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/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
fastdnaml-1.2.2/scripts/ae2dnaml-14-else
fastdnaml-1.2.2/scripts/ae2dnaml:15: comm=`echo $0 | sed -e 's&^.*/&&g'`
fastdnaml-1.2.2/scripts/ae2dnaml-16- optprm="[ "'"'"dnaml_opt1 [ | dnaml_opt2 [...]]"'"'" ]"
##############################################
fastdnaml-1.2.2/scripts/ae2dnaml-30-
fastdnaml-1.2.2/scripts/ae2dnaml:31:id=`eval "cat < $temp_file | $opts | out.PID -o $1 fastDNAml"`
fastdnaml-1.2.2/scripts/ae2dnaml-32-
##############################################
fastdnaml-1.2.2/scripts/clean_jumbles-4-#
fastdnaml-1.2.2/scripts/clean_jumbles:5:comm=`echo $0 | sed 's&^.*/&&g'`
fastdnaml-1.2.2/scripts/clean_jumbles-6-nosummaryflag="-nosummary"
##############################################
fastdnaml-1.2.2/scripts/clean_jumbles-29-
fastdnaml-1.2.2/scripts/clean_jumbles:30:if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -eq 0; then
fastdnaml-1.2.2/scripts/clean_jumbles-31- echo "$comm: No files found of form $out.(jumble_seed)"
##############################################
fastdnaml-1.2.2/scripts/clean_jumbles-117-
fastdnaml-1.2.2/scripts/clean_jumbles:118:if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
fastdnaml-1.2.2/scripts/clean_jumbles-119- pids=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
##############################################
fastdnaml-1.2.2/scripts/n_files-4-for fileName in "$@"; do
fastdnaml-1.2.2/scripts/n_files:5: if test -f "$fileName"; then nFile=`expr $nFile + 1`; fi
fastdnaml-1.2.2/scripts/n_files-6-done
##############################################
fastdnaml-1.2.2/scripts/out.PID-20- if test $# -lt 1; then
fastdnaml-1.2.2/scripts/out.PID:21: comm=`echo $0 | sed -e 's&^.*/&&g'`
fastdnaml-1.2.2/scripts/out.PID-22- echo "
##############################################
fastdnaml-1.2.2/scripts/restart-11- tail -2`
fastdnaml-1.2.2/scripts/restart:12:nFound=`echo $lastTwoEnds | wc -w`
fastdnaml-1.2.2/scripts/restart-13-if test $nFound -eq 0; then
##############################################
fastdnaml-1.2.2/scripts/restart-25-else
fastdnaml-1.2.2/scripts/restart:26: penultimateEnd=`echo $lastTwoEnds | sed 's/^\([0-9]*\).*$/\1/'`
fastdnaml-1.2.2/scripts/restart:27: lastStart=`expr $penultimateEnd + 1`
fastdnaml-1.2.2/scripts/restart-28- tail +$lastStart "$file"
##############################################
fastdnaml-1.2.2/scripts/trees2NEXUS-13- for file in $*; do
fastdnaml-1.2.2/scripts/trees2NEXUS:14: i=`expr $i + 1`
fastdnaml-1.2.2/scripts/trees2NEXUS-15- sed -e 's/^/ utree '"$i"' = /' $file
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_boot-5-
fastdnaml-1.2.2/scripts/fastDNAml_boot:6:comm=`echo "$0" | sed -e 's&^.*/&&g'`
fastdnaml-1.2.2/scripts/fastDNAml_boot-7-bootflag="-boots"
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_boot-93-if test -f "$1"; then
fastdnaml-1.2.2/scripts/fastDNAml_boot:94: root=`echo "$1" | sed -e 's/\.phylip$//' -e 's/\.phy$//'`; in="$1"
fastdnaml-1.2.2/scripts/fastDNAml_boot-95-elif test -f "$1.phy"; then
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_boot-102-
fastdnaml-1.2.2/scripts/fastDNAml_boot:103:seed=`echo $seed | awk '{printf("%09d",$1)}'`
fastdnaml-1.2.2/scripts/fastDNAml_boot:104:out=`echo "${root}_$seed" | sed -e 's&^.*/&&'`
fastdnaml-1.2.2/scripts/fastDNAml_boot-105-
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_boot-112- while
fastdnaml-1.2.2/scripts/fastDNAml_boot:113: if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
fastdnaml-1.2.2/scripts/fastDNAml_boot:114: nJumble=`grep '^Ln Likelihood' $out.[0-9]* /dev/null | wc -l`
fastdnaml-1.2.2/scripts/fastDNAml_boot-115- nBest=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_boot-134-
fastdnaml-1.2.2/scripts/fastDNAml_boot:135: if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -eq 0; then
fastdnaml-1.2.2/scripts/fastDNAml_boot-136- echo "$comm: No files found for $out"
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_boot-169-
fastdnaml-1.2.2/scripts/fastDNAml_boot:170: if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
fastdnaml-1.2.2/scripts/fastDNAml_boot-171- pids=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_boot-181- fi
fastdnaml-1.2.2/scripts/fastDNAml_boot:182: remaining=`expr $remaining - 1`
fastdnaml-1.2.2/scripts/fastDNAml_boot-183-fi
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_loop-5-
fastdnaml-1.2.2/scripts/fastDNAml_loop:6:comm=`echo "$0" | sed -e 's&^.*/&&'`
fastdnaml-1.2.2/scripts/fastDNAml_loop-7-cleanflag="-noclean"
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_loop-71-if test -f "$1"; then
fastdnaml-1.2.2/scripts/fastDNAml_loop:72: root=`echo "$1" | sed -e 's/\.phylip$//' -e 's/\.phy$//'`; in="$1"
fastdnaml-1.2.2/scripts/fastDNAml_loop-73-elif test -f "$1.phy"; then
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_loop-80-
fastdnaml-1.2.2/scripts/fastDNAml_loop:81:out=`echo "$root" | sed -e 's&^.*/&&'`
fastdnaml-1.2.2/scripts/fastDNAml_loop-82-
##############################################
fastdnaml-1.2.2/scripts/fastDNAml_loop-104- nJumble=0
fastdnaml-1.2.2/scripts/fastDNAml_loop:105: elif test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
fastdnaml-1.2.2/scripts/fastDNAml_loop:106: nJumble=`grep '^Ln Likelihood' $out.[0-9]* /dev/null | wc -l`
fastdnaml-1.2.2/scripts/fastDNAml_loop-107- nBest=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
##############################################
fastdnaml-1.2.2/scripts/iterate_rates-19-
fastdnaml-1.2.2/scripts/iterate_rates:20:root=`echo "$root0" | sed 's&^.*/\([^/][^/]*\)$&\1&'`
fastdnaml-1.2.2/scripts/iterate_rates-21-
##############################################
fastdnaml-1.2.2/scripts/iterate_rates-23-
fastdnaml-1.2.2/scripts/iterate_rates:24:tree1=`ls -1 ${root}_*.tree | tail -1`
fastdnaml-1.2.2/scripts/iterate_rates-25-if test -z "$tree1"; then
##############################################
fastdnaml-1.2.2/scripts/iterate_rates-32-else
fastdnaml-1.2.2/scripts/iterate_rates:33: v0=`echo "$tree1" | sed 's/^.*_\([0-9][0-9]*)\.tree$/\1/'`
fastdnaml-1.2.2/scripts/iterate_rates:34: v1=`expr $v0 + 1`
fastdnaml-1.2.2/scripts/iterate_rates-35-fi
##############################################
fastdnaml-1.2.2/debian/patches/scripts.patch-15-+
fastdnaml-1.2.2/debian/patches/scripts.patch:16: comm=`echo "$0" | sed -e 's&^.*/&&g'`
fastdnaml-1.2.2/debian/patches/scripts.patch-17- bootflag="-boots"
##############################################
fastdnaml-1.2.2/debian/patches/scripts.patch-27-+
fastdnaml-1.2.2/debian/patches/scripts.patch:28: comm=`echo "$0" | sed -e 's&^.*/&&'`
fastdnaml-1.2.2/debian/patches/scripts.patch-29- cleanflag="-noclean"
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-2-#
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:3:comm=`echo "$0" | sed -e 's&^.*/&&g'`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-4-bootflag="-boots"
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-90-if test -f "$1"; then
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:91: root=`echo "$1" | sed -e 's/\.phylip$//' -e 's/\.phy$//'`; in="$1"
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-92-elif test -f "$1.phy"; then
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-99-
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:100:seed=`echo $seed | awk '{printf("%09d",$1)}'`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:101:out=`echo "${root}_$seed" | sed -e 's&^.*/&&'`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-102-
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-109- while
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:110: if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:111: nJumble=`grep '^Ln Likelihood' $out.[0-9]* /dev/null | wc -l`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-112- nBest=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-131-
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:132: if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -eq 0; then
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-133- echo "$comm: No files found for $out"
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-166-
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:167: if test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-168- pids=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-178- fi
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot:179: remaining=`expr $remaining - 1`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_boot-180-fi
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop-2-#
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop:3:comm=`echo "$0" | sed -e 's&^.*/&&'`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop-4-cleanflag="-noclean"
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop-68-if test -f "$1"; then
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop:69: root=`echo "$1" | sed -e 's/\.phylip$//' -e 's/\.phy$//'`; in="$1"
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop-70-elif test -f "$1.phy"; then
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop-77-
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop:78:out=`echo "$root" | sed -e 's&^.*/&&'`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop-79-
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop-101- nJumble=0
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop:102: elif test `ls -d $out.[0-9]* 2>/dev/null | wc -l` -gt 0; then
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop:103: nJumble=`grep '^Ln Likelihood' $out.[0-9]* /dev/null | wc -l`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/fastDNAml_loop-104- nBest=`grep '^Ln Likelihood' $out.[0-9]* /dev/null |
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates-17-
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates:18:root=`echo "$root0" | sed 's&^.*/\([^/][^/]*\)$&\1&'`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates-19-
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates-21-
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates:22:tree1=`ls -1 ${root}_*.tree | tail -1`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates-23-if test -z "$tree1"; then
##############################################
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates-30-else
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates:31: v0=`echo "$tree1" | sed 's/^.*_\([0-9][0-9]*)\.tree$/\1/'`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates:32: v1=`expr $v0 + 1`
fastdnaml-1.2.2/.pc/scripts.patch/scripts/iterate_rates-33-fi