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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
freebayes-1.3.2/paper/main.tex-511-
freebayes-1.3.2/paper/main.tex:512:For accurate variant detection via resequencing, we require that the locus in question is sequencable. That is, we require that the reference is accurate, that we have an accurate model of copy number at the locus, that we have genomic coverage, and that reads can be aligned to the alleles of interest in the region. In a case where these conditions are met, we assume $S = true$. Where it is not, $S = false$.
freebayes-1.3.2/paper/main.tex-513-
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freebayes-1.3.2/src/Utility.cpp-524- // Berghel, Hal ; Roach, David : "An Extension of Ukkonen's
freebayes-1.3.2/src/Utility.cpp:525: // Enhanced Dynamic Programming ASM Algorithm"
freebayes-1.3.2/src/Utility.cpp-526- // (http://www.acm.org/~hlb/publications/asm/asm.html)
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freebayes-1.3.2/src/levenshtein.cpp-75- // Berghel, Hal ; Roach, David : "An Extension of Ukkonen's
freebayes-1.3.2/src/levenshtein.cpp:76: // Enhanced Dynamic Programming ASM Algorithm"
freebayes-1.3.2/src/levenshtein.cpp-77- // (http://www.acm.org/~hlb/publications/asm/asm.html)
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freebayes-1.3.2/ttmath/ttmathbig.h-137- we have following types:
freebayes-1.3.2/ttmath/ttmathbig.h:138: asm_vc_32 - with asm code designed for Microsoft Visual C++ (32 bits)
freebayes-1.3.2/ttmath/ttmathbig.h:139: asm_gcc_32 - with asm code designed for GCC (32 bits)
freebayes-1.3.2/ttmath/ttmathbig.h:140: asm_vc_64 - with asm for VC (64 bit)
freebayes-1.3.2/ttmath/ttmathbig.h:141: asm_gcc_64 - with asm for GCC (64 bit)
freebayes-1.3.2/ttmath/ttmathbig.h:142: no_asm_32 - pure C++ version (32 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathbig.h:143: no_asm_64 - pure C++ version (64 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathbig.h-144- */
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freebayes-1.3.2/ttmath/ttmathtypes.h-107-/*!
freebayes-1.3.2/ttmath/ttmathtypes.h:108: asm version of the library is available by default only for:
freebayes-1.3.2/ttmath/ttmathtypes.h-109- x86 and amd64 platforms and for Microsoft Visual and GCC compilers
freebayes-1.3.2/ttmath/ttmathtypes.h-110-
freebayes-1.3.2/ttmath/ttmathtypes.h:111: but you can force using asm version (the same asm as for Microsoft Visual)
freebayes-1.3.2/ttmath/ttmathtypes.h:112: by defining TTMATH_FORCEASM macro
freebayes-1.3.2/ttmath/ttmathtypes.h:113: you have to be sure that your compiler accept such an asm format
freebayes-1.3.2/ttmath/ttmathtypes.h-114-*/
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freebayes-1.3.2/ttmath/ttmathtypes.h-127-
freebayes-1.3.2/ttmath/ttmathtypes.h:128: asm version is available only for x86 or amd64 platforms
freebayes-1.3.2/ttmath/ttmathtypes.h-129- */
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freebayes-1.3.2/ttmath/ttmathtypes.h-136- /*!
freebayes-1.3.2/ttmath/ttmathtypes.h:137: another compilers than MS VC or GCC or CLANG (LLVM) by default use no asm version
freebayes-1.3.2/ttmath/ttmathtypes.h-138- (CLANG defines __GNUC__ too)
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freebayes-1.3.2/ttmath/ttmathtypes.h-319- lib type codes:
freebayes-1.3.2/ttmath/ttmathtypes.h:320: asm_vc_32 - with asm code designed for Microsoft Visual C++ (32 bits)
freebayes-1.3.2/ttmath/ttmathtypes.h:321: asm_gcc_32 - with asm code designed for GCC (32 bits)
freebayes-1.3.2/ttmath/ttmathtypes.h:322: asm_vc_64 - with asm for VC (64 bit)
freebayes-1.3.2/ttmath/ttmathtypes.h:323: asm_gcc_64 - with asm for GCC (64 bit)
freebayes-1.3.2/ttmath/ttmathtypes.h:324: no_asm_32 - pure C++ version (32 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathtypes.h:325: no_asm_64 - pure C++ version (64 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathtypes.h-326- */
##############################################
freebayes-1.3.2/ttmath/ttmathuint_noasm.h-57- we have following types:
freebayes-1.3.2/ttmath/ttmathuint_noasm.h:58: asm_vc_32 - with asm code designed for Microsoft Visual C++ (32 bits)
freebayes-1.3.2/ttmath/ttmathuint_noasm.h:59: asm_gcc_32 - with asm code designed for GCC (32 bits)
freebayes-1.3.2/ttmath/ttmathuint_noasm.h:60: asm_vc_64 - with asm for VC (64 bit)
freebayes-1.3.2/ttmath/ttmathuint_noasm.h:61: asm_gcc_64 - with asm for GCC (64 bit)
freebayes-1.3.2/ttmath/ttmathuint_noasm.h:62: no_asm_32 - pure C++ version (32 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathuint_noasm.h:63: no_asm_64 - pure C++ version (64 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathuint_noasm.h-64- */
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freebayes-1.3.2/ttmath/ttmathuint_noasm.h-101-
freebayes-1.3.2/ttmath/ttmathuint_noasm.h:102: this method is created only when TTMATH_NOASM macro is defined
freebayes-1.3.2/ttmath/ttmathuint_noasm.h-103- */
##############################################
freebayes-1.3.2/ttmath/ttmathuint_noasm.h-288-
freebayes-1.3.2/ttmath/ttmathuint_noasm.h:289: this method is created only when TTMATH_NOASM macro is defined
freebayes-1.3.2/ttmath/ttmathuint_noasm.h-290- */
##############################################
freebayes-1.3.2/ttmath/ttmathuint_x86.h-65- we have following types:
freebayes-1.3.2/ttmath/ttmathuint_x86.h:66: asm_vc_32 - with asm code designed for Microsoft Visual C++ (32 bits)
freebayes-1.3.2/ttmath/ttmathuint_x86.h:67: asm_gcc_32 - with asm code designed for GCC (32 bits)
freebayes-1.3.2/ttmath/ttmathuint_x86.h:68: asm_vc_64 - with asm for VC (64 bit)
freebayes-1.3.2/ttmath/ttmathuint_x86.h:69: asm_gcc_64 - with asm for GCC (64 bit)
freebayes-1.3.2/ttmath/ttmathuint_x86.h:70: no_asm_32 - pure C++ version (32 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathuint_x86.h:71: no_asm_64 - pure C++ version (64 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathuint_x86.h-72- */
##############################################
freebayes-1.3.2/ttmath/ttmathuint_x86.h-783- /*
freebayes-1.3.2/ttmath/ttmathuint_x86.h:784: the asm code is nearly the same as in AddVector
freebayes-1.3.2/ttmath/ttmathuint_x86.h-785- only two instructions 'adc' are changed to 'sbb'
##############################################
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h-84- we have following types:
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h:85: asm_vc_32 - with asm code designed for Microsoft Visual C++ (32 bits)
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h:86: asm_gcc_32 - with asm code designed for GCC (32 bits)
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h:87: asm_vc_64 - with asm for VC (64 bit)
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h:88: asm_gcc_64 - with asm for GCC (64 bit)
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h:89: no_asm_32 - pure C++ version (32 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h:90: no_asm_64 - pure C++ version (64 bit) - without any asm code
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h-91- */
##############################################
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h-578-
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h:579: // the asm code is nearly the same as in AddVector
freebayes-1.3.2/ttmath/ttmathuint_x86_64.h-580- // only two instructions 'adc' are changed to 'sbb'
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freebayes-1.3.2/ttmath/ttmathuint_x86_64_msvc.asm-311-
freebayes-1.3.2/ttmath/ttmathuint_x86_64_msvc.asm:312:; the same asm code as in addvector_x64 only two instructions 'adc' changed to 'sbb'
freebayes-1.3.2/ttmath/ttmathuint_x86_64_msvc.asm-313-
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freebayes-1.3.2/debian/createmanpages-4-
freebayes-1.3.2/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
freebayes-1.3.2/debian/createmanpages-6-
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freebayes-1.3.2/debian/rules-20- mkdir -p $(CURDIR)/test/bash-tap/
freebayes-1.3.2/debian/rules:21: for bt in $(CURDIR)/debian/bash-tap/* ; do ln -s $${bt} $(CURDIR)/test/bash-tap/`basename $${bt}` ; done
freebayes-1.3.2/debian/rules-22- ln -s $(CURDIR)/debian/test-simple-bash/lib test/test-simple-bash