===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
jellyfish-2.3.0/README.md-74-
jellyfish-2.3.0/README.md:75:This will install the python binding in `$HOME/lib/python2.7/site-packages` (adjust based on your Python version).
jellyfish-2.3.0/README.md-76-
##############################################
jellyfish-2.3.0/config.rpath-48-host="$1"
jellyfish-2.3.0/config.rpath:49:host_cpu=`echo "$host" | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
jellyfish-2.3.0/config.rpath:50:host_vendor=`echo "$host" | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
jellyfish-2.3.0/config.rpath:51:host_os=`echo "$host" | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
jellyfish-2.3.0/config.rpath-52-
##############################################
jellyfish-2.3.0/config.rpath-225- case $host_os in aix4.[012]|aix4.[012].*)
jellyfish-2.3.0/config.rpath:226: collect2name=`${CC} -print-prog-name=collect2`
jellyfish-2.3.0/config.rpath-227- if test -f "$collect2name" && \
##############################################
jellyfish-2.3.0/config.rpath-349- hardcode_direct=yes
jellyfish-2.3.0/config.rpath:350: if test -z "`echo __ELF__ | $CC -E - | grep __ELF__`" || test "$host_os-$host_cpu" = "openbsd2.8-powerpc"; then
jellyfish-2.3.0/config.rpath-351- hardcode_libdir_flag_spec='${wl}-rpath,$libdir'
##############################################
jellyfish-2.3.0/config.rpath-514-sed_quote_subst='s/\(["`$\\]\)/\\\1/g'
jellyfish-2.3.0/config.rpath:515:escaped_wl=`echo "X$wl" | sed -e 's/^X//' -e "$sed_quote_subst"`
jellyfish-2.3.0/config.rpath:516:shlibext=`echo "$shrext" | sed -e 's,^\.,,'`
jellyfish-2.3.0/config.rpath:517:escaped_hardcode_libdir_flag_spec=`echo "X$hardcode_libdir_flag_spec" | sed -e 's/^X//' -e "$sed_quote_subst"`
jellyfish-2.3.0/config.rpath-518-
##############################################
jellyfish-2.3.0/m4/m4-ax_ext.m4-107- then
jellyfish-2.3.0/m4/m4-ax_ext.m4:108: eax_cpuid0=`echo $ax_cv_gcc_x86_cpuid_0x00000000 | cut -d ":" -f 1`
jellyfish-2.3.0/m4/m4-ax_ext.m4-109- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_ext.m4-114- then
jellyfish-2.3.0/m4/m4-ax_ext.m4:115: eax_cpuid80000000=`echo $ax_cv_gcc_x86_cpuid_0x80000000 | cut -d ":" -f 1`
jellyfish-2.3.0/m4/m4-ax_ext.m4-116- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_ext.m4-123- then
jellyfish-2.3.0/m4/m4-ax_ext.m4:124: ecx_cpuid1=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 3`
jellyfish-2.3.0/m4/m4-ax_ext.m4:125: edx_cpuid1=`echo $ax_cv_gcc_x86_cpuid_0x00000001 | cut -d ":" -f 4`
jellyfish-2.3.0/m4/m4-ax_ext.m4-126- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_ext.m4-134- then
jellyfish-2.3.0/m4/m4-ax_ext.m4:135: ebx_cpuid7=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 2`
jellyfish-2.3.0/m4/m4-ax_ext.m4:136: ecx_cpuid7=`echo $ax_cv_gcc_x86_cpuid_0x00000007 | cut -d ":" -f 3`
jellyfish-2.3.0/m4/m4-ax_ext.m4-137- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_ext.m4-145- then
jellyfish-2.3.0/m4/m4-ax_ext.m4:146: ecx_cpuid80000001=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 3`
jellyfish-2.3.0/m4/m4-ax_ext.m4:147: edx_cpuid80000001=`echo $ax_cv_gcc_x86_cpuid_0x80000001 | cut -d ":" -f 4`
jellyfish-2.3.0/m4/m4-ax_ext.m4-148- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_ext.m4-187- if test x"$ax_cv_gcc_x86_avx_xgetbv_0x00000000" != x"unknown"; then
jellyfish-2.3.0/m4/m4-ax_ext.m4:188: xgetbv_eax=`echo $ax_cv_gcc_x86_avx_xgetbv_0x00000000 | cut -d ":" -f 1`
jellyfish-2.3.0/m4/m4-ax_ext.m4-189- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-76- if test -z "$PERL_EXT_PREFIX" ; then
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4:77: [PERL_EXT_PREFIX=`$PERL -MConfig -e 'print $Config{prefix};'`];
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-78- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-87- if test -z "$PERL_EXT_INC" ; then
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4:88: [PERL_EXT_INC=`$PERL -MConfig -e 'print $Config{archlibexp}, "/CORE";'`];
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-89- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-99- if test -z "$1" -o "x$1" = xNONE ; then
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4:100: [PERL_EXT_LIB=`$PERL -MConfig -e 'print $Config{sitearch};'`];
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-101- else
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4:102: [PERL_EXT_LIB=`$PERL -MConfig -e 'print $ARGV.shift, "/lib/perl/", $Config{api_versionstring};' $1`]
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-103- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-113- if test -z "$PERL_EXT_CPPFLAGS" ; then
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4:114: [PERL_EXT_CPPFLAGS=`$PERL -MConfig -e 'print $Config{cppflags};'`];
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-115- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-124- if test -z "$PERL_EXT_LDFLAGS" ; then
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4:125: [PERL_EXT_LDFLAGS=`$PERL -MConfig -e 'print $Config{lddlflags};'`];
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-126- fi
##############################################
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-131- *darwin*)
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4:132: PERL_EXT_LDFLAGS=`echo ${PERL_EXT_LDFLAGS} | sed -e "s,-arch [[^ ]]*,,g"`
jellyfish-2.3.0/m4/m4-ax_perl_ext.m4-133- ;;
##############################################
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-74- AC_MSG_CHECKING([SWIG version])
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:75: [swig_version=`$SWIG -version 2>&1 | grep 'SWIG Version' | sed 's/.*\([0-9][0-9]*\.[0-9][0-9]*\.[0-9][0-9]*\).*/\1/g'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-76- AC_MSG_RESULT([$swig_version])
##############################################
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-79- [required=$1]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:80: [required_major=`echo $required | sed 's/[^0-9].*//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-81- if test -z "$required_major" ; then
##############################################
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-83- fi
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:84: [required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:85: [required_minor=`echo $required | sed 's/[^0-9].*//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-86- if test -z "$required_minor" ; then
##############################################
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-88- fi
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:89: [required=`echo $required | sed 's/[0-9]*[^0-9]//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:90: [required_patch=`echo $required | sed 's/[^0-9].*//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-91- if test -z "$required_patch" ; then
##############################################
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-95- [available=$swig_version]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:96: [available_major=`echo $available | sed 's/[^0-9].*//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-97- if test -z "$available_major" ; then
##############################################
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-99- fi
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:100: [available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:101: [available_minor=`echo $available | sed 's/[^0-9].*//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-102- if test -z "$available_minor" ; then
##############################################
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-104- fi
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:105: [available=`echo $available | sed 's/[0-9]*[^0-9]//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:106: [available_patch=`echo $available | sed 's/[^0-9].*//'`]
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-107- if test -z "$available_patch" ; then
##############################################
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-123- AC_MSG_CHECKING([for SWIG library])
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4:124: SWIG_LIB=`$SWIG -swiglib`
jellyfish-2.3.0/m4/m4-ax_pkg_swig.m4-125- AC_MSG_RESULT([$SWIG_LIB])
##############################################
jellyfish-2.3.0/m4/m4-ax_python_devel.m4-144- AC_MSG_CHECKING([for the distutils Python package])
jellyfish-2.3.0/m4/m4-ax_python_devel.m4:145: ac_distutils_result=`$PYTHON -c "import distutils" 2>&1`
jellyfish-2.3.0/m4/m4-ax_python_devel.m4-146- if test -z "$ac_distutils_result"; then
##############################################
jellyfish-2.3.0/m4/m4-ax_python_devel.m4-234- # use the official shared library
jellyfish-2.3.0/m4/m4-ax_python_devel.m4:235: ac_python_library=`echo "$ac_python_library" | sed "s/^lib//"`
jellyfish-2.3.0/m4/m4-ax_python_devel.m4-236- PYTHON_LDFLAGS="-L$ac_python_libdir -l$ac_python_library"
##############################################
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-72- AC_MSG_CHECKING([for Ruby version])
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4:73: [RUBY_VERSION=`$RUBY -e 'print RUBY_VERSION'`];
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-74- AC_MSG_RESULT([$RUBY_VERSION])
##############################################
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-81- AS_IF([test -z "$RUBY_EXT_LIB"],
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4:82: AS_IF([test -z "$1" -o "x$1" = xNONE], [RUBY_EXT_LIB=`$RUBY -rrbconfig -e 'print RbConfig::expand(RbConfig::CONFIG.fetch("sitearchdir"))'`],
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4:83: [RUBY_EXT_LIB=`$RUBY -rrbconfig -e 'print(ARGV.fetch(0), "/lib/ruby/", RbConfig::CONFIG.fetch("ruby_version"))' $1`]))
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-84- AC_MSG_RESULT([$RUBY_EXT_LIB])
##############################################
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-91- AS_IF([test -z "$RUBY_EXT_CFLAGS"],
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4:92: [RUBY_EXT_CFLAGS="-I`$RUBY -rrbconfig -e 'print RbConfig::expand(RbConfig::CONFIG.fetch("rubyhdrdir"))'`"]
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4:93: [RUBY_EXT_CFLAGS="$RUBY_EXT_CFLAGS -I`$RUBY -rrbconfig -e 'print RbConfig::CONFIG.has_key?("rubyarchhdrdir") ? RbConfig::expand(RbConfig::CONFIG.fetch("rubyarchhdrdir")) : File.join(RbConfig::expand(RbConfig::CONFIG.fetch("rubyhdrdir")), RbConfig::CONFIG.fetch("arch"))'`"])
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-94- AC_MSG_RESULT([$RUBY_EXT_CFLAGS])
##############################################
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-101- AS_IF([test -z "$RUBY_EXT_LIBS"],
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4:102: [RUBY_EXT_LIBS="`$RUBY -rrbconfig -e 'print RbConfig::expand(RbConfig::CONFIG.fetch("LIBRUBYARG_SHARED"))'` `$RUBY -rrbconfig -e 'print RbConfig::expand(RbConfig::CONFIG.fetch("LIBS"))'`"])
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-103- AC_MSG_RESULT([$RUBY_EXT_LIBS])
##############################################
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-111- *darwin*)
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4:112: RUBY_EXT_LDFLAGS=`echo ${RUBY_EXT_LDFLAGS} | sed -e "s,-arch [[^ ]]*,,g"`
jellyfish-2.3.0/m4/m4-ax_ruby_ext.m4-113- RUBY_EXT_LDFLAGS="${RUBY_EXT_LDFLAGS} -bundle -undefined dynamic_lookup"
##############################################
jellyfish-2.3.0/swig/Readme.md-19-`pkg-config --exists jellyfish-2.0 && echo OK` prints `OK`), then the
jellyfish-2.3.0/swig/Readme.md:20:bindings can be installed as follows. (`$PREFIX` should be set to the
jellyfish-2.3.0/swig/Readme.md-21-desired installation location)
##############################################
jellyfish-2.3.0/swig/perl5/Makefile.PL-8- my ($cmd) = @_;
jellyfish-2.3.0/swig/perl5/Makefile.PL:9: my $res = `pkg-config $cmd`;
jellyfish-2.3.0/swig/perl5/Makefile.PL-10- if($?) {
##############################################
jellyfish-2.3.0/swig/Tuprules.tup-118-else
jellyfish-2.3.0/swig/Tuprules.tup:119: PERL_CFLAGS = `perl -MConfig -e 'print("-I$Config{archlibexp}/CORE")'`
jellyfish-2.3.0/swig/Tuprules.tup-120-endif
##############################################
jellyfish-2.3.0/swig/Tuprules.tup-124-else
jellyfish-2.3.0/swig/Tuprules.tup:125: PERL_LIBS = `perl -MConfig -e 'print($Config{ccdlflags})'`
jellyfish-2.3.0/swig/Tuprules.tup-126-endif
##############################################
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc-4252- } else {
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc:4253: printf(", where %s = %s\n", kTypeParamLabel, test_case.type_param());
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc-4254- }
##############################################
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc-6033- // the output easy to parse by a program.
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc:6034: PrintOnOneLine(test_case->type_param(), kMaxParamLength);
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc-6035- }
##############################################
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc-6042- // output easy to parse by a program.
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc:6043: PrintOnOneLine(test_info->value_param(), kMaxParamLength);
jellyfish-2.3.0/unit_tests/gtest/src/gtest-all.cc-6044- }
##############################################
jellyfish-2.3.0/unit_tests/test_mer_dna.cc-415- for(std::string::const_iterator it = this->GetParam().begin(); it < this->GetParam().end(); ++it, ++i) {
jellyfish-2.3.0/unit_tests/test_mer_dna.cc:416: sprintf(str + this->GetParam().size() - i, "%.*s", i, this->GetParam().c_str());
jellyfish-2.3.0/unit_tests/test_mer_dna.cc-417- typename TypeParam::Type m(str);
##############################################
jellyfish-2.3.0/debian/patches/portability.patch-3-Bug-Debian: https://bugs.debian.org/871697
jellyfish-2.3.0/debian/patches/portability.patch:4:Description: Replace asm statements by C code to increase portability
jellyfish-2.3.0/debian/patches/portability.patch-5-Note: Does not work as described - needs verification
##############################################
jellyfish-2.3.0/debian/tests/run-unit-test-4-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
jellyfish-2.3.0/debian/tests/run-unit-test:5: AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
jellyfish-2.3.0/debian/tests/run-unit-test-6- trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
##############################################
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/Tuprules.tup-118-else
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/Tuprules.tup:119: PERL_CFLAGS = `perl -MConfig -e 'print("-I$Config{archlibexp}/CORE")'`
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/Tuprules.tup-120-endif
##############################################
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/Tuprules.tup-124-else
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/Tuprules.tup:125: PERL_LIBS = `perl -MConfig -e 'print($Config{ccdlflags})'`
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/Tuprules.tup-126-endif
##############################################
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/perl5/Makefile.PL-8- my ($cmd) = @_;
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/perl5/Makefile.PL:9: my $res = `pkg-config $cmd`;
jellyfish-2.3.0/.pc/fix_replacement_of_-L_option.patch/swig/perl5/Makefile.PL-10- if($?) {