=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== mmseqs2-12-113e3+ds/cmake/GetGitRevisionDescription.cmake-76- @ONLY) mmseqs2-12-113e3+ds/cmake/GetGitRevisionDescription.cmake:77: include("${GIT_DATA}/grabRef.cmake") mmseqs2-12-113e3+ds/cmake/GetGitRevisionDescription.cmake-78- ############################################## mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-367- supplied C version. Also, the case of x86 using gcc is special-cased mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h:368: to an asm instruction, so is already as fast as it can be, and so mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-369- this setting has no effect. Similarly for Win32 under recent MS compilers. mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h:370: (On most x86s, the asm version is only slightly faster than the C version.) mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-371- ############################################## mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-2754- mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h:2755:/* assign tree index for size S to variable I. Use x86 asm if possible */ mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-2756-#if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__)) ############################################## mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-2857- mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h:2858:/* index corresponding to given bit. Use x86 asm if possible */ mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-2859- ############################################## mmseqs2-12-113e3+ds/src/commons/Parameters.cpp-257- PARAM_SUBDB_MODE(PARAM_SUBDB_MODE_ID, "--subdb-mode", "Subdb mode", "Subdb mode 0: copy data 1: soft link data and write index", typeid(int), (void *) &subDbMode, "^[0-1]{1}$"), mmseqs2-12-113e3+ds/src/commons/Parameters.cpp:258: PARAM_TAR_INCLUDE(PARAM_TAR_INCLUDE_ID, "--tar-include", "Tar Inclusion Regex", "Include file names based on this regex", typeid(std::string), (void *) &tarInclude, "^.*$"), mmseqs2-12-113e3+ds/src/commons/Parameters.cpp-259- PARAM_TAR_EXCLUDE(PARAM_TAR_EXCLUDE_ID, "--tar-exclude", "Tar Exclusion Regex", "Exclude file names based on this regex", typeid(std::string), (void *) &tarExclude, "^.*$"), ############################################## mmseqs2-12-113e3+ds/src/workflow/Databases.cpp-149- "Kalamari contains over 250 genomes chosen to be representative of agents tracked by genome-based foodborne disease surveillance, common contaminants, and diverse phyla and bacterial genera.", mmseqs2-12-113e3+ds/src/workflow/Databases.cpp:150: "Katz et al: Kraken with Kalamari: Contamination Detection. ASM Poster, 270 (2018)", mmseqs2-12-113e3+ds/src/workflow/Databases.cpp-151- "https://github.com/lskatz/Kalamari", ############################################## mmseqs2-12-113e3+ds/debian/missing-sources/userguide/Home.md-1310-The corresponding index file (file extension `.index`) looks like this. The first column is the numeric sequence identfier, second the offset and thrid the length. mmseqs2-12-113e3+ds/debian/missing-sources/userguide/Home.md:1311:The length contains the null byte and the new line. So the real sequence sequence is two shorted (`$3 - 2`). mmseqs2-12-113e3+ds/debian/missing-sources/userguide/Home.md-1312- ############################################## mmseqs2-12-113e3+ds/debian/missing-sources/userguide/MMseqs2-Developer-Guide.md-223- mmseqs2-12-113e3+ds/debian/missing-sources/userguide/MMseqs2-Developer-Guide.md:224:`BASE_DIR="$HOME/clone/regression_test”` mmseqs2-12-113e3+ds/debian/missing-sources/userguide/MMseqs2-Developer-Guide.md:225:`MMSEQSSSE="$HOME/clone/build/src/mmseqs”` mmseqs2-12-113e3+ds/debian/missing-sources/userguide/MMseqs2-Developer-Guide.md:226:`MMSEQSAVX="$HOME/clone/build_avx2/src/mmseqs"` mmseqs2-12-113e3+ds/debian/missing-sources/userguide/MMseqs2-Developer-Guide.md-227- ############################################## mmseqs2-12-113e3+ds/.pc/spelling/src/commons/Parameters.cpp-257- PARAM_SUBDB_MODE(PARAM_SUBDB_MODE_ID, "--subdb-mode", "Subdb mode", "Subdb mode 0: copy data 1: soft link data and write index", typeid(int), (void *) &subDbMode, "^[0-1]{1}$"), mmseqs2-12-113e3+ds/.pc/spelling/src/commons/Parameters.cpp:258: PARAM_TAR_INCLUDE(PARAM_TAR_INCLUDE_ID, "--tar-include", "Tar Inclusion Regex", "Include file names based on this regex", typeid(std::string), (void *) &tarInclude, "^.*$"), mmseqs2-12-113e3+ds/.pc/spelling/src/commons/Parameters.cpp-259- PARAM_TAR_EXCLUDE(PARAM_TAR_EXCLUDE_ID, "--tar-exclude", "Tar Exclusion Regex", "Exclude file names based on this regex", typeid(std::string), (void *) &tarExclude, "^.*$"),