note: Parameter 'a' can be declared with const
head hisat2-2.2.1/gbwt_graph.h:1569:49: style: Parameter 'a' can be declared as reference to const. However it seems that 'PathEdgeTo' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     hisat2-2.2.1/gbwt_graph.h:2610:102: note: You might need to cast the function pointer here
     hisat2-2.2.1/gbwt_graph.h:1569:49: note: Parameter 'a' can be declared as reference to const
2.8 hisat2-2.2.1/gbwt_graph.h:1569:49: style: Parameter 'a' can be declared with const. However it seems that 'PathEdgeTo' is a callback function, if 'a' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
     hisat2-2.2.1/gbwt_graph.h:2610:102: note: You might need to cast the function pointer here
     hisat2-2.2.1/gbwt_graph.h:1569:49: note: Parameter 'a' can be declared with const
head hisat2-2.2.1/gbwt_graph.h:2314:46: style: Variable 'ref_nodes' can be declared as reference to const [constVariable]
2.8 hisat2-2.2.1/gbwt_graph.h:2314:46: style: Variable 'ref_nodes' can be declared with const [constVariable]
head hisat2-2.2.1/gbwt_graph.h:2341:46: style: Variable 'ref_nodes' can be declared as reference to const [constVariable]
2.8 hisat2-2.2.1/gbwt_graph.h:2341:46: style: Variable 'ref_nodes' can be declared with const [constVariable]
head hisat2-2.2.1/gbwt_graph.h:2343:46: style: Variable 'nodes' can be declared as reference to const [constVariable]
2.8 hisat2-2.2.1/gbwt_graph.h:2343:46: style: Variable 'nodes' can be declared with const [constVariable]
head hisat2-2.2.1/gfm.h:306:2: style: Class 'GFMFileOpenException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/gfm.h:3740:61: style: Parameter 'tloc' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/gfm.h:3740:61: style: Parameter 'tloc' can be declared with const [constParameter]
head hisat2-2.2.1/gfm.h:3740:87: style: Parameter 'bloc' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/gfm.h:3740:87: style: Parameter 'bloc' can be declared with const [constParameter]
head hisat2-2.2.1/gfm.h:4592:21: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:4753:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:4775:21: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:5072:21: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:5197:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:5217:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:5444:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:6067:28: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:6160:32: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:6309:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:6349:36: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/gfm.h:6846:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:1060:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:1202:22: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:1284:23: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:1433:21: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:1452:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:391:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:413:21: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:701:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:819:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hgfm.h:839:24: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:1255:27: style: Variable 'next_ed' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:1290:43: style: Variable 'ii_ed' can be declared as reference to const [constVariable]
2.8 hisat2-2.2.1/hi_aligner.h:4019:26: style: Parameter 'rds' can be declared with const [constParameter]
head hisat2-2.2.1/hi_aligner.h:4019:39: style: Parameter 'nofw' can be declared as const array [constParameter]
2.8 hisat2-2.2.1/hi_aligner.h:4019:39: style: Parameter 'nofw' can be declared with const [constParameter]
head hisat2-2.2.1/hi_aligner.h:4019:53: style: Parameter 'norc' can be declared as const array [constParameter]
2.8 hisat2-2.2.1/hi_aligner.h:4019:53: style: Parameter 'norc' can be declared with const [constParameter]
head hisat2-2.2.1/hi_aligner.h:4019:71: style: Parameter 'minsc' can be declared as const array [constParameter]
2.8 hisat2-2.2.1/hi_aligner.h:4019:71: style: Parameter 'minsc' can be declared with const [constParameter]
head hisat2-2.2.1/hi_aligner.h:4019:90: style: Parameter 'maxpen' can be declared as const array [constParameter]
2.8 hisat2-2.2.1/hi_aligner.h:4019:90: style: Parameter 'maxpen' can be declared with const [constParameter]
head hisat2-2.2.1/hi_aligner.h:4102:25: style: Variable 'rs_size' can be declared as const array [constVariable]
2.8 hisat2-2.2.1/hi_aligner.h:4102:25: style: Variable 'rs_size' can be declared with const [constVariable]
head hisat2-2.2.1/hi_aligner.h:4174:25: style: Variable 'fwi' can be declared as const array [constVariable]
2.8 hisat2-2.2.1/hi_aligner.h:4174:25: style: Variable 'fwi' can be declared with const [constVariable]
head hisat2-2.2.1/hi_aligner.h:4187:46: style: Variable 'partialHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:4199:46: style: Variable 'partialHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:4236:42: style: Variable 'partialHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:4262:42: style: Variable 'partialHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:5036:34: style: Variable 'partialHit_j' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:5044:34: style: Variable 'partialHit_j' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:5045:34: style: Variable 'partialHit_k' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hi_aligner.h:6283:77: style: Parameter 'sink' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/hi_aligner.h:6283:77: style: Parameter 'sink' can be declared with const [constParameter]
head hisat2-2.2.1/hisat2_build.cpp:821:32: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hisat2_repeat.cpp:714:33: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/hisat2_repeat.cpp:858:32: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/multikey_qsort.h:252:14: style: Parameter 's' can be declared as pointer to const [constParameter]
2.8 hisat2-2.2.1/multikey_qsort.h:252:14: style: Parameter 's' can be declared with const [constParameter]
head hisat2-2.2.1/multikey_qsort.h:291:14: style: Parameter 's' can be declared as pointer to const [constParameter]
2.8 hisat2-2.2.1/multikey_qsort.h:291:14: style: Parameter 's' can be declared with const [constParameter]
head hisat2-2.2.1/multikey_qsort.h:323:53: style: Parameter 's' can be declared as pointer to const [constParameter]
2.8 hisat2-2.2.1/multikey_qsort.h:323:53: style: Parameter 's' can be declared with const [constParameter]
head hisat2-2.2.1/multikey_qsort.h:877:14: style: Parameter 's' can be declared as pointer to const [constParameter]
2.8 hisat2-2.2.1/multikey_qsort.h:877:14: style: Parameter 's' can be declared with const [constParameter]
head hisat2-2.2.1/random_util.h:50:2: style: Class 'Random1toN' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hisat2-2.2.1/reference.cpp:219:28: style: Variable 'e' can be declared as reference to const [constVariable]
head hisat2-2.2.1/reference.cpp:475:14: style: Condition 'count>0' is always true [knownConditionTrueFalse]
     hisat2-2.2.1/reference.cpp:470:12: note: Assuming that condition 'count==0' is not redundant
     hisat2-2.2.1/reference.cpp:475:14: note: Condition 'count>0' is always true
head hisat2-2.2.1/reference.cpp:639:14: style: Condition 'count>0' is always true [knownConditionTrueFalse]
     hisat2-2.2.1/reference.cpp:633:12: note: Assuming that condition 'count==0' is not redundant
     hisat2-2.2.1/reference.cpp:639:14: note: Condition 'count>0' is always true
head hisat2-2.2.1/repeat.h:343:40: style: Variable 'allele' can be declared as reference to const [constVariable]
head hisat2-2.2.1/repeat_builder.cpp:142:35: style: Parameter 'coordHelper' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/repeat_builder.cpp:142:35: style: Parameter 'coordHelper' can be declared with const [constParameter]
head hisat2-2.2.1/repeat_builder.cpp:2030:29: style: Variable 'range2' can be declared as reference to const [constVariable]
head hisat2-2.2.1/repeat_builder.cpp:2099:39: style: Parameter 'coordHelper' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/repeat_builder.cpp:2099:39: style: Parameter 'coordHelper' can be declared with const [constParameter]
head hisat2-2.2.1/repeat_builder.cpp:3455:20: style: Variable 'repeat' can be declared as reference to const [constVariable]
head hisat2-2.2.1/repeat_builder.cpp:352:22: style: Parameter 'array' can be declared as const array [constParameter]
2.8 hisat2-2.2.1/repeat_builder.cpp:352:22: style: Parameter 'array' can be declared with const [constParameter]
head hisat2-2.2.1/repeat_builder.cpp:3555:34: style: Variable 'seed' can be declared as reference to const [constVariable]
head hisat2-2.2.1/repeat_builder.cpp:3565:34: style: Variable 'seed' can be declared as reference to const [constVariable]
head hisat2-2.2.1/repeat_builder.cpp:387:17: style: Variable 'nameline' can be declared as reference to const [constVariable]
head hisat2-2.2.1/repeat_builder.cpp:600:65: style: Parameter 'snp' can be declared as reference to const [constParameter]
2.8 hisat2-2.2.1/repeat_builder.cpp:600:65: style: Parameter 'snp' can be declared with const [constParameter]
head hisat2-2.2.1/repeat_builder.cpp:932:29: style: Variable 'range2' can be declared as reference to const [constVariable]
head hisat2-2.2.1/repeat_kmer.h:355:35: style: Variable 'position' can be declared as reference to const [constVariable]
head hisat2-2.2.1/repeat_kmer.h:384:35: style: Variable 'position' can be declared as reference to const [constVariable]
head hisat2-2.2.1/rfm.h:459:21: style: Variable 'ref' can be declared as reference to const [constVariable]
head hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::matchBonuses' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::mmpens' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/scoring.h:140:5: warning: Member variable 'Scoring::npens' is not initialized in the constructor. [uninitMemberVar]
head hisat2-2.2.1/splice_site.cpp:168:23: style: Variable 'pool' can be declared as reference to const [constVariable]
head hisat2-2.2.1/splice_site_new.cpp:656:23: style: Variable 'pool' can be declared as reference to const [constVariable]
head hisat2-2.2.1/spliced_aligner.h:1040:41: style: Variable 'tempHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/spliced_aligner.h:1727:41: style: Variable 'tempHit' can be declared as reference to const [constVariable]
head hisat2-2.2.1/spliced_aligner.h:175:33: style: Variable 'genomeHit_j' can be declared as reference to const [constVariable]
head hisat2-2.2.1/spliced_aligner.h:176:33: style: Variable 'genomeHit_k' can be declared as reference to const [constVariable]
head hisat2-2.2.1/timer.h:37:2: style: Class 'Timer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]


DONE