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              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("${GIT_DATA}/grabRef.cmake")
mmseqs2-12-113e3+ds/cmake/GetGitRevisionDescription.cmake-78-
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mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-367-  supplied C version. Also, the case of x86 using gcc is special-cased
mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h:368:  to an asm instruction, so is already as fast as it can be, and so
mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-369-  this setting has no effect. Similarly for Win32 under recent MS compilers.
mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h:370:  (On most x86s, the asm version is only slightly faster than the C version.)
mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-371-
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mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-2754-
mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h:2755:/* assign tree index for size S to variable I. Use x86 asm if possible  */
mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-2756-#if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
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mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-2857-
mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h:2858:/* index corresponding to given bit. Use x86 asm if possible */
mmseqs2-12-113e3+ds/lib/nedmalloc/malloc.c.h-2859-
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mmseqs2-12-113e3+ds/src/commons/Parameters.cpp-257-        PARAM_SUBDB_MODE(PARAM_SUBDB_MODE_ID, "--subdb-mode", "Subdb mode", "Subdb mode 0: copy data 1: soft link data and write index", typeid(int), (void *) &subDbMode, "^[0-1]{1}$"),
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, "^.*$"),
mmseqs2-12-113e3+ds/src/commons/Parameters.cpp-259-        PARAM_TAR_EXCLUDE(PARAM_TAR_EXCLUDE_ID, "--tar-exclude", "Tar Exclusion Regex", "Exclude file names based on this regex", typeid(std::string), (void *) &tarExclude, "^.*$"),
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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",
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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 (`$3 - 2`).
mmseqs2-12-113e3+ds/debian/missing-sources/userguide/Home.md-1312-
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mmseqs2-12-113e3+ds/debian/missing-sources/userguide/MMseqs2-Developer-Guide.md-223-
mmseqs2-12-113e3+ds/debian/missing-sources/userguide/MMseqs2-Developer-Guide.md:224:`BASE_DIR="$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-
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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, "^.*$"),