=========================================================== .___ __ __ _________________ __ __ __| _/|__|/ |_ / ___\_` __ \__ \ | | \/ __ | | \\_ __\ / /_/ > | \// __ \| | / /_/ | | || | \___ /|__| (____ /____/\____ | |__||__| /_____/ \/ \/ grep rough audit - static analysis tool v2.8 written by @Wireghoul =================================[justanotherhacker.com]=== biobambam2-2.0.177+ds/bumpversion.sh-1-#! /bin/bash biobambam2-2.0.177+ds/bumpversion.sh:2:VERSION=`grep AC_INIT < configure.ac | awk -F',' '{print $2}'` biobambam2-2.0.177+ds/bumpversion.sh:3:FIRST=`echo $VERSION | awk -F'.' '{print $1}'` biobambam2-2.0.177+ds/bumpversion.sh:4:SECOND=`echo $VERSION | awk -F'.' '{print $2}'` biobambam2-2.0.177+ds/bumpversion.sh:5:THIRD=`echo $VERSION | awk -F'.' '{print $3}'` biobambam2-2.0.177+ds/bumpversion.sh:6:NEXTTHIRD=`expr ${THIRD} + 1` biobambam2-2.0.177+ds/bumpversion.sh-7-export DEBEMAIL=germant@miltenyibiotec.de ############################################## biobambam2-2.0.177+ds/m4/ltsugar.m4-68-m4_define([lt_combine], biobambam2-2.0.177+ds/m4/ltsugar.m4:69:[m4_if(m4_eval([$# > 3]), [1], biobambam2-2.0.177+ds/m4/ltsugar.m4-70- [m4_pushdef([_Lt_sep], [m4_define([_Lt_sep], m4_defn([lt_car]))])]]dnl ############################################## biobambam2-2.0.177+ds/release.sh-16-git checkout master biobambam2-2.0.177+ds/release.sh:17:VERSION=`grep <configure.ac "AC_INIT" | perl -p -e "s/.*AC_INIT\(//" | awk -F ',' '{print $2}'` biobambam2-2.0.177+ds/release.sh-18-DATE=`date +"%Y%m%d%H%M%S"` ############################################## biobambam2-2.0.177+ds/removespace.sh-2-for i in `find src -regex .*\\\.[ch]pp` `find src -regex .*\\\.[ch]` ; do biobambam2-2.0.177+ds/removespace.sh:3: ORIG=`cat $i` biobambam2-2.0.177+ds/removespace.sh:4: PATCHED=`perl -p -e "s/(\s*)($)/\n/" < ${i}` biobambam2-2.0.177+ds/removespace.sh-5- ############################################## biobambam2-2.0.177+ds/test/dupsingle.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/dupsingle.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/dupsingle.sh-3-pushd ${SCRIPTDIR} ############################################## biobambam2-2.0.177+ds/test/dupsinglemarked.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/dupsinglemarked.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/dupsinglemarked.sh-3-pushd ${SCRIPTDIR} ############################################## biobambam2-2.0.177+ds/test/dupsinglemarkedsortedqreset.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/dupsinglemarkedsortedqreset.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/dupsinglemarkedsortedqreset.sh-3-pushd ${SCRIPTDIR} ############################################## biobambam2-2.0.177+ds/test/sorttestshort.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/sorttestshort.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/sorttestshort.sh-3-pushd ${SCRIPTDIR} ############################################## biobambam2-2.0.177+ds/test/testdupsingle.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/testdupsingle.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/testdupsingle.sh-3-pushd ${SCRIPTDIR} ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-3-pushd ${SCRIPTDIR} ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-22-for i in `reset | ./bamtosam | head -n 1 | egrep "^@HD"` ; do biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:23: if [ ! -z "`echo $i | egrep \"^SO:\"`" ] ; then biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:24: SORTORDER=`echo $i | perl -p -e "s/^SO://"` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-25- fi ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-32-# check reset by column biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:33:COL2=`reset | ./bamtosam | egrep -v "^@" | awk -F '\t' '{print $2}' | sort -u` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:34:COL2CNT=`echo $COL2 | wc -l` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-35- ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-43- biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:44:COL3=`reset | ./bamtosam | egrep -v "^@" | awk -F '\t' '{print $3}' | sort -u` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:45:COL3CNT=`echo "${COL3}" | wc -l` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-46- ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-54- biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:55:COL4=`reset | ./bamtosam | egrep -v "^@" | awk -F '\t' '{print $4}' | sort -u` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:56:COL4CNT=`echo "${COL4}" | wc -l` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-57- ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-65- biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:66:COL5=`reset | ./bamtosam | egrep -v "^@" | awk -F '\t' '{print $5}' | sort -u` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:67:COL5CNT=`echo "${COL5}" | wc -l` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-68- ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-76- biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:77:COL6=`reset | ./bamtosam | egrep -v "^@" | awk -F '\t' '{print $6}' | sort -u` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:78:COL6CNT=`echo "${COL6}" | wc -l` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-79- ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-87- biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:88:COL7=`reset | ./bamtosam | egrep -v "^@" | awk -F '\t' '{print $7}' | sort -u` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:89:COL7CNT=`echo "${COL7}" | wc -l` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-90- ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-98- biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:99:COL8=`reset | ./bamtosam | egrep -v "^@" | awk -F '\t' '{print $8}' | sort -u` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:100:COL8CNT=`echo "${COL8}" | wc -l` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-101- ############################################## biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-109- biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:110:COL9=`reset | ./bamtosam | egrep -v "^@" | awk -F '\t' '{print $9}' | sort -u` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh:111:COL9CNT=`echo "${COL9}" | wc -l` biobambam2-2.0.177+ds/test/testdupsinglemarkedsortedqreset.sh-112- ############################################## biobambam2-2.0.177+ds/test/testshortsort.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/testshortsort.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/testshortsort.sh-3-pushd ${SCRIPTDIR} ############################################## biobambam2-2.0.177+ds/test/testshortsortcoordinate.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/testshortsortcoordinate.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/testshortsortcoordinate.sh-3-pushd ${SCRIPTDIR} ############################################## biobambam2-2.0.177+ds/test/testshortsortqueryname.sh-1-#! /bin/bash biobambam2-2.0.177+ds/test/testshortsortqueryname.sh:2:SCRIPTDIR=`dirname "${BASH_SOURCE[0]}"` biobambam2-2.0.177+ds/test/testshortsortqueryname.sh-3-pushd ${SCRIPTDIR}