2022-06-28 17:01
ftp://ftp.de.debian.org/debian/pool/main/h/hhsuite/hhsuite_3.3.0+ds.orig.tar.xz
cppcheck-options: --library=posix --library=gnu  --showtime=top5 --check-library --inconclusive --enable=style,information --template=daca2 -D__GNUC__ --platform=unix64 -rp=temp -j2
platform: Linux-5.4.0-110-generic-x86_64-with-glibc2.29
python: 3.8.10
client-version: 1.3.24
compiler: g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
cppcheck: head 2.8
head-info: 2223cd2 (2022-06-28 14:02:02 +0200)
count: 773 769
elapsed-time: 753.1 1194.0
head-timing-info:
 Overall time: 0s

old-timing-info:
 Overall time: 0s

head results:
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:162:18: portability: Non reentrant function 'readdir' called. For threadsafe applications it is recommended to use the reentrant replacement function 'readdir_r'. [prohibitedreaddirCalled]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:115:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:115:5: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:222:5: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:222:5: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:291:5: portability: %ld in format string (no. 1) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:411:8: portability: %zd in format string (no. 2) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:411:8: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:479:10: warning: Either the condition 'index_fh==NULL' is redundant or there is possible null pointer dereference: index_fh. [nullPointerRedundantCheck]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:477:15: note: Assuming that condition 'index_fh==NULL' is not redundant
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:479:10: note: Null pointer dereference
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:142:67: style:inconclusive: Function 'ffindex_insert_dir' argument 3 names different: declaration 'offset' definition 'start_offset'. [funcArgNamesDifferent]
hh-suite-3.3.0/lib/ffindex/src/ffindex.h:59:67: note: Function 'ffindex_insert_dir' argument 3 names different: declaration 'offset' definition 'start_offset'.
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:142:67: note: Function 'ffindex_insert_dir' argument 3 names different: declaration 'offset' definition 'start_offset'.
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:389:71: style:inconclusive: Function 'ffindex_fopen_by_name' argument 3 names different: declaration 'name' definition 'filename'. [funcArgNamesDifferent]
hh-suite-3.3.0/lib/ffindex/src/ffindex.h:63:71: note: Function 'ffindex_fopen_by_name' argument 3 names different: declaration 'name' definition 'filename'.
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:389:71: note: Function 'ffindex_fopen_by_name' argument 3 names different: declaration 'name' definition 'filename'.
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:447:63: style:inconclusive: Function 'ffindex_unlink' argument 2 names different: declaration 'entry_name' definition 'name_to_unlink'. [funcArgNamesDifferent]
hh-suite-3.3.0/lib/ffindex/src/ffindex.h:89:63: note: Function 'ffindex_unlink' argument 2 names different: declaration 'entry_name' definition 'name_to_unlink'.
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:447:63: note: Function 'ffindex_unlink' argument 2 names different: declaration 'entry_name' definition 'name_to_unlink'.
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:48:73: style: Parameter 'mode' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/lib/ffindex/src/ffindex.c:279:36: error: Uninitialized variables: &search.offset, &search.length [uninitvar]
hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:13: portability: %ld in format string (no. 2) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:13: portability: %ld in format string (no. 3) requires 'long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:172:13: warning: %lld in format string (no. 4) requires 'long long' but the argument type is 'signed long'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:169:28: style: Local variable 'tv' shadows outer variable [shadowVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:94:20: note: Shadowed declaration
hh-suite-3.3.0/lib/ffindex/src/ffindex_apply_mpi.c:169:28: note: Shadow variable
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta.c:77:5: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta.c:122:24: style: Variable 'seq_id_length' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta.c:123:19: style: Variable 'count_ws' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta.c:127:23: style: Variable 'entry_length' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_build.c:117:5: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex_build.c:150:5: warning: Repositioning operation performed on a file opened in append mode has no effect. [seekOnAppendedFile]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta_with_split.c:100:5: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta_with_split.c:68:9: warning: Size of pointer 'substr' used instead of size of its data. [pointerSize]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta_with_split.c:158:24: style: Variable 'seq_id_length' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta_with_split.c:159:19: style: Variable 'count_ws' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta_with_split.c:163:24: style: Variable 'header_length' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta_with_split.c:164:18: style: Variable 'is_header' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_from_fasta_with_split.c:167:26: style: Variable 'sequence_length' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/lib/ffindex/src/ffindex_modify.c:90:5: portability: %zd in format string (no. 3) requires 'ssize_t' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_sint]
hh-suite-3.3.0/lib/ffindex/src/ffindex_unpack.c:74:32: warning: Either the condition 'entry==NULL' is redundant or there is possible null pointer dereference: entry. [nullPointerRedundantCheck]
hh-suite-3.3.0/lib/ffindex/src/ffindex_unpack.c:74:14: note: Assuming that condition 'entry==NULL' is not redundant
hh-suite-3.3.0/lib/ffindex/src/ffindex_unpack.c:74:32: note: Null pointer dereference
hh-suite-3.3.0/lib/ffindex/src/ffindex_reduce.c:80:32: warning: Either the condition 'entry==NULL' is redundant or there is possible null pointer dereference: entry. [nullPointerRedundantCheck]
hh-suite-3.3.0/lib/ffindex/src/ffindex_reduce.c:80:14: note: Assuming that condition 'entry==NULL' is not redundant
hh-suite-3.3.0/lib/ffindex/src/ffindex_reduce.c:80:32: note: Null pointer dereference
hh-suite-3.3.0/src/a3m_database_extract.cpp:178:32: warning: Either the condition 'entry==NULL' is redundant or there is possible null pointer dereference: entry. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/a3m_database_extract.cpp:178:14: note: Assuming that condition 'entry==NULL' is not redundant
hh-suite-3.3.0/src/a3m_database_extract.cpp:178:32: note: Null pointer dereference
hh-suite-3.3.0/src/a3m_compress.cpp:136:20: style: Array index 'index' is used before limits check. [arrayIndexThenCheck]
hh-suite-3.3.0/src/a3m_compress.cpp:142:20: style: Array index 'index' is used before limits check. [arrayIndexThenCheck]
hh-suite-3.3.0/src/a3m_compress.cpp:407:36: style: Array index 'index' is used before limits check. [arrayIndexThenCheck]
hh-suite-3.3.0/src/a3m_compress.cpp:444:36: style: Array index 'index' is used before limits check. [arrayIndexThenCheck]
hh-suite-3.3.0/src/a3m_compress.cpp:556:14: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/a3m_compress.cpp:580:14: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/a3m_compress.cpp:265:15: style: Variable 'last_char' is reassigned a value before the old one has been used. [redundantAssignment]
hh-suite-3.3.0/src/a3m_compress.cpp:259:17: note: last_char is assigned
hh-suite-3.3.0/src/a3m_compress.cpp:265:15: note: last_char is overwritten
hh-suite-3.3.0/src/a3m_compress.cpp:81:12: warning: Redundant assignment of 'line' to itself. [selfAssignment]
hh-suite-3.3.0/src/a3m_compress.cpp:522:10: style:inconclusive: Same expression used in consecutive assignments of 'first_pipe_index' and 'second_pipe_index'. [duplicateAssignExpression]
hh-suite-3.3.0/src/a3m_compress.cpp:523:10: note: Same expression used in consecutive assignments of 'first_pipe_index' and 'second_pipe_index'.
hh-suite-3.3.0/src/a3m_compress.cpp:522:10: note: Same expression used in consecutive assignments of 'first_pipe_index' and 'second_pipe_index'.
hh-suite-3.3.0/src/a3m_compress.cpp:247:59: style:inconclusive: Function 'extract_a3m' argument 6 names different: declaration 'ffindex_header_data' definition 'ffindex_header_database_data'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/a3m_compress.h:32:61: note: Function 'extract_a3m' argument 6 names different: declaration 'ffindex_header_data' definition 'ffindex_header_database_data'.
hh-suite-3.3.0/src/a3m_compress.cpp:247:59: note: Function 'extract_a3m' argument 6 names different: declaration 'ffindex_header_data' definition 'ffindex_header_database_data'.
hh-suite-3.3.0/src/a3m_compress.cpp:357:17: style:inconclusive: Function 'compress_sequence' argument 2 names different: declaration 'sequence' definition 'aligned_sequence'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/a3m_compress.h:28:53: note: Function 'compress_sequence' argument 2 names different: declaration 'sequence' definition 'aligned_sequence'.
hh-suite-3.3.0/src/a3m_compress.cpp:357:17: note: Function 'compress_sequence' argument 2 names different: declaration 'sequence' definition 'aligned_sequence'.
hh-suite-3.3.0/src/a3m_compress.cpp:521:47: style:inconclusive: Function 'getShortIdFromHeader' argument 1 names different: declaration 'header' definition 'id'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/a3m_compress.h:47:47: note: Function 'getShortIdFromHeader' argument 1 names different: declaration 'header' definition 'id'.
hh-suite-3.3.0/src/a3m_compress.cpp:521:47: note: Function 'getShortIdFromHeader' argument 1 names different: declaration 'header' definition 'id'.
hh-suite-3.3.0/src/a3m_compress.cpp:356:51: performance: Function parameter 'id' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/a3m_compress.cpp:478:11: style: Parameter 'full_sequence' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/src/a3m_compress.cpp:407:36: warning: Either the condition 'index<aligned_sequence.size()' is redundant or 'index' can have the value greater or equal to aligned_sequence.size(). Expression 'aligned_sequence[index]' cause access out of bounds. [containerOutOfBounds]
hh-suite-3.3.0/src/a3m_compress.cpp:401:88: note: Assuming that condition 'index<aligned_sequence.size()' is not redundant
hh-suite-3.3.0/src/a3m_compress.cpp:407:36: note: Access out of bounds
hh-suite-3.3.0/src/a3m_compress.cpp:444:36: warning: Either the condition 'index<aligned_sequence.size()' is redundant or 'index' can have the value greater or equal to aligned_sequence.size(). Expression 'aligned_sequence[index]' cause access out of bounds. [containerOutOfBounds]
hh-suite-3.3.0/src/a3m_compress.cpp:438:88: note: Assuming that condition 'index<aligned_sequence.size()' is not redundant
hh-suite-3.3.0/src/a3m_compress.cpp:444:36: note: Access out of bounds
hh-suite-3.3.0/src/a3m_database_filter.cpp:146:19: style: Array index 'index' is used before limits check. [arrayIndexThenCheck]
hh-suite-3.3.0/src/a3m_database_filter.cpp:135:32: warning: Either the condition 'entry==NULL' is redundant or there is possible null pointer dereference: entry. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/a3m_database_filter.cpp:135:14: note: Assuming that condition 'entry==NULL' is not redundant
hh-suite-3.3.0/src/a3m_database_filter.cpp:135:32: note: Null pointer dereference
hh-suite-3.3.0/src/a3m_database_reduce.cpp:144:32: warning: Either the condition 'entry==NULL' is redundant or there is possible null pointer dereference: entry. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/a3m_database_reduce.cpp:144:14: note: Assuming that condition 'entry==NULL' is not redundant
hh-suite-3.3.0/src/a3m_database_reduce.cpp:144:32: note: Null pointer dereference
hh-suite-3.3.0/src/cs/log.h:35:3: warning: Member variable 'Log::level' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/cs/exception.h:32:3: style: Class 'Exception' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/ran.h:34:3: style: Struct 'Ran' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/utils.h:128:16: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/utils.h:129:16: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/utils.h:130:16: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/utils.h:146:13: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/utils.h:149:14: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/utils.h:208:13: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/utils.h:211:14: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/matrix.h:93:16: style: The scope of the variable 'nel' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/matrix.h:143:10: style: The scope of the variable 'i' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/matrix.h:143:12: style: The scope of the variable 'nel' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/matrix.h:160:14: style: The scope of the variable 'nel' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/ran.h:65:16: style: The scope of the variable 'x' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/ran.h:65:18: style: The scope of the variable 'y' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/application.cc:34:14: warning: Member variable 'Application::out_' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/cs/application.cc:34:14: warning: Member variable 'Application::argc_' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/cs/application.cc:34:14: warning: Member variable 'Application::argv_' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/cs/getopt_pp.h:403:7: performance: Variable '_it' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hh-suite-3.3.0/src/cs/getopt_pp.h:286:3: style: Class 'OptionPresent' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/getopt_pp.h:402:5: style: Class '_iterator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/getopt_pp.h:290:18: style: The function 'operator()' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/getopt_pp.h:65:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/getopt_pp.h:290:18: note: Function in derived class
hh-suite-3.3.0/src/cs/getopt_pp.h:208:27: style: The function 'operator()' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/getopt_pp.h:112:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/getopt_pp.h:208:27: note: Function in derived class
hh-suite-3.3.0/src/cs/getopt_pp.h:137:27: style: The function '_assign' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/getopt_pp.h:99:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/getopt_pp.h:137:27: note: Function in derived class
hh-suite-3.3.0/src/cs/getopt_pp.h:112:18: style: The function 'operator()' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/getopt_pp.h:65:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/getopt_pp.h:112:18: note: Function in derived class
hh-suite-3.3.0/src/cs/blosum_matrix.h:37:3: style: Class 'BlosumMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/context_library-inl.h:112:26: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
hh-suite-3.3.0/src/cs/context_library-inl.h:109:17: note: Assignment 'sum=0.0', assigned value is 0.0
hh-suite-3.3.0/src/cs/context_library-inl.h:110:24: note: Assuming condition is false
hh-suite-3.3.0/src/cs/context_library-inl.h:112:26: note: Invalid argument
hh-suite-3.3.0/src/cs/crf_state-inl.h:152:28: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
hh-suite-3.3.0/src/cs/crf_state-inl.h:147:24: note: Assignment 'sum=0.0', assigned value is 0.0
hh-suite-3.3.0/src/cs/crf_state-inl.h:148:26: note: Assuming condition is false
hh-suite-3.3.0/src/cs/crf_state-inl.h:152:28: note: Invalid argument
hh-suite-3.3.0/src/cs/crf_pseudocounts-inl.h:58:28: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
hh-suite-3.3.0/src/cs/crf_pseudocounts-inl.h:55:19: note: Assignment 'sum=0.0', assigned value is 0.0
hh-suite-3.3.0/src/cs/crf_pseudocounts-inl.h:56:26: note: Assuming condition is false
hh-suite-3.3.0/src/cs/crf_pseudocounts-inl.h:58:28: note: Invalid argument
hh-suite-3.3.0/src/cs/crf_pseudocounts-inl.h:99:28: warning: Invalid log() argument nr 1. The value is 0 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
hh-suite-3.3.0/src/cs/crf_pseudocounts-inl.h:96:19: note: Assignment 'sum=0.0', assigned value is 0.0
hh-suite-3.3.0/src/cs/crf_pseudocounts-inl.h:97:26: note: Assuming condition is false
hh-suite-3.3.0/src/cs/crf_pseudocounts-inl.h:99:28: note: Invalid argument
hh-suite-3.3.0/src/cs/pseudocounts.h:166:10: performance:inconclusive: Technically the member function 'cs::Pseudocounts::AdmixTo' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/pseudocounts-inl.h:59:25: note: Technically the member function 'cs::Pseudocounts::AdmixTo' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/pseudocounts.h:166:10: note: Technically the member function 'cs::Pseudocounts::AdmixTo' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/pseudocounts.h:169:10: performance:inconclusive: Technically the member function 'cs::Pseudocounts::AdmixTo' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/pseudocounts-inl.h:70:25: note: Technically the member function 'cs::Pseudocounts::AdmixTo' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/pseudocounts.h:169:10: note: Technically the member function 'cs::Pseudocounts::AdmixTo' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/cstranslate_app.h:75:10: style:inconclusive: Technically the member function 'cs::CSTranslateAppOptions::Validate' can be const. [functionConst]
hh-suite-3.3.0/src/cs/cstranslate_app.h:523:10: performance:inconclusive: Technically the member function 'CSTranslateApp < cs :: AA >::WriteStateSequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/cstranslate_app.h:543:10: performance:inconclusive: Technically the member function 'CSTranslateApp < cs :: AA >::WriteStateProfile' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/cstranslate_app.h:605:10: performance:inconclusive: Technically the member function 'CSTranslateApp < cs :: AA >::BuildSequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment.h:80:10: performance:inconclusive: Technically the member function 'Alignment < cs :: AA >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment-inl.h:137:22: note: Technically the member function 'Alignment < cs :: AA >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:80:10: note: Technically the member function 'Alignment < cs :: AA >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:95:9: performance:inconclusive: Technically the member function 'Alignment < cs :: AA >::ReadPsi' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment-inl.h:212:22: note: Technically the member function 'Alignment < cs :: AA >::ReadPsi' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:95:9: note: Technically the member function 'Alignment < cs :: AA >::ReadPsi' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:80:10: performance:inconclusive: Technically the member function 'Alignment < AS219 >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment-inl.h:137:22: note: Technically the member function 'Alignment < AS219 >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:80:10: note: Technically the member function 'Alignment < AS219 >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:95:9: performance:inconclusive: Technically the member function 'Alignment < AS219 >::ReadPsi' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment-inl.h:212:22: note: Technically the member function 'Alignment < AS219 >::ReadPsi' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:95:9: note: Technically the member function 'Alignment < AS219 >::ReadPsi' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:80:10: performance:inconclusive: Technically the member function 'Alignment < cs :: AS219 >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment-inl.h:137:22: note: Technically the member function 'Alignment < cs :: AS219 >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:80:10: note: Technically the member function 'Alignment < cs :: AS219 >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:95:9: performance:inconclusive: Technically the member function 'Alignment < cs :: AS219 >::ReadPsi' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment-inl.h:212:22: note: Technically the member function 'Alignment < cs :: AS219 >::ReadPsi' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:95:9: note: Technically the member function 'Alignment < cs :: AS219 >::ReadPsi' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:80:10: performance:inconclusive: Technically the member function 'Alignment < AA >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment-inl.h:137:22: note: Technically the member function 'Alignment < AA >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:80:10: note: Technically the member function 'Alignment < AA >::FilterSequencesByHeaders' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:95:9: performance:inconclusive: Technically the member function 'Alignment < AA >::ReadPsi' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/cs/alignment-inl.h:212:22: note: Technically the member function 'Alignment < AA >::ReadPsi' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/alignment.h:95:9: note: Technically the member function 'Alignment < AA >::ReadPsi' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/cs/context_profile.h:31:5: style: Struct 'Color' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/context_profile.h:34:5: style: Struct 'Color' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/pseudocounts.h:53:5: style: Struct 'ConstantAdmix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/crf_pseudocounts.h:36:3: style: Class 'CrfPseudocounts' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/library_pseudocounts.h:37:5: style: Class 'LibraryPseudocounts' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/pssm.h:36:3: style: Struct 'Pssm' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/profile.h:40:5: style: Class 'Profile < AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/sequence.h:38:5: style: Class 'Sequence < AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/sequence.h:50:5: style: Class 'Sequence < AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/crf_state.h:51:5: style: Struct 'CrfState < cs :: AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/emission.h:37:5: style: Class 'Emission < cs :: AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/count_profile.h:48:5: style: Struct 'CountProfile < cs :: AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/count_profile.h:51:5: style: Struct 'CountProfile < cs :: AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/count_profile.h:48:5: style: Struct 'CountProfile < AS219 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/count_profile.h:51:5: style: Struct 'CountProfile < AS219 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/count_profile.h:48:5: style: Struct 'CountProfile < cs :: AS219 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/count_profile.h:51:5: style: Struct 'CountProfile < cs :: AS219 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/count_profile.h:48:5: style: Struct 'CountProfile < AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/count_profile.h:51:5: style: Struct 'CountProfile < AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/alignment.h:112:5: style: Class 'Alignment < cs :: AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/alignment.h:112:5: style: Class 'Alignment < AS219 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/alignment.h:112:5: style: Class 'Alignment < cs :: AS219 >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/alignment.h:112:5: style: Class 'Alignment < AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/crf.h:65:5: style: Class 'Crf < cs :: AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/cs/pseudocounts.h:56:20: style: The function 'operator()' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:43:20: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:56:20: note: Function in derived class
hh-suite-3.3.0/src/cs/pseudocounts.h:60:20: style: The function 'GetTargetNeffParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:45:20: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:60:20: note: Function in derived class
hh-suite-3.3.0/src/cs/pseudocounts.h:64:18: style: The function 'SetTargetNeffParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:47:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:64:18: note: Function in derived class
hh-suite-3.3.0/src/cs/pseudocounts.h:77:20: style: The function 'operator()' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:43:20: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:77:20: note: Function in derived class
hh-suite-3.3.0/src/cs/pseudocounts.h:81:20: style: The function 'GetTargetNeffParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:45:20: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:81:20: note: Function in derived class
hh-suite-3.3.0/src/cs/pseudocounts.h:85:18: style: The function 'SetTargetNeffParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:47:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:85:18: note: Function in derived class
hh-suite-3.3.0/src/cs/pseudocounts.h:97:20: style: The function 'operator()' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:43:20: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:97:20: note: Function in derived class
hh-suite-3.3.0/src/cs/pseudocounts.h:106:27: style: The function 'GetTargetNeffParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:45:20: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:106:27: note: Function in derived class
hh-suite-3.3.0/src/cs/pseudocounts.h:110:25: style: The function 'SetTargetNeffParam' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:47:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/pseudocounts.h:110:25: note: Function in derived class
hh-suite-3.3.0/src/cs/crf_pseudocounts.h:40:16: style: The function 'AddToSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:160:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/crf_pseudocounts.h:40:16: note: Function in derived class
hh-suite-3.3.0/src/cs/crf_pseudocounts.h:42:16: style: The function 'AddToProfile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:163:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/crf_pseudocounts.h:42:16: note: Function in derived class
hh-suite-3.3.0/src/cs/library_pseudocounts.h:41:18: style: The function 'AddToSequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:160:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/library_pseudocounts.h:41:18: note: Function in derived class
hh-suite-3.3.0/src/cs/library_pseudocounts.h:43:18: style: The function 'AddToProfile' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/pseudocounts.h:163:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/library_pseudocounts.h:43:18: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_app.h:130:17: style: The function 'Run' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/application.h:60:15: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_app.h:130:17: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_app.h:367:18: style: The function 'ParseOptions' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/application.h:62:16: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_app.h:367:18: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_app.h:394:18: style: The function 'PrintOptions' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/application.h:64:16: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_app.h:394:18: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_app.h:422:18: style: The function 'PrintBanner' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/application.h:68:16: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_app.h:422:18: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_app.h:427:18: style: The function 'PrintUsage' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/application.h:66:16: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_app.h:427:18: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_app.h:441:26: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/cs/cstranslate_app.h:476:24: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/cs/pssm.h:60:24: portability:inconclusive: Casting from double * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/pssm.h:85:25: portability:inconclusive: Casting from double * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/cs/alignment-inl.h:791:10: style: The scope of the variable 'change' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/cstranslate_app.h:289:23: style: The scope of the variable 'a3m_string' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/profile-inl.h:80:16: style: The scope of the variable 'i' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/profile-inl.h:119:12: style: The scope of the variable 'i' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/profile-inl.h:119:14: style: The scope of the variable 'nel' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/profile-inl.h:135:16: style: The scope of the variable 'nel' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/sequence-inl.h:114:9: style: The scope of the variable 'c' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/emission.h:95:9: style: The scope of the variable 'sum' can be reduced. [variableScope]
hh-suite-3.3.0/src/cs/crf_state-inl.h:111:67: style:inconclusive: Function 'operator<<' argument 2 names different: declaration 'crf' definition 'state'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/cs/crf_state.h:115:67: note: Function 'operator<<' argument 2 names different: declaration 'crf' definition 'state'.
hh-suite-3.3.0/src/cs/crf_state-inl.h:111:67: note: Function 'operator<<' argument 2 names different: declaration 'crf' definition 'state'.
hh-suite-3.3.0/src/cs/sequence-inl.h:37:31: style:inconclusive: Function 'Sequence < AA >' argument 1 names different: declaration 'fin' definition 'in'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/cs/sequence.h:47:29: note: Function 'Sequence < AA >' argument 1 names different: declaration 'fin' definition 'in'.
hh-suite-3.3.0/src/cs/sequence-inl.h:37:31: note: Function 'Sequence < AA >' argument 1 names different: declaration 'fin' definition 'in'.
hh-suite-3.3.0/src/cs/sequence-inl.h:110:32: style:inconclusive: Function 'Read' argument 1 names different: declaration 'in' definition 'fin'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/cs/sequence.h:89:21: note: Function 'Read' argument 1 names different: declaration 'in' definition 'fin'.
hh-suite-3.3.0/src/cs/sequence-inl.h:110:32: note: Function 'Read' argument 1 names different: declaration 'in' definition 'fin'.
hh-suite-3.3.0/src/cs/crf_state-inl.h:79:33: style:inconclusive: Function 'Write' argument 1 names different: declaration 'fin' definition 'fout'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/cs/crf_state.h:95:22: note: Function 'Write' argument 1 names different: declaration 'fin' definition 'fout'.
hh-suite-3.3.0/src/cs/crf_state-inl.h:79:33: note: Function 'Write' argument 1 names different: declaration 'fin' definition 'fout'.
hh-suite-3.3.0/src/cs/alignment-inl.h:445:36: style:inconclusive: Function 'Resize' argument 1 names different: declaration 'num_seqs' definition 'nseqs'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/cs/alignment.h:74:23: note: Function 'Resize' argument 1 names different: declaration 'num_seqs' definition 'nseqs'.
hh-suite-3.3.0/src/cs/alignment-inl.h:445:36: note: Function 'Resize' argument 1 names different: declaration 'num_seqs' definition 'nseqs'.
hh-suite-3.3.0/src/cs/alignment-inl.h:445:50: style:inconclusive: Function 'Resize' argument 2 names different: declaration 'num_cols' definition 'ncols'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/cs/alignment.h:74:40: note: Function 'Resize' argument 2 names different: declaration 'num_cols' definition 'ncols'.
hh-suite-3.3.0/src/cs/alignment-inl.h:445:50: note: Function 'Resize' argument 2 names different: declaration 'num_cols' definition 'ncols'.
hh-suite-3.3.0/src/cs/sequence-inl.h:115:17: style: Local variable 'header' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/cs/sequence.h:74:24: note: Shadowed declaration
hh-suite-3.3.0/src/cs/sequence-inl.h:115:17: note: Shadow variable
hh-suite-3.3.0/src/cs/alignment-inl.h:65:18: style: Local variable 'nseqs' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/cs/alignment.h:138:12: note: Shadowed declaration
hh-suite-3.3.0/src/cs/alignment-inl.h:65:18: note: Shadow variable
hh-suite-3.3.0/src/cs/alignment-inl.h:66:18: style: Local variable 'ncols' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/cs/alignment.h:141:12: note: Shadowed declaration
hh-suite-3.3.0/src/cs/alignment-inl.h:66:18: note: Shadow variable
hh-suite-3.3.0/src/cs/alignment-inl.h:243:21: style: Local variable 'name' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/cs/alignment.h:156:17: note: Shadowed declaration
hh-suite-3.3.0/src/cs/alignment-inl.h:243:21: note: Shadow variable
hh-suite-3.3.0/src/cs/alignment-inl.h:248:21: style: Local variable 'seq' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/cs/alignment.h:128:14: note: Shadowed declaration
hh-suite-3.3.0/src/cs/alignment-inl.h:248:21: note: Shadow variable
hh-suite-3.3.0/src/cs/alignment-inl.h:286:18: style: Local variable 'nseqs' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/cs/alignment.h:138:12: note: Shadowed declaration
hh-suite-3.3.0/src/cs/alignment-inl.h:286:18: note: Shadow variable
hh-suite-3.3.0/src/cs/alignment-inl.h:336:31: style: Local variable 'match' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/cs/alignment.h:121:14: note: Shadowed declaration
hh-suite-3.3.0/src/cs/alignment-inl.h:336:31: note: Shadow variable
hh-suite-3.3.0/src/cs/alignment-inl.h:425:25: style: Local variable 'header' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/cs/alignment.h:150:17: note: Shadowed declaration
hh-suite-3.3.0/src/cs/alignment-inl.h:425:25: note: Shadow variable
hh-suite-3.3.0/src/cs/context_profile.h:34:23: performance: Function parameter 'coldef' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/cs/cstranslate_app.h:508:64: performance: Function parameter 'outfile' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/cs/cstranslate_app.h:530:68: performance: Function parameter 'outfile' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/cs/cstranslate_app.h:605:45: style: Parameter 'as_profile' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/cs/alignment-inl.h:791:17: style: Variable 'change' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/cs/crf_state-inl.h:139:17: style: Variable 'mean' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/cs/crf_state-inl.h:141:14: style: Variable 'mean' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/cs/crf_state-inl.h:144:10: style: Variable 'mean' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/cs/crf_state-inl.h:53:21: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/cs/context_profile-inl.h:115:21: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/cs/count_profile-inl.h:86:19: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:31:3: style: The class 'CSTranslateMpiApp < cs :: AA >' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:38:17: style: The function 'Run' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/cstranslate_app.h:130:17: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:38:17: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:218:18: style: The function 'ParseOptions' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/cstranslate_app.h:367:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:218:18: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:238:18: style: The function 'PrintOptions' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/cstranslate_app.h:394:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:238:18: note: Function in derived class
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:263:18: style: The function 'PrintUsage' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/cs/cstranslate_app.h:427:18: note: Virtual function in base class
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:263:18: note: Function in derived class
hh-suite-3.3.0/src/cs/log.cc:33:42: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled]
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:57:47: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/cs/log.cc:41:39: style:inconclusive: Function 'get' argument 1 names different: declaration 'level' definition 'log_level'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/cs/log.h:37:36: note: Function 'get' argument 1 names different: declaration 'level' definition 'log_level'.
hh-suite-3.3.0/src/cs/log.cc:41:39: note: Function 'get' argument 1 names different: declaration 'level' definition 'log_level'.
hh-suite-3.3.0/src/cs/cstranslate_mpi_app.h:156:21: style: The scope of the variable 'a3m_string' can be reduced. [variableScope]
hh-suite-3.3.0/src/ffindexdatabase.cpp:8:7: warning: Class 'FFindexDatabase' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/ffindexdatabase.cpp:8:7: warning: Class 'FFindexDatabase' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hhdecl.h:107:3: style: Struct 'Params' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/util-inl.h:415:23: style: Redundant condition: If 'EXPR > 32', the comparison 'EXPR != '\0'' is always true. [redundantCondition]
hh-suite-3.3.0/src/util-inl.h:466:23: style: Redundant condition: If 'EXPR > 32', the comparison 'EXPR != '\0'' is always true. [redundantCondition]
hh-suite-3.3.0/src/util-inl.h:483:23: style: Redundant condition: If 'EXPR > 32', the comparison 'EXPR != '\0'' is always true. [redundantCondition]
hh-suite-3.3.0/src/util-inl.h:573:25: style: Redundant condition: If 'EXPR > 32', the comparison 'EXPR != '\0'' is always true. [redundantCondition]
hh-suite-3.3.0/src/util-inl.h:591:25: style: Redundant condition: If 'EXPR > 32', the comparison 'EXPR != '\0'' is always true. [redundantCondition]
hh-suite-3.3.0/src/ffindexdatabase.cpp:21:12: warning:inconclusive: Either the condition 'db_index_fh==NULL' is redundant or there is possible null pointer dereference: db_index_fh. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/ffindexdatabase.cpp:15:21: note: Assuming that condition 'db_index_fh==NULL' is not redundant
hh-suite-3.3.0/src/ffindexdatabase.cpp:21:12: note: Null pointer dereference
hh-suite-3.3.0/src/util.h:49:18: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/util.h:53:14: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/util-inl.h:86:13: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/util-inl.h:125:16: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/util-inl.h:126:15: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/util-inl.h:127:15: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/util-inl.h:174:15: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/util-inl.h:175:15: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/util-inl.h:195:13: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/util-inl.h:199:14: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/hhutil-inl.h:434:12: style: Redundant initialization for 'result'. The initialized value is overwritten before it is read. [redundantInitialization]
hh-suite-3.3.0/src/hhutil-inl.h:393:26: note: result is initialized
hh-suite-3.3.0/src/hhutil-inl.h:434:12: note: result is overwritten
hh-suite-3.3.0/src/hhutil-inl.h:399:15: style: Redundant initialization for 'maskedMax'. The initialized value is overwritten before it is read. [redundantInitialization]
hh-suite-3.3.0/src/hhutil-inl.h:394:26: note: maskedMax is initialized
hh-suite-3.3.0/src/hhutil-inl.h:399:15: note: maskedMax is overwritten
hh-suite-3.3.0/src/hhutil-inl.h:400:15: style: Redundant initialization for 'maskedMin'. The initialized value is overwritten before it is read. [redundantInitialization]
hh-suite-3.3.0/src/hhutil-inl.h:395:26: note: maskedMin is initialized
hh-suite-3.3.0/src/hhutil-inl.h:400:15: note: maskedMin is overwritten
hh-suite-3.3.0/src/util-inl.h:680:8: style: The scope of the variable 'chr' can be reduced. [variableScope]
hh-suite-3.3.0/src/util-inl.h:295:69: style: Parameter 'def_array' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/src/util-inl.h:532:20: style: Variable 'sptr' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/util-inl.h:551:20: style: Variable 'sptr' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hash.h:351:14: error: Returning object that will be invalid when returning. [returnDanglingLifetime]
hh-suite-3.3.0/src/hash.h:351:14: note: Address of variable taken here.
hh-suite-3.3.0/src/hash.h:351:14: note: Returning object that will be invalid when returning.
hh-suite-3.3.0/src/list.h:308:3: error: Found a exit path from function with non-void return type that has missing return statement [missingReturn]
hh-suite-3.3.0/src/hash.h:48:3: warning:inconclusive: Member variable 'Pair::key' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:202:12: warning: Member variable 'Hash::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:210:12: warning: Member variable 'Hash::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:221:12: warning: Member variable 'Hash::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/list.h:304:30: error: No 'return' statement in non-void function causes undefined behavior. [operatorEqMissingReturnStatement]
hh-suite-3.3.0/src/list.h:55:10: performance:inconclusive: Technically the member function 'List::SwapContent' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/list.h:87:9: style:inconclusive: Technically the member function 'List::ReadLast' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:115:9: style:inconclusive: Technically the member function 'List::ReadCurrent' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:430:23: note: Technically the member function 'List::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:115:9: note: Technically the member function 'List::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:157:9: style:inconclusive: Technically the member function 'List::Size' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:162:10: style:inconclusive: Technically the member function 'List::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:165:10: style:inconclusive: Technically the member function 'List::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:170:10: style:inconclusive: Technically the member function 'List::Start' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:175:9: style:inconclusive: Technically the member function 'List::GetPos' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:535:16: note: Technically the member function 'List::GetPos' can be const.
hh-suite-3.3.0/src/list.h:175:9: note: Technically the member function 'List::GetPos' can be const.
hh-suite-3.3.0/src/hash.h:164:7: style:inconclusive: Technically the member function 'Hash::End' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:175:7: style:inconclusive: Technically the member function 'Hash::Size' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:178:7: style:inconclusive: Technically the member function 'Hash::MaxLen' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:261:3: warning: Class 'List' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/list.h:68:5: style: Class 'List' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:31:9: style: Class 'ListEl' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hash.h:97:3: style: Class 'Hash' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hash.h:46:9: style: Class 'Pair' is unsafe, 'Pair::key' can leak by wrong usage. [unsafeClassCanLeak]
hh-suite-3.3.0/src/hash.h:307:14: style: The scope of the variable 'pairp' can be reduced. [variableScope]
hh-suite-3.3.0/src/list.h:592:39: style:inconclusive: Function 'AppendCopy' argument 1 names different: declaration 'list' definition 'list2'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/list.h:193:32: note: Function 'AppendCopy' argument 1 names different: declaration 'list' definition 'list2'.
hh-suite-3.3.0/src/list.h:592:39: note: Function 'AppendCopy' argument 1 names different: declaration 'list' definition 'list2'.
hh-suite-3.3.0/src/hash.h:221:33: style:inconclusive: Function 'Hash' argument 2 names different: declaration 'n' definition 'f'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hash.h:98:24: note: Function 'Hash' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hash.h:221:33: note: Function 'Hash' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hash.h:268:37: style:inconclusive: Function 'New' argument 2 names different: declaration 'n' definition 'f'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hash.h:106:28: note: Function 'New' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hash.h:268:37: note: Function 'New' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/list.h:304:51: style: Parameter 'l' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hash.h:49:22: style: Parameter 'd' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hash.h:50:13: style: Parameter 'l' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hash.h:50:30: style: Parameter 'd' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/list.h:165:20: style: Parameter 'curr' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/src/hash.h:324:14: error: Returning pointer that will be invalid when returning. [returnDanglingLifetime]
hh-suite-3.3.0/src/hash.h:324:14: note: Address of variable taken here.
hh-suite-3.3.0/src/hash.h:324:14: note: Returning pointer that will be invalid when returning.
hh-suite-3.3.0/src/hash.h:351:14: error: Returning pointer that will be invalid when returning. [returnDanglingLifetime]
hh-suite-3.3.0/src/hash.h:351:14: note: Address of variable taken here.
hh-suite-3.3.0/src/hash.h:351:14: note: Returning pointer that will be invalid when returning.
hh-suite-3.3.0/src/hash.h:574:15: error: Using pointer that is a temporary. [danglingTemporaryLifetime]
hh-suite-3.3.0/src/hash.h:573:11: note: Address of variable taken here.
hh-suite-3.3.0/src/hash.h:573:26: note: Temporary created here.
hh-suite-3.3.0/src/hash.h:574:15: note: Using pointer that is a temporary.
hh-suite-3.3.0/src/hash.h:586:16: error: Using pointer that is a temporary. [danglingTemporaryLifetime]
hh-suite-3.3.0/src/hash.h:573:11: note: Address of variable taken here.
hh-suite-3.3.0/src/hash.h:573:26: note: Temporary created here.
hh-suite-3.3.0/src/hash.h:586:16: note: Using pointer that is a temporary.
hh-suite-3.3.0/src/hash.h:593:10: error: Using pointer that is a temporary. [danglingTemporaryLifetime]
hh-suite-3.3.0/src/hash.h:573:11: note: Address of variable taken here.
hh-suite-3.3.0/src/hash.h:573:26: note: Temporary created here.
hh-suite-3.3.0/src/hash.h:593:10: note: Using pointer that is a temporary.
hh-suite-3.3.0/src/hhalignment.cpp:20:12: warning: Member variable 'Alignment::N_filtered' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:20:12: warning: Member variable 'Alignment::N_ss' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:20:12: warning: Member variable 'Alignment::kss_dssp' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:20:12: warning: Member variable 'Alignment::ksa_dssp' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:20:12: warning: Member variable 'Alignment::kss_pred' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:20:12: warning: Member variable 'Alignment::kss_conf' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:20:12: warning: Member variable 'Alignment::kfirst' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:20:12: warning: Member variable 'Alignment::n_display' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:80:23: warning: Member variable 'Alignment::readCommentLine' is not assigned a value in 'Alignment::operator='. [operatorEqVarError]
hh-suite-3.3.0/src/hhalignment.cpp:80:23: warning: Member variable 'Alignment::nseqs' is not assigned a value in 'Alignment::operator='. [operatorEqVarError]
hh-suite-3.3.0/src/hhalignment.cpp:80:23: warning: Member variable 'Alignment::maxseq' is not assigned a value in 'Alignment::operator='. [operatorEqVarError]
hh-suite-3.3.0/src/hhalignment.cpp:80:23: warning: Member variable 'Alignment::maxres' is not assigned a value in 'Alignment::operator='. [operatorEqVarError]
hh-suite-3.3.0/src/hash.h:202:12: warning: Member variable 'Hash < Hit >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:210:12: warning: Member variable 'Hash < Hit >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:221:12: warning: Member variable 'Hash < Hit >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:48:3: warning:inconclusive: Member variable 'Pair < Hit >::key' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhalignment.cpp:80:23: style: 'operator=' should return reference to 'this' instance. [operatorEqRetRefThis]
hh-suite-3.3.0/src/hhalignment.cpp:80:23: warning: 'operator=' should check for assignment to self to avoid problems with dynamic memory. [operatorEqToSelf]
hh-suite-3.3.0/src/hhhit.h:151:17: style:inconclusive: Technically the member function 'Hit::CalcProbab' can be const. [functionConst]
hh-suite-3.3.0/src/hhhmm.h:162:7: style:inconclusive: Technically the member function 'HMM::Warning' can be const. [functionConst]
hh-suite-3.3.0/src/hhalignment.h:136:10: performance:inconclusive: Technically the member function 'Alignment::initX' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhalignment.cpp:69:19: note: Technically the member function 'Alignment::initX' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhalignment.h:136:10: note: Technically the member function 'Alignment::initX' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hash.h:164:7: style:inconclusive: Technically the member function 'Hash < Hit >::End' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:175:7: style:inconclusive: Technically the member function 'Hash < Hit >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:178:7: style:inconclusive: Technically the member function 'Hash < Hit >::MaxLen' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:55:10: performance:inconclusive: Technically the member function 'List < Pair < Hit > >::SwapContent' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/list.h:87:9: style:inconclusive: Technically the member function 'List < Pair < Hit > >::ReadLast' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:115:9: style:inconclusive: Technically the member function 'List < Pair < Hit > >::ReadCurrent' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:430:23: note: Technically the member function 'List < Pair < Hit > >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:115:9: note: Technically the member function 'List < Pair < Hit > >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:157:9: style:inconclusive: Technically the member function 'List < Pair < Hit > >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:162:10: style:inconclusive: Technically the member function 'List < Pair < Hit > >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:165:10: style:inconclusive: Technically the member function 'List < Pair < Hit > >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:170:10: style:inconclusive: Technically the member function 'List < Pair < Hit > >::Start' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:175:9: style:inconclusive: Technically the member function 'List < Pair < Hit > >::GetPos' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:535:16: note: Technically the member function 'List < Pair < Hit > >::GetPos' can be const.
hh-suite-3.3.0/src/list.h:175:9: note: Technically the member function 'List < Pair < Hit > >::GetPos' can be const.
hh-suite-3.3.0/src/hhalignment.cpp:21:3: warning: Class 'Alignment' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash < Hit >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash < Hit >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < Hit >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < Hit >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < Hit >' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
hh-suite-3.3.0/src/list.h:261:3: warning: Class 'List < Pair < Hit > >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhdatabase.h:39:5: style: Class 'HHblitsDatabase' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hhdatabase.h:82:5: style: Class 'HHEntry' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hash.h:97:3: style: Class 'Hash < Hit >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:68:5: style: Class 'List < Pair < Hit > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:31:9: style: Class 'ListEl < Pair < Hit > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hhdatabase.h:103:10: style: The function 'getTemplateA3M' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/hhdatabase.h:85:18: note: Virtual function in base class
hh-suite-3.3.0/src/hhdatabase.h:103:10: note: Function in derived class
hh-suite-3.3.0/src/hhdatabase.h:105:10: style: The function 'getTemplateHMM' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/hhdatabase.h:87:18: note: Virtual function in base class
hh-suite-3.3.0/src/hhdatabase.h:105:10: note: Function in derived class
hh-suite-3.3.0/src/hhdatabase.h:108:11: style: The function 'getName' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/hhdatabase.h:90:19: note: Virtual function in base class
hh-suite-3.3.0/src/hhdatabase.h:108:11: note: Function in derived class
hh-suite-3.3.0/src/hhdatabase.h:121:10: style: The function 'getTemplateA3M' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/hhdatabase.h:85:18: note: Virtual function in base class
hh-suite-3.3.0/src/hhdatabase.h:121:10: note: Function in derived class
hh-suite-3.3.0/src/hhdatabase.h:123:10: style: The function 'getTemplateHMM' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/hhdatabase.h:87:18: note: Virtual function in base class
hh-suite-3.3.0/src/hhdatabase.h:123:10: note: Function in derived class
hh-suite-3.3.0/src/hhdatabase.h:126:11: style: The function 'getName' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/hhdatabase.h:90:19: note: Virtual function in base class
hh-suite-3.3.0/src/hhdatabase.h:126:11: note: Function in derived class
hh-suite-3.3.0/src/hhalignment.cpp:3614:21: style: Expression is always true because 'else if' condition is opposite to previous condition at line 3593. [multiCondition]
hh-suite-3.3.0/src/hhalignment.cpp:3593:21: note: first condition
hh-suite-3.3.0/src/hhalignment.cpp:3614:21: note: else if condition is opposite to first condition
hh-suite-3.3.0/src/hash.h:46:9: style: Class 'Pair < Hit >' is unsafe, 'Pair < Hit >::key' can leak by wrong usage. [unsafeClassCanLeak]
hh-suite-3.3.0/src/util-inl.h:391:14: warning: Either the condition 'line' is redundant or there is possible null pointer dereference: str. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/hhhmm.h:170:9: note: Assuming that condition 'line' is not redundant
hh-suite-3.3.0/src/hhhmm.h:168:21: note: Calling function 'fgetline', 1st argument 'line' value is 0
hh-suite-3.3.0/src/util-inl.h:391:14: note: Null pointer dereference
hh-suite-3.3.0/src/hhalignment.cpp:72:16: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhalignment.cpp:1875:31: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhalignment.cpp:1876:31: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhalignment.cpp:2440:14: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhalignment.cpp:2446:22: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhalignment.cpp:2520:37: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhalignment.cpp:824:7: style: The scope of the variable 'a' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:1613:7: style: The scope of the variable 'diffNmax_prev' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:1712:11: style: The scope of the variable 'qsc_sum' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:2049:7: style: The scope of the variable 'ni' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:2050:7: style: The scope of the variable 'naa' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:2206:11: style: The scope of the variable 'maxw' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:2207:9: style: The scope of the variable 'maxa' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:2286:9: style: The scope of the variable 'nn' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:3823:10: style: The scope of the variable 'j' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:3824:7: style: The scope of the variable 'a' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:3825:7: style: The scope of the variable 'naa' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:3826:9: style: The scope of the variable 'n' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:3828:7: style: The scope of the variable 'ncol' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhalignment.cpp:3829:8: style: The scope of the variable 'change' can be reduced. [variableScope]
hh-suite-3.3.0/src/hash.h:221:33: style:inconclusive: Function 'Hash < Hit >' argument 2 names different: declaration 'n' definition 'f'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hash.h:98:24: note: Function 'Hash < Hit >' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hash.h:221:33: note: Function 'Hash < Hit >' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hhalignment.cpp:181:7: style: Local variable 'l' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.h:52:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:181:7: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:765:12: style: Local variable 'copy_pos' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:647:7: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:765:12: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:773:11: style: Local variable 'cur_name' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:655:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:773:11: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:1719:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:1627:7: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:1719:16: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:1755:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:1627:7: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:1755:16: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:1891:18: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:1627:7: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:1891:18: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:2470:20: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:2415:10: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:2470:20: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:2475:20: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:2415:10: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:2475:20: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:2642:13: style: Local variable 'sum' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:2424:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:2642:13: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:3010:20: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:2964:10: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:3010:20: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:3217:20: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:3172:10: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:3217:20: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:3222:20: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:3172:10: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:3222:20: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:3484:7: style: Local variable 'l' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.h:52:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:3484:7: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:3858:20: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:3823:10: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:3858:20: note: Shadow variable
hh-suite-3.3.0/src/hhalignment.cpp:3863:20: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhalignment.cpp:3823:10: note: Shadowed declaration
hh-suite-3.3.0/src/hhalignment.cpp:3863:20: note: Shadow variable
hh-suite-3.3.0/src/hash.h:102:24: performance: Function parameter 'f' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/hash.h:103:24: performance: Function parameter 'f' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/hash.h:221:33: performance: Function parameter 'f' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/hash.h:268:37: performance: Function parameter 'f' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/list.h:73:19: performance: Function parameter 'null' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/list.h:137:24: performance: Function parameter 'd' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/list.h:31:21: performance: Function parameter 'd' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/list.h:37:21: performance: Function parameter 'd' should be passed by const reference. [passedByValue]
hh-suite-3.3.0/src/hhhit-inl.h:38:39: style: Parameter 'a' can be declared as const array [constParameter]
hh-suite-3.3.0/src/hhhit-inl.h:55:41: style: Parameter 'a' can be declared as const array [constParameter]
hh-suite-3.3.0/src/hhalignment.cpp:2027:38: style: Parameter 'keep_orig' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/src/hhalignment.cpp:2951:56: style: Parameter 'in' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/src/hhalignment.cpp:3159:56: style: Parameter 'in' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/src/hhalignment.cpp:3708:34: style: Parameter 'Xk' can be declared as const array [constParameter]
hh-suite-3.3.0/src/hhalignment.cpp:3708:44: style: Parameter 'Ik' can be declared as const array [constParameter]
hh-suite-3.3.0/src/hhviterbi.h:216:17: performance:inconclusive: Technically the member function 'Viterbi::read_scoreline_sscore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhviterbi.h:242:21: performance:inconclusive: Technically the member function 'Viterbi::scoreLookup30' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoder.h:129:7: performance:inconclusive: Technically the member function 'PosteriorDecoder::initializeBacktrace' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhbacktracemac.cpp:273:24: note: Technically the member function 'PosteriorDecoder::initializeBacktrace' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:129:7: note: Technically the member function 'PosteriorDecoder::initializeBacktrace' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhhmmsimd.h:12:5: style: Class 'HMMSimd' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hhbacktracemac.cpp:14:49: style: Parameter 'q' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhbacktracemac.cpp:14:57: style: Parameter 't' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhbacktracemac.cpp:14:77: style: Parameter 'p_mm' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:48: style:inconclusive: Function 'backwardAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:123:31: note: Function 'backwardAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'.
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:48: note: Function 'backwardAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'.
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:57: style:inconclusive: Function 'backwardAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:123:43: note: Function 'backwardAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'.
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:57: note: Function 'backwardAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'.
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:66: style:inconclusive: Function 'backwardAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:123:56: note: Function 'backwardAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'.
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:66: note: Function 'backwardAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'.
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:11:82: style:inconclusive: Function 'backwardAlgorithm' argument 5 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:124:20: note: Function 'backwardAlgorithm' argument 5 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'.
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:11:82: note: Function 'backwardAlgorithm' argument 5 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'.
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:21:14: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:14:12: note: Shadowed declaration
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:21:14: note: Shadow variable
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:33:14: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:14:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:33:14: note: Shadow variable
hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:66: style: Parameter 'hit' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhhitlist.h:38:3: warning: Member variable 'HitList::score' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhitlist.h:38:3: warning: Member variable 'HitList::weight' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhitlist.h:38:3: warning: Member variable 'HitList::N_searched' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:202:12: warning: Member variable 'Hash < float >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:202:12: warning: Member variable 'Hash < float >::fail' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:210:12: warning: Member variable 'Hash < float >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:221:12: warning: Member variable 'Hash < float >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:48:3: warning:inconclusive: Member variable 'Pair < float >::key' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:48:3: warning:inconclusive: Member variable 'Pair < float >::data' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhfullalignment.h:35:8: performance:inconclusive: Technically the member function 'FullAlignment::ScoreChr' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhfullalignment.h:36:8: performance:inconclusive: Technically the member function 'FullAlignment::PosteriorChr' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hash.h:164:7: style:inconclusive: Technically the member function 'Hash < float >::End' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:175:7: style:inconclusive: Technically the member function 'Hash < float >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:178:7: style:inconclusive: Technically the member function 'Hash < float >::MaxLen' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:55:10: performance:inconclusive: Technically the member function 'List < Hit >::SwapContent' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/list.h:87:9: style:inconclusive: Technically the member function 'List < Hit >::ReadLast' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:115:9: style:inconclusive: Technically the member function 'List < Hit >::ReadCurrent' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:430:23: note: Technically the member function 'List < Hit >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:115:9: note: Technically the member function 'List < Hit >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:157:9: style:inconclusive: Technically the member function 'List < Hit >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:162:10: style:inconclusive: Technically the member function 'List < Hit >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:165:10: style:inconclusive: Technically the member function 'List < Hit >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:170:10: style:inconclusive: Technically the member function 'List < Hit >::Start' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:175:9: style:inconclusive: Technically the member function 'List < Hit >::GetPos' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:535:16: note: Technically the member function 'List < Hit >::GetPos' can be const.
hh-suite-3.3.0/src/list.h:175:9: note: Technically the member function 'List < Hit >::GetPos' can be const.
hh-suite-3.3.0/src/list.h:55:10: performance:inconclusive: Technically the member function 'List < Pair < float > >::SwapContent' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/list.h:87:9: style:inconclusive: Technically the member function 'List < Pair < float > >::ReadLast' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:115:9: style:inconclusive: Technically the member function 'List < Pair < float > >::ReadCurrent' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:430:23: note: Technically the member function 'List < Pair < float > >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:115:9: note: Technically the member function 'List < Pair < float > >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:157:9: style:inconclusive: Technically the member function 'List < Pair < float > >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:162:10: style:inconclusive: Technically the member function 'List < Pair < float > >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:165:10: style:inconclusive: Technically the member function 'List < Pair < float > >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:170:10: style:inconclusive: Technically the member function 'List < Pair < float > >::Start' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:175:9: style:inconclusive: Technically the member function 'List < Pair < float > >::GetPos' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:535:16: note: Technically the member function 'List < Pair < float > >::GetPos' can be const.
hh-suite-3.3.0/src/list.h:175:9: note: Technically the member function 'List < Pair < float > >::GetPos' can be const.
hh-suite-3.3.0/src/hhviterbirunner.h:32:3: warning: Class 'ViterbiConsumerThread' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhviterbirunner.h:32:3: warning: Class 'ViterbiConsumerThread' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash < float >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash < float >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < float >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < float >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < float >' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
hh-suite-3.3.0/src/list.h:261:3: warning: Class 'List < Hit >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/list.h:261:3: warning: Class 'List < Pair < float > >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhalign.h:15:5: style: Class 'HHalign' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hash.h:97:3: style: Class 'Hash < float >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:68:5: style: Class 'List < Hit >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:68:5: style: Class 'List < Pair < float > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:31:9: style: Class 'ListEl < Hit >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:31:9: style: Class 'ListEl < Pair < float > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hhalign.h:19:18: style: The function 'run' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
hh-suite-3.3.0/src/hhblits.h:109:16: note: Virtual function in base class
hh-suite-3.3.0/src/hhalign.h:19:18: note: Function in derived class
hh-suite-3.3.0/src/hash.h:46:9: style: Class 'Pair < float >' is unsafe, 'Pair < float >::key' can leak by wrong usage. [unsafeClassCanLeak]
hh-suite-3.3.0/src/hash.h:221:33: style:inconclusive: Function 'Hash < float >' argument 2 names different: declaration 'n' definition 'f'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hash.h:98:24: note: Function 'Hash < float >' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hash.h:221:33: note: Function 'Hash < float >' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hhviterbirunner.h:23:52: style: Parameter 'par' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhblits_ca3m.cpp:73:7: error: Memory leak: db.data_fh [memleak]
hh-suite-3.3.0/src/hhblits_ca3m.cpp:68:7: error: Memory leak: db.index_fh [memleak]
hh-suite-3.3.0/src/hhblits_mpi.cpp:76:13: error: Memory leak: db.data_fh [memleak]
hh-suite-3.3.0/src/hhblits_mpi.cpp:71:13: error: Memory leak: db.index_fh [memleak]
hh-suite-3.3.0/src/hhblits_mpi.cpp:131:44: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits_omp.cpp:73:13: error: Memory leak: db.data_fh [memleak]
hh-suite-3.3.0/src/hhblits_omp.cpp:68:13: error: Memory leak: db.index_fh [memleak]
hh-suite-3.3.0/src/hhblits_omp.cpp:119:9: style: Variable 'threads' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhconsensus.cpp:399:13: warning: Either the condition '!outf' is redundant or there is possible null pointer dereference: outf. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/hhconsensus.cpp:389:11: note: Assuming that condition '!outf' is not redundant
hh-suite-3.3.0/src/hhconsensus.cpp:399:13: note: Null pointer dereference
hh-suite-3.3.0/src/hhconsensus.cpp:400:12: warning: Either the condition '!outf' is redundant or there is possible null pointer dereference: outf. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/hhconsensus.cpp:389:11: note: Assuming that condition '!outf' is not redundant
hh-suite-3.3.0/src/hhconsensus.cpp:400:12: note: Null pointer dereference
hh-suite-3.3.0/src/hhconsensus.cpp:36:23: style: Parameter 'par' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhdatabase.cpp:75:3: warning: Class 'HHblitsDatabase' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhdatabase.cpp:75:3: warning: Class 'HHblitsDatabase' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hhdatabase.cpp:465:33: warning: Class 'HHFileEntry' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhdatabase.cpp:465:33: warning: Class 'HHFileEntry' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hhdatabase.cpp:149:62: style:inconclusive: Function 'initNoPrefilter' argument 1 names different: declaration 'new_prefilter_hits' definition 'new_entries'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhdatabase.h:43:49: note: Function 'initNoPrefilter' argument 1 names different: declaration 'new_prefilter_hits' definition 'new_entries'.
hh-suite-3.3.0/src/hhdatabase.cpp:149:62: note: Function 'initNoPrefilter' argument 1 names different: declaration 'new_prefilter_hits' definition 'new_entries'.
hh-suite-3.3.0/src/hhdatabase.cpp:176:46: style:inconclusive: Function 'prefilter_db' argument 12 names different: declaration 'maxnumdb' definition 'maxnumbdb'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhdatabase.h:52:85: note: Function 'prefilter_db' argument 12 names different: declaration 'maxnumdb' definition 'maxnumbdb'.
hh-suite-3.3.0/src/hhdatabase.cpp:176:46: note: Function 'prefilter_db' argument 12 names different: declaration 'maxnumdb' definition 'maxnumbdb'.
hh-suite-3.3.0/src/hhdatabase.cpp:195:85: style:inconclusive: Function 'getEntriesFromNames' argument 1 names different: declaration 'names' definition 'hits'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhdatabase.h:71:73: note: Function 'getEntriesFromNames' argument 1 names different: declaration 'names' definition 'hits'.
hh-suite-3.3.0/src/hhdatabase.cpp:195:85: note: Function 'getEntriesFromNames' argument 1 names different: declaration 'names' definition 'hits'.
hh-suite-3.3.0/src/hhdatabase.cpp:396:36: style:inconclusive: Function 'getTemplateHMM' argument 1 names different: declaration 'inf' definition 'dbf'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhdatabase.h:93:31: note: Function 'getTemplateHMM' argument 1 names different: declaration 'inf' definition 'dbf'.
hh-suite-3.3.0/src/hhdatabase.cpp:396:36: note: Function 'getTemplateHMM' argument 1 names different: declaration 'inf' definition 'dbf'.
hh-suite-3.3.0/src/hhdatabase.cpp:341:22: style: Local variable 'entry' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhdatabase.h:113:22: note: Shadowed declaration
hh-suite-3.3.0/src/hhdatabase.cpp:341:22: note: Shadow variable
hh-suite-3.3.0/src/hhdatabase.cpp:156:62: style: Parameter 'selected_templates' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhdatabase.cpp:560:49: style: Parameter 'entries' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhdecl.h:145:16: style:inconclusive: Member variable 'Parameters::argv' is in the wrong place in the initializer list. [initializerList]
hh-suite-3.3.0/src/hhdecl.cpp:7:73: note: Member variable 'Parameters::argv' is in the wrong place in the initializer list.
hh-suite-3.3.0/src/hhdecl.h:145:16: note: Member variable 'Parameters::argv' is in the wrong place in the initializer list.
hh-suite-3.3.0/src/hhfilter.cpp:186:10: warning: Either the condition '!inf' is redundant or there is possible null pointer dereference: inf. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/hhfilter.cpp:176:9: note: Assuming that condition '!inf' is not redundant
hh-suite-3.3.0/src/hhfilter.cpp:186:10: note: Null pointer dereference
hh-suite-3.3.0/src/hhfilter.cpp:34:23: style: Parameter 'par' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:16:9: style: The scope of the variable 'Pmax_i' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:10:47: style:inconclusive: Function 'forwardAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:121:30: note: Function 'forwardAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'.
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:10:47: note: Function 'forwardAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'.
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:10:56: style:inconclusive: Function 'forwardAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:121:43: note: Function 'forwardAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'.
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:10:56: note: Function 'forwardAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'.
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:10:65: style:inconclusive: Function 'forwardAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:121:56: note: Function 'forwardAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'.
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:10:65: note: Function 'forwardAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'.
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:11:43: style:inconclusive: Function 'forwardAlgorithm' argument 5 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:122:20: note: Function 'forwardAlgorithm' argument 5 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'.
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:11:43: note: Function 'forwardAlgorithm' argument 5 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'.
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:44:11: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:13:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:44:11: note: Shadow variable
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:190:12: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:13:6: note: Shadowed declaration
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:190:12: note: Shadow variable
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:191:9: style: Local variable 'jmin' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:18:6: note: Shadowed declaration
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:191:9: note: Shadow variable
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:202:14: style: Local variable 'j' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:13:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:202:14: note: Shadow variable
hh-suite-3.3.0/src/hhforwardalgorithm.cpp:188:17: style: Variable 'ffprob' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhfullalignment.cpp:32:16: warning: Member variable 'FullAlignment::identities' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhfullalignment.cpp:32:16: warning: Member variable 'FullAlignment::score_sim' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhfullalignment.cpp:32:16: warning: Member variable 'FullAlignment::symbol' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhfullalignment.cpp:32:16: warning: Member variable 'FullAlignment::posterior' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhfullalignment.h:21:8: style:inconclusive: Technically the member function 'FullAlignment::PrintA2M' can be const. [functionConst]
hh-suite-3.3.0/src/hhfullalignment.cpp:394:21: note: Technically the member function 'FullAlignment::PrintA2M' can be const.
hh-suite-3.3.0/src/hhfullalignment.h:21:8: note: Technically the member function 'FullAlignment::PrintA2M' can be const.
hh-suite-3.3.0/src/hhfullalignment.cpp:33:3: warning: Class 'FullAlignment' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhfullalignment.cpp:33:3: warning: Class 'FullAlignment' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hhfullalignment.cpp:195:70: style: Parameter 'hit' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhfullalignment.cpp:209:59: style: Parameter 'hit' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhfullalignment.cpp:120:19: style: Variable 'prev_state' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhfunc.cpp:41:22: style: Condition 'input_format==0' is always true [knownConditionTrueFalse]
hh-suite-3.3.0/src/hhfunc.cpp:38:20: note: Assignment 'input_format=0', assigned value is 0
hh-suite-3.3.0/src/hhfunc.cpp:41:22: note: Condition 'input_format==0' is always true
hh-suite-3.3.0/src/hhfunc.cpp:114:10: warning: Either the condition '!inf' is redundant or there is possible null pointer dereference: inf. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/hhfunc.cpp:107:9: note: Assuming that condition '!inf' is not redundant
hh-suite-3.3.0/src/hhfunc.cpp:114:10: note: Null pointer dereference
hh-suite-3.3.0/src/hhfunc.cpp:220:20: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhfunc.cpp:10:32: style: Parameter 'par' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhfunc.cpp:120:34: style: Parameter 'par' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhfunc.cpp:120:45: style: Parameter 'input_format' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhfunc.cpp:164:37: style: Parameter 'par' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhfunc.cpp:103:13: style: Variable 'path[0]' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhhalfalignment.cpp:17:3: warning: Class 'HalfAlignment' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhhalfalignment.cpp:17:3: warning: Class 'HalfAlignment' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hhhalfalignment.cpp:175:8: style: The scope of the variable 'c' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhalfalignment.cpp:246:8: style: The scope of the variable 'state' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhalfalignment.cpp:315:7: style: The scope of the variable 'omitted' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhalfalignment.cpp:312:33: style:inconclusive: Function 'Print' argument 1 names different: declaration 'outfile' definition 'alnfile'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhhalfalignment.h:29:20: note: Function 'Print' argument 1 names different: declaration 'outfile' definition 'alnfile'.
hh-suite-3.3.0/src/hhhalfalignment.cpp:312:33: note: Function 'Print' argument 1 names different: declaration 'outfile' definition 'alnfile'.
hh-suite-3.3.0/src/hhhalfalignment.cpp:185:10: style: Local variable 'h' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhalfalignment.h:78:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhhalfalignment.cpp:185:10: note: Shadow variable
hh-suite-3.3.0/src/hhhalfalignment.cpp:243:42: style: Parameter 'hit' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhhalfalignment.cpp:371:12: error: Memory is allocated but not initialized: tmp_name [uninitdata]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::fam' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::sfam' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::fold' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::cl' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::score' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::score_aass' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::score_ss' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::Pval' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::Pvalt' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::logPval' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::logPvalt' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::Eval' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::logEval' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::Probab' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::Pforward' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::L' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::irep' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::lastrep' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::n_display' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::nss_dssp' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::nsa_dssp' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::nss_pred' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::nss_conf' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::nfirst' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::ncons' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::nsteps' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::i1' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::i2' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::j1' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::j2' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::matched_cols' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::qsc' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::state' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:8:6: warning: Member variable 'Hit::min_overlap' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhhit.cpp:235:54: style:inconclusive: Function 'initHitFromHMM' argument 3 names different: declaration 'nseqdis' definition 'par_nseqdis'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhhit.h:128:51: note: Function 'initHitFromHMM' argument 3 names different: declaration 'nseqdis' definition 'par_nseqdis'.
hh-suite-3.3.0/src/hhhit.cpp:235:54: note: Function 'initHitFromHMM' argument 3 names different: declaration 'nseqdis' definition 'par_nseqdis'.
hh-suite-3.3.0/src/hhhit.cpp:95:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhit.h:81:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhhit.cpp:95:16: note: Shadow variable
hh-suite-3.3.0/src/hhhit.cpp:105:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhit.h:81:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhhit.cpp:105:16: note: Shadow variable
hh-suite-3.3.0/src/hhhit.cpp:115:16: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhit.h:81:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhhit.cpp:115:16: note: Shadow variable
hh-suite-3.3.0/src/hhhit.cpp:137:6: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhit.h:81:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhhit.cpp:137:6: note: Shadow variable
hh-suite-3.3.0/src/hhhit.cpp:153:8: style: Local variable 'state' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhit.h:145:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhhit.cpp:153:8: note: Shadow variable
hh-suite-3.3.0/src/hhhit.cpp:145:4: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hash.h:202:12: warning: Member variable 'Hash < int >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:202:12: warning: Member variable 'Hash < int >::fail' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:210:12: warning: Member variable 'Hash < int >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:221:12: warning: Member variable 'Hash < int >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:48:3: warning:inconclusive: Member variable 'Pair < int >::key' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:48:3: warning:inconclusive: Member variable 'Pair < int >::data' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:164:7: style:inconclusive: Technically the member function 'Hash < int >::End' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:175:7: style:inconclusive: Technically the member function 'Hash < int >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:178:7: style:inconclusive: Technically the member function 'Hash < int >::MaxLen' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:55:10: performance:inconclusive: Technically the member function 'List < Pair < int > >::SwapContent' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/list.h:87:9: style:inconclusive: Technically the member function 'List < Pair < int > >::ReadLast' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:115:9: style:inconclusive: Technically the member function 'List < Pair < int > >::ReadCurrent' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:430:23: note: Technically the member function 'List < Pair < int > >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:115:9: note: Technically the member function 'List < Pair < int > >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:157:9: style:inconclusive: Technically the member function 'List < Pair < int > >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:162:10: style:inconclusive: Technically the member function 'List < Pair < int > >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:165:10: style:inconclusive: Technically the member function 'List < Pair < int > >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:170:10: style:inconclusive: Technically the member function 'List < Pair < int > >::Start' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:175:9: style:inconclusive: Technically the member function 'List < Pair < int > >::GetPos' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:535:16: note: Technically the member function 'List < Pair < int > >::GetPos' can be const.
hh-suite-3.3.0/src/list.h:175:9: note: Technically the member function 'List < Pair < int > >::GetPos' can be const.
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash < int >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash < int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < int >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < int >' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
hh-suite-3.3.0/src/list.h:261:3: warning: Class 'List < Pair < int > >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:97:3: style: Class 'Hash < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:68:5: style: Class 'List < Pair < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:31:9: style: Class 'ListEl < Pair < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hash.h:46:9: style: Class 'Pair < int >' is unsafe, 'Pair < int >::key' can leak by wrong usage. [unsafeClassCanLeak]
hh-suite-3.3.0/src/hhhitlist.cpp:466:10: style: The scope of the variable 'alpha' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhitlist.cpp:275:54: style:inconclusive: Function 'PrintM8File' argument 2 names different: declaration 'outputstream' definition 'outbuffer'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhhitlist.h:67:47: note: Function 'PrintM8File' argument 2 names different: declaration 'outputstream' definition 'outbuffer'.
hh-suite-3.3.0/src/hhhitlist.cpp:275:54: note: Function 'PrintM8File' argument 2 names different: declaration 'outputstream' definition 'outbuffer'.
hh-suite-3.3.0/src/hhhitlist.cpp:325:57: style:inconclusive: Function 'PrintScoreFile' argument 2 names different: declaration 'outputstream' definition 'outbuffer'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhhitlist.h:64:50: note: Function 'PrintScoreFile' argument 2 names different: declaration 'outputstream' definition 'outbuffer'.
hh-suite-3.3.0/src/hhhitlist.cpp:325:57: note: Function 'PrintScoreFile' argument 2 names different: declaration 'outputstream' definition 'outbuffer'.
hh-suite-3.3.0/src/hash.h:221:33: style:inconclusive: Function 'Hash < int >' argument 2 names different: declaration 'n' definition 'f'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hash.h:98:24: note: Function 'Hash < int >' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hash.h:221:33: note: Function 'Hash < int >' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hhhitlist.cpp:466:16: style: Variable 'alpha' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhhmm.cpp:112:11: style: 'operator=' should return reference to 'this' instance. [operatorEqRetRefThis]
hh-suite-3.3.0/src/hhhmm.h:25:13: style:inconclusive: Member variable 'HMM::maxres' is in the wrong place in the initializer list. [initializerList]
hh-suite-3.3.0/src/hhhmm.cpp:12:61: note: Member variable 'HMM::maxres' is in the wrong place in the initializer list.
hh-suite-3.3.0/src/hhhmm.h:25:13: note: Member variable 'HMM::maxres' is in the wrong place in the initializer list.
hh-suite-3.3.0/src/hhhmm.h:88:8: style:inconclusive: Technically the member function 'HMM::fillCountProfile' can be const. [functionConst]
hh-suite-3.3.0/src/hhhmm.cpp:1839:11: note: Technically the member function 'HMM::fillCountProfile' can be const.
hh-suite-3.3.0/src/hhhmm.h:88:8: note: Technically the member function 'HMM::fillCountProfile' can be const.
hh-suite-3.3.0/src/hhhmm.h:110:8: performance:inconclusive: Technically the member function 'HMM::IncludeNullModelInHMM' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhhmm.cpp:2055:11: note: Technically the member function 'HMM::IncludeNullModelInHMM' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhhmm.h:110:8: note: Technically the member function 'HMM::IncludeNullModelInHMM' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhhmm.cpp:13:2: warning: Class 'HMM' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhhmm.cpp:35:10: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhhmm.cpp:37:11: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhhmm.cpp:1721:8: style: The scope of the variable 'sum' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhmm.cpp:1723:8: style: The scope of the variable 'p0' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhmm.cpp:1723:12: style: The scope of the variable 'p1' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhmm.cpp:1723:16: style: The scope of the variable 'p2' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhmm.cpp:1873:8: style: The scope of the variable 'sum' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhhmm.cpp:321:8: style: Local variable 'l' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhmm.h:156:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhhmm.cpp:321:8: note: Shadow variable
hh-suite-3.3.0/src/hhhmm.cpp:322:8: style: Local variable 'i' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhmm.cpp:206:6: note: Shadowed declaration
hh-suite-3.3.0/src/hhhmm.cpp:322:8: note: Shadow variable
hh-suite-3.3.0/src/hhhmm.cpp:874:10: style: Local variable 'ptr' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhhmm.cpp:698:8: note: Shadowed declaration
hh-suite-3.3.0/src/hhhmm.cpp:874:10: note: Shadow variable
hh-suite-3.3.0/src/hhhmm.cpp:1873:8: style: Variable 'sum' is not assigned a value. [unassignedVariable]
hh-suite-3.3.0/src/hhhmm.cpp:2122:12: style: Variable 'pnul[a]' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhhmmsimd.cpp:29:5: warning: Class 'HMMSimd' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhhmmsimd.cpp:31:14: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhhmmsimd.cpp:48:9: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhhmmsimd.cpp:50:24: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhhmmsimd.cpp:51:24: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhhmmsimd.cpp:94:25: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhhmmsimd.cpp:108:25: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoder.h:125:7: style:inconclusive: Technically the member function 'PosteriorDecoder::macAlgorithm' can be const. [functionConst]
hh-suite-3.3.0/src/hhmacalgorithm.cpp:17:24: note: Technically the member function 'PosteriorDecoder::macAlgorithm' can be const.
hh-suite-3.3.0/src/hhposteriordecoder.h:125:7: note: Technically the member function 'PosteriorDecoder::macAlgorithm' can be const.
hh-suite-3.3.0/src/hhmacalgorithm.cpp:28:9: style: The scope of the variable 'jmin' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhmacalgorithm.cpp:28:14: style: The scope of the variable 'jmax' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhmacalgorithm.cpp:17:43: style:inconclusive: Function 'macAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:125:26: note: Function 'macAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'.
hh-suite-3.3.0/src/hhmacalgorithm.cpp:17:43: note: Function 'macAlgorithm' argument 1 names different: declaration 'q_hmm' definition 'q'.
hh-suite-3.3.0/src/hhmacalgorithm.cpp:17:52: style:inconclusive: Function 'macAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:125:39: note: Function 'macAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'.
hh-suite-3.3.0/src/hhmacalgorithm.cpp:17:52: note: Function 'macAlgorithm' argument 2 names different: declaration 't_hmm' definition 't'.
hh-suite-3.3.0/src/hhmacalgorithm.cpp:17:61: style:inconclusive: Function 'macAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:125:52: note: Function 'macAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'.
hh-suite-3.3.0/src/hhmacalgorithm.cpp:17:61: note: Function 'macAlgorithm' argument 3 names different: declaration 'hit_vec' definition 'hit'.
hh-suite-3.3.0/src/hhmacalgorithm.cpp:40:38: style: Variable 'term4' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhmake.cpp:354:38: style: Unused variable: qav [unusedVariable]
hh-suite-3.3.0/src/hhposteriordecoder.h:90:16: style:inconclusive: Member variable 'PosteriorDecoder::S73' is in the wrong place in the initializer list. [initializerList]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:47:3: note: Member variable 'PosteriorDecoder::S73' is in the wrong place in the initializer list.
hh-suite-3.3.0/src/hhposteriordecoder.h:90:16: note: Member variable 'PosteriorDecoder::S73' is in the wrong place in the initializer list.
hh-suite-3.3.0/src/hhposteriordecoder.h:70:7: performance:inconclusive: Technically the member function 'PosteriorDecoder::excludeMACAlignment' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:248:24: note: Technically the member function 'PosteriorDecoder::excludeMACAlignment' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:70:7: note: Technically the member function 'PosteriorDecoder::excludeMACAlignment' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:132:10: performance:inconclusive: Technically the member function 'PosteriorDecoder::maskViterbiAlignment' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:211:24: note: Technically the member function 'PosteriorDecoder::maskViterbiAlignment' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:132:10: note: Technically the member function 'PosteriorDecoder::maskViterbiAlignment' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:135:7: style:inconclusive: Technically the member function 'PosteriorDecoder::restoreHitValues' can be const. [functionConst]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:286:24: note: Technically the member function 'PosteriorDecoder::restoreHitValues' can be const.
hh-suite-3.3.0/src/hhposteriordecoder.h:135:7: note: Technically the member function 'PosteriorDecoder::restoreHitValues' can be const.
hh-suite-3.3.0/src/hhposteriordecoder.h:138:7: performance:inconclusive: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:310:24: note: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:138:7: note: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:139:7: performance:inconclusive: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:319:24: note: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:139:7: note: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:140:7: performance:inconclusive: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:300:24: note: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:140:7: note: Technically the member function 'PosteriorDecoder::printVector' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:143:7: performance:inconclusive: Technically the member function 'PosteriorDecoder::exclude_regions' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:122:24: note: Technically the member function 'PosteriorDecoder::exclude_regions' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:143:7: note: Technically the member function 'PosteriorDecoder::exclude_regions' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:144:14: performance:inconclusive: Technically the member function 'PosteriorDecoder::exclude_template_regions' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:138:24: note: Technically the member function 'PosteriorDecoder::exclude_template_regions' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.h:144:14: note: Technically the member function 'PosteriorDecoder::exclude_template_regions' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoder.cpp:66:8: warning: Class 'PosteriorDecoder' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:66:8: warning: Class 'PosteriorDecoder' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:50:17: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:51:17: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:53:19: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:54:19: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:56:21: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:314:26: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:323:22: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:162:88: style:inconclusive: Function 'initializeForAlignment' argument 4 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoder.h:131:71: note: Function 'initializeForAlignment' argument 4 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'.
hh-suite-3.3.0/src/hhposteriordecoder.cpp:162:88: note: Function 'initializeForAlignment' argument 4 names different: declaration 'viterbi_matrix' definition 'celloff_matrix'.
hh-suite-3.3.0/src/hhposteriordecoder.cpp:122:61: style: Parameter 'q_hmm' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:122:74: style: Parameter 't_hmm' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:138:70: style: Parameter 'q_hmm' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:138:83: style: Parameter 't_hmm' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhposteriordecoder.cpp:270:47: style: Parameter 'curr_hit' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhposteriordecoderrunner.h:29:16: style:inconclusive: Member variable 'PosteriorDecoderRunner::S73' is in the wrong place in the initializer list. [initializerList]
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:38:35: note: Member variable 'PosteriorDecoderRunner::S73' is in the wrong place in the initializer list.
hh-suite-3.3.0/src/hhposteriordecoderrunner.h:29:16: note: Member variable 'PosteriorDecoderRunner::S73' is in the wrong place in the initializer list.
hh-suite-3.3.0/src/hhposteriordecoderrunner.h:45:7: performance:inconclusive: Technically the member function 'PosteriorDecoderRunner::initializeQueryHMMTransitions' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:147:30: note: Technically the member function 'PosteriorDecoderRunner::initializeQueryHMMTransitions' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoderrunner.h:45:7: note: Technically the member function 'PosteriorDecoderRunner::initializeQueryHMMTransitions' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoderrunner.h:46:7: performance:inconclusive: Technically the member function 'PosteriorDecoderRunner::cleanupThread' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:138:30: note: Technically the member function 'PosteriorDecoderRunner::cleanupThread' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoderrunner.h:46:7: note: Technically the member function 'PosteriorDecoderRunner::cleanupThread' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:27:15: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:28:15: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:89:17: style: The scope of the variable 'format_tmp' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:33:53: style:inconclusive: Function 'PosteriorDecoderRunner' argument 3 names different: declaration 'n_threadsconst' definition 'n_threads'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhposteriordecoderrunner.h:18:20: note: Function 'PosteriorDecoderRunner' argument 3 names different: declaration 'n_threadsconst' definition 'n_threads'.
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:33:53: note: Function 'PosteriorDecoderRunner' argument 3 names different: declaration 'n_threadsconst' definition 'n_threads'.
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:79:28: style: Local variable 'hits' shadows outer argument [shadowArgument]
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:43:77: note: Shadowed declaration
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:79:28: note: Shadow variable
hh-suite-3.3.0/src/hhposteriordecoderrunner.cpp:61:76: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hh-suite-3.3.0/src/hash.h:202:12: warning: Member variable 'Hash < char >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:202:12: warning: Member variable 'Hash < char >::fail' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:210:12: warning: Member variable 'Hash < char >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:221:12: warning: Member variable 'Hash < char >::key_len' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:48:3: warning:inconclusive: Member variable 'Pair < char >::key' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hash.h:48:3: warning:inconclusive: Member variable 'Pair < char >::data' is not initialized in the constructor. [uninitMemberVar]
hh-suite-3.3.0/src/hhprefilter.h:124:7: style:inconclusive: Technically the member function 'Prefilter::stripe_query_profile' can be const. [functionConst]
hh-suite-3.3.0/src/hhprefilter.cpp:356:17: note: Technically the member function 'Prefilter::stripe_query_profile' can be const.
hh-suite-3.3.0/src/hhprefilter.h:124:7: note: Technically the member function 'Prefilter::stripe_query_profile' can be const.
hh-suite-3.3.0/src/hash.h:164:7: style:inconclusive: Technically the member function 'Hash < char >::End' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:175:7: style:inconclusive: Technically the member function 'Hash < char >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/hash.h:178:7: style:inconclusive: Technically the member function 'Hash < char >::MaxLen' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:55:10: performance:inconclusive: Technically the member function 'List < Pair < char > >::SwapContent' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/list.h:87:9: style:inconclusive: Technically the member function 'List < Pair < char > >::ReadLast' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:115:9: style:inconclusive: Technically the member function 'List < Pair < char > >::ReadCurrent' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:430:23: note: Technically the member function 'List < Pair < char > >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:115:9: note: Technically the member function 'List < Pair < char > >::ReadCurrent' can be const.
hh-suite-3.3.0/src/list.h:157:9: style:inconclusive: Technically the member function 'List < Pair < char > >::Size' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:162:10: style:inconclusive: Technically the member function 'List < Pair < char > >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:165:10: style:inconclusive: Technically the member function 'List < Pair < char > >::End' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:170:10: style:inconclusive: Technically the member function 'List < Pair < char > >::Start' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:175:9: style:inconclusive: Technically the member function 'List < Pair < char > >::GetPos' can be const. [functionConst]
hh-suite-3.3.0/src/list.h:535:16: note: Technically the member function 'List < Pair < char > >::GetPos' can be const.
hh-suite-3.3.0/src/list.h:175:9: note: Technically the member function 'List < Pair < char > >::GetPos' can be const.
hh-suite-3.3.0/src/hhprefilter.cpp:41:3: warning: Class 'Prefilter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhprefilter.cpp:41:3: warning: Class 'Prefilter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash < char >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:225:3: warning: Class 'Hash < char >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < char >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < char >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hash.h:50:34: warning: Class 'Pair < char >' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
hh-suite-3.3.0/src/list.h:261:3: warning: Class 'List < Pair < char > >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hash.h:97:3: style: Class 'Hash < char >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:68:5: style: Class 'List < Pair < char > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/list.h:31:9: style: Class 'ListEl < Pair < char > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
hh-suite-3.3.0/src/hash.h:46:9: style: Class 'Pair < char >' is unsafe, 'Pair < char >::key' can leak by wrong usage. [unsafeClassCanLeak]
hh-suite-3.3.0/src/hhprefilter.cpp:42:10: warning:inconclusive: Either the condition '!fin' is redundant or there is possible null pointer dereference: fin. [nullPointerRedundantCheck]
hh-suite-3.3.0/src/hhprefilter.cpp:38:7: note: Assuming that condition '!fin' is not redundant
hh-suite-3.3.0/src/hhprefilter.cpp:42:10: note: Null pointer dereference
hh-suite-3.3.0/src/hhprefilter.cpp:33:20: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:81:29: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:230:32: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:317:11: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:318:12: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:319:13: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:323:16: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:366:24: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:447:23: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:463:20: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:582:35: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhprefilter.cpp:228:13: style: The scope of the variable 'qji' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhprefilter.cpp:229:13: style: The scope of the variable 's_prev_it' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhprefilter.cpp:229:25: style: The scope of the variable 's_curr_it' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhprefilter.cpp:280:55: style:inconclusive: Function 'init_no_prefiltering' argument 1 names different: declaration 'cs219_database' definition 'query_database'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhprefilter.h:77:52: note: Function 'init_no_prefiltering' argument 1 names different: declaration 'cs219_database' definition 'query_database'.
hh-suite-3.3.0/src/hhprefilter.cpp:280:55: note: Function 'init_no_prefiltering' argument 1 names different: declaration 'cs219_database' definition 'query_database'.
hh-suite-3.3.0/src/hash.h:221:33: style:inconclusive: Function 'Hash < char >' argument 2 names different: declaration 'n' definition 'f'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hash.h:98:24: note: Function 'Hash < char >' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hash.h:221:33: note: Function 'Hash < char >' argument 2 names different: declaration 'n' definition 'f'.
hh-suite-3.3.0/src/hhprefilter.cpp:76:17: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhprefilter.cpp:77:23: style: Variable 'end_query' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhprefilter.cpp:78:20: style: Variable 'end_db' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhprefilter.cpp:102:13: style: Unused variable: edge [unusedVariable]
hh-suite-3.3.0/src/hhprefilter.cpp:494:66: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hh-suite-3.3.0/src/hhprefilter.cpp:546:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hh-suite-3.3.0/src/hhprefilter.cpp:561:46: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hh-suite-3.3.0/src/hhsearch.cpp:20:17: style: Variable 'argc' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhsearch.cpp:21:20: style: Variable 'argv' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhutil.cpp:154:15: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhutil.cpp:165:15: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhutil.cpp:77:23: portability: Casting from float * to unsigned int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/hhutil.cpp:104:14: portability: Casting between unsigned int * and float * which have an incompatible binary data representation. [invalidPointerCast]
hh-suite-3.3.0/src/hhutil.cpp:116:23: portability: Casting from float * to unsigned int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
hh-suite-3.3.0/src/hhutil.cpp:143:14: portability: Casting between unsigned int * and float * which have an incompatible binary data representation. [invalidPointerCast]
hh-suite-3.3.0/src/hhviterbi.cpp:23:33: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbi.cpp:43:22: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbi.cpp:63:22: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbi.cpp:64:22: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbi.cpp:202:22: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbi.cpp:203:22: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbi.cpp:323:9: style: The scope of the variable 'min_overlap' can be reduced. [variableScope]
hh-suite-3.3.0/src/hhviterbi.cpp:13:22: style:inconclusive: Function 'Viterbi' argument 1 names different: declaration 'maxres' definition 'max_seq_length'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhviterbi.h:53:17: note: Function 'Viterbi' argument 1 names different: declaration 'maxres' definition 'max_seq_length'.
hh-suite-3.3.0/src/hhviterbi.cpp:13:22: note: Function 'Viterbi' argument 1 names different: declaration 'maxres' definition 'max_seq_length'.
hh-suite-3.3.0/src/hhviterbi.cpp:62:15: style: Parameter 'i_steps' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/src/hhviterbi.cpp:62:30: style: Parameter 'j_steps' can be declared as pointer to const [constParameter]
hh-suite-3.3.0/src/hhviterbi.cpp:83:81: style: Parameter 'start_i' can be declared as const array [constParameter]
hh-suite-3.3.0/src/hhviterbi.cpp:83:109: style: Parameter 'start_j' can be declared as const array [constParameter]
hh-suite-3.3.0/src/hhviterbi.cpp:197:15: style: Parameter 'alignmentScore' can be declared as const array [constParameter]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:177:48: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:182:47: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:183:47: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:184:47: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:185:47: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:186:47: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:187:47: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:188:47: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:222:51: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:223:51: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:224:51: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:225:51: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:226:51: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:227:51: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:228:51: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:277:45: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:288:53: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:289:53: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:290:53: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:291:53: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:292:53: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:293:53: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:294:40: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:295:40: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:296:40: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:297:40: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:298:40: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:396:27: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:397:27: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:398:27: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:399:27: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbialgorithm.cpp:400:27: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhviterbirunner.h:65:7: performance:inconclusive: Technically the member function 'ViterbiRunner::merge_thread_results' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhviterbirunner.cpp:249:21: note: Technically the member function 'ViterbiRunner::merge_thread_results' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhviterbirunner.h:65:7: note: Technically the member function 'ViterbiRunner::merge_thread_results' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhviterbirunner.h:79:8: performance:inconclusive: Technically the member function 'ViterbiRunner::calculateEarlyStop' can be static (but you may consider moving to unnamed namespace). [functionStatic]
hh-suite-3.3.0/src/hhviterbirunner.cpp:213:22: note: Technically the member function 'ViterbiRunner::calculateEarlyStop' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhviterbirunner.h:79:8: note: Technically the member function 'ViterbiRunner::calculateEarlyStop' can be static (but you may consider moving to unnamed namespace).
hh-suite-3.3.0/src/hhviterbirunner.cpp:104:14: style: Local variable 'alignment' shadows outer function [shadowFunction]
hh-suite-3.3.0/src/hhviterbirunner.h:55:19: note: Shadowed declaration
hh-suite-3.3.0/src/hhviterbirunner.cpp:104:14: note: Shadow variable
hh-suite-3.3.0/src/hhviterbirunner.cpp:213:53: style: Parameter 'par' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhviterbirunner.cpp:213:85: style: Parameter 'all_hits' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhviterbirunner.cpp:233:29: style: Variable 'current_hit.logEval' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/util.cpp:282:8: debug: Wrong data detected by condition !tok->next()->astOperand1() [DacaWrongData]
hh-suite-3.3.0/src/util.cpp:282:18: debug: Wrong data detected by condition !tok->next()->astOperand2() [DacaWrongData]
hh-suite-3.3.0/src/util.cpp:282:27: error: Uninitialized variable: i [uninitvar]
hh-suite-3.3.0/src/hhblits.cpp:12:5: performance: Variable 'dbs' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
hh-suite-3.3.0/src/hhblits.cpp:40:5: warning: Class 'HHblits' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
hh-suite-3.3.0/src/hhblits.cpp:40:5: warning: Class 'HHblits' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
hh-suite-3.3.0/src/hhblits.cpp:257:8: style: The if condition is the same as the previous if condition [duplicateCondition]
hh-suite-3.3.0/src/hhblits.cpp:243:9: note: First condition
hh-suite-3.3.0/src/hhblits.cpp:257:8: note: Second condition
hh-suite-3.3.0/src/hhblits.cpp:843:37: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:851:38: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:938:37: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:939:49: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:940:32: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:1309:45: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:1385:44: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:1388:36: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:1706:45: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:1783:44: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:1786:36: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:2036:29: style: C-style pointer casting [cstyleCast]
hh-suite-3.3.0/src/hhblits.cpp:11:30: style:inconclusive: Function 'HHblits' argument 1 names different: declaration 'parameters' definition 'par'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhblits.h:73:23: note: Function 'HHblits' argument 1 names different: declaration 'parameters' definition 'par'.
hh-suite-3.3.0/src/hhblits.cpp:11:30: note: Function 'HHblits' argument 1 names different: declaration 'parameters' definition 'par'.
hh-suite-3.3.0/src/hhblits.cpp:1850:43: style:inconclusive: Function 'writePairwiseAlisFile' argument 1 names different: declaration 'pairwieseAlisFile' definition 'pairwiseAlisFile'. [funcArgNamesDifferent]
hh-suite-3.3.0/src/hhblits.h:89:36: note: Function 'writePairwiseAlisFile' argument 1 names different: declaration 'pairwieseAlisFile' definition 'pairwiseAlisFile'.
hh-suite-3.3.0/src/hhblits.cpp:1850:43: note: Function 'writePairwiseAlisFile' argument 1 names different: declaration 'pairwieseAlisFile' definition 'pairwiseAlisFile'.
hh-suite-3.3.0/src/hhblits.cpp:1227:17: style: Local variable 'hit_cur' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1071:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1227:17: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1246:31: style: Local variable 'viterbirunner' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1215:23: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1246:31: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1247:34: style: Local variable 'hits_to_add' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1216:26: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1247:34: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1296:21: style: Local variable 'hit_cur' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1071:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1296:21: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1379:17: style: Local variable 'hit_cur' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1071:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1379:17: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1624:17: style: Local variable 'hit_cur' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1462:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1624:17: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1643:31: style: Local variable 'viterbirunner' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1612:23: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1643:31: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1644:34: style: Local variable 'hits_to_add' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1613:26: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1644:34: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1693:21: style: Local variable 'hit_cur' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1462:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1693:21: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:1777:17: style: Local variable 'hit_cur' shadows outer variable [shadowVariable]
hh-suite-3.3.0/src/hhblits.cpp:1462:9: note: Shadowed declaration
hh-suite-3.3.0/src/hhblits.cpp:1777:17: note: Shadow variable
hh-suite-3.3.0/src/hhblits.cpp:11:66: style: Parameter 'databases' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhblits.cpp:890:53: style: Parameter 'hits' can be declared as reference to const [constParameter]
hh-suite-3.3.0/src/hhblits.cpp:81:20: style: Variable 'argc' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhblits.cpp:82:23: style: Variable 'argv' is assigned a value that is never used. [unreadVariable]
hh-suite-3.3.0/src/hhblits.cpp:988:46: style: Unused variable: alignments [unusedVariable]
hh-suite-3.3.0/src/hhblits.cpp:172:47: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
hh-suite-3.3.0/src/hhblits.cpp:1828:51: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
diff:
head hh-suite-3.3.0/lib/ffindex/src/ffindex.c:48:73: style: Parameter 'mode' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/lib/ffindex/src/ffindex.c:48:73: style: Parameter 'mode' can be declared with const [constParameter]
head hh-suite-3.3.0/src/a3m_compress.cpp:478:11: style: Parameter 'full_sequence' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/src/a3m_compress.cpp:478:11: style: Parameter 'full_sequence' can be declared with const [constParameter]
head hh-suite-3.3.0/src/cs/blosum_matrix.h:37:3: style: Class 'BlosumMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hh-suite-3.3.0/src/cs/context_profile.h:31:5: style: Struct 'Color' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hh-suite-3.3.0/src/cs/cstranslate_app.h:605:45: style: Parameter 'as_profile' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/cs/cstranslate_app.h:605:45: style: Parameter 'as_profile' can be declared with const [constParameter]
head hh-suite-3.3.0/src/cs/sequence.h:38:5: style: Class 'Sequence < AA >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hh-suite-3.3.0/src/hash.h:49:22: style: Parameter 'd' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hash.h:49:22: style: Parameter 'd' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hash.h:50:13: style: Parameter 'l' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hash.h:50:13: style: Parameter 'l' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hash.h:50:30: style: Parameter 'd' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hash.h:50:30: style: Parameter 'd' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhalignment.cpp:2027:38: style: Parameter 'keep_orig' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/src/hhalignment.cpp:2027:38: style: Parameter 'keep_orig' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhalignment.cpp:2951:56: style: Parameter 'in' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/src/hhalignment.cpp:2951:56: style: Parameter 'in' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhalignment.cpp:3159:56: style: Parameter 'in' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/src/hhalignment.cpp:3159:56: style: Parameter 'in' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhalignment.cpp:3708:34: style: Parameter 'Xk' can be declared as const array [constParameter]
2.8 hh-suite-3.3.0/src/hhalignment.cpp:3708:34: style: Parameter 'Xk' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhalignment.cpp:3708:44: style: Parameter 'Ik' can be declared as const array [constParameter]
2.8 hh-suite-3.3.0/src/hhalignment.cpp:3708:44: style: Parameter 'Ik' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhbacktracemac.cpp:14:49: style: Parameter 'q' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhbacktracemac.cpp:14:49: style: Parameter 'q' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhbacktracemac.cpp:14:57: style: Parameter 't' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhbacktracemac.cpp:14:57: style: Parameter 't' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhbacktracemac.cpp:14:77: style: Parameter 'p_mm' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhbacktracemac.cpp:14:77: style: Parameter 'p_mm' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:66: style: Parameter 'hit' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhbackwardalgorithm.cpp:10:66: style: Parameter 'hit' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhblits.cpp:11:66: style: Parameter 'databases' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhblits.cpp:11:66: style: Parameter 'databases' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhblits.cpp:890:53: style: Parameter 'hits' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhblits.cpp:890:53: style: Parameter 'hits' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhconsensus.cpp:36:23: style: Parameter 'par' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhconsensus.cpp:36:23: style: Parameter 'par' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhdatabase.cpp:156:62: style: Parameter 'selected_templates' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhdatabase.cpp:156:62: style: Parameter 'selected_templates' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhdatabase.cpp:560:49: style: Parameter 'entries' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhdatabase.cpp:560:49: style: Parameter 'entries' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhdecl.h:107:3: style: Struct 'Params' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head hh-suite-3.3.0/src/hhfilter.cpp:34:23: style: Parameter 'par' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhfilter.cpp:34:23: style: Parameter 'par' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhfullalignment.cpp:195:70: style: Parameter 'hit' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhfullalignment.cpp:195:70: style: Parameter 'hit' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhfullalignment.cpp:209:59: style: Parameter 'hit' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhfullalignment.cpp:209:59: style: Parameter 'hit' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhfunc.cpp:10:32: style: Parameter 'par' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhfunc.cpp:10:32: style: Parameter 'par' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhfunc.cpp:120:34: style: Parameter 'par' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhfunc.cpp:120:34: style: Parameter 'par' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhfunc.cpp:120:45: style: Parameter 'input_format' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhfunc.cpp:120:45: style: Parameter 'input_format' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhfunc.cpp:164:37: style: Parameter 'par' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhfunc.cpp:164:37: style: Parameter 'par' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhhalfalignment.cpp:243:42: style: Parameter 'hit' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhhalfalignment.cpp:243:42: style: Parameter 'hit' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhhit-inl.h:38:39: style: Parameter 'a' can be declared as const array [constParameter]
2.8 hh-suite-3.3.0/src/hhhit-inl.h:38:39: style: Parameter 'a' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhhit-inl.h:55:41: style: Parameter 'a' can be declared as const array [constParameter]
2.8 hh-suite-3.3.0/src/hhhit-inl.h:55:41: style: Parameter 'a' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhposteriordecoder.cpp:122:61: style: Parameter 'q_hmm' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhposteriordecoder.cpp:122:61: style: Parameter 'q_hmm' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhposteriordecoder.cpp:122:74: style: Parameter 't_hmm' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhposteriordecoder.cpp:122:74: style: Parameter 't_hmm' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhposteriordecoder.cpp:138:70: style: Parameter 'q_hmm' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhposteriordecoder.cpp:138:70: style: Parameter 'q_hmm' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhposteriordecoder.cpp:138:83: style: Parameter 't_hmm' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhposteriordecoder.cpp:138:83: style: Parameter 't_hmm' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhposteriordecoder.cpp:270:47: style: Parameter 'curr_hit' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhposteriordecoder.cpp:270:47: style: Parameter 'curr_hit' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhviterbi.cpp:197:15: style: Parameter 'alignmentScore' can be declared as const array [constParameter]
2.8 hh-suite-3.3.0/src/hhviterbi.cpp:197:15: style: Parameter 'alignmentScore' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhviterbi.cpp:62:15: style: Parameter 'i_steps' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/src/hhviterbi.cpp:62:15: style: Parameter 'i_steps' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhviterbi.cpp:62:30: style: Parameter 'j_steps' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/src/hhviterbi.cpp:62:30: style: Parameter 'j_steps' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhviterbi.cpp:83:109: style: Parameter 'start_j' can be declared as const array [constParameter]
2.8 hh-suite-3.3.0/src/hhviterbi.cpp:83:109: style: Parameter 'start_j' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhviterbi.cpp:83:81: style: Parameter 'start_i' can be declared as const array [constParameter]
2.8 hh-suite-3.3.0/src/hhviterbi.cpp:83:81: style: Parameter 'start_i' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhviterbirunner.cpp:213:53: style: Parameter 'par' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhviterbirunner.cpp:213:53: style: Parameter 'par' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhviterbirunner.cpp:213:85: style: Parameter 'all_hits' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhviterbirunner.cpp:213:85: style: Parameter 'all_hits' can be declared with const [constParameter]
head hh-suite-3.3.0/src/hhviterbirunner.h:23:52: style: Parameter 'par' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/hhviterbirunner.h:23:52: style: Parameter 'par' can be declared with const [constParameter]
head hh-suite-3.3.0/src/list.h:165:20: style: Parameter 'curr' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/src/list.h:165:20: style: Parameter 'curr' can be declared with const [constParameter]
head hh-suite-3.3.0/src/list.h:304:51: style: Parameter 'l' can be declared as reference to const [constParameter]
2.8 hh-suite-3.3.0/src/list.h:304:51: style: Parameter 'l' can be declared with const [constParameter]
head hh-suite-3.3.0/src/util-inl.h:295:69: style: Parameter 'def_array' can be declared as pointer to const [constParameter]
2.8 hh-suite-3.3.0/src/util-inl.h:295:69: style: Parameter 'def_array' can be declared with const [constParameter]


DONE