===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
genometools-1.6.1+ds/doc/manuals/execcommand.pl-96- print STDERR "run $argstring\n";
genometools-1.6.1+ds/doc/manuals/execcommand.pl:97: my($retcode) = system($argstring);
genometools-1.6.1+ds/doc/manuals/execcommand.pl-98- $retcode = $? >> 8;
##############################################
genometools-1.6.1+ds/doc/manuals/findemptyoutfiles.sh-4-do
genometools-1.6.1+ds/doc/manuals/findemptyoutfiles.sh:5: filesize=`cat ${filename} | wc -l`
genometools-1.6.1+ds/doc/manuals/findemptyoutfiles.sh-6- if test $filesize -eq 1
##############################################
genometools-1.6.1+ds/scripts/sed_all-20-then
genometools-1.6.1+ds/scripts/sed_all:21: echo "Usage: `basename $0` sed_command file [...]" >&2
genometools-1.6.1+ds/scripts/sed_all-22- echo "Apply \"sed_command\" to each \"file\" and replace it afterwards." >&2
##############################################
genometools-1.6.1+ds/scripts/sed_all-39- else
genometools-1.6.1+ds/scripts/sed_all:40: echo "`basename $0`: sed command failed, removing tmpfile"
genometools-1.6.1+ds/scripts/sed_all-41- rm -f $TMPFILE
##############################################
genometools-1.6.1+ds/scripts/hop.sh-330-function f_pos_stats {
genometools-1.6.1+ds/scripts/hop.sh:331: count_all () { RETVAL=`grep '^'$2 $1 | wc -l`; }
genometools-1.6.1+ds/scripts/hop.sh-332- count_all_pos () { RETVAL=`awk '/^'$2'/ && ('${FIELD[S_HEND]}' == "'$3'")' $1 \
genometools-1.6.1+ds/scripts/hop.sh-333- | wc -l`; }
genometools-1.6.1+ds/scripts/hop.sh:334: count () { RETVAL=`awk '/^'$2'/ && ('${FIELD[S_CHAR]}' == "'$3'")' $1 | wc -l`; }
genometools-1.6.1+ds/scripts/hop.sh-335- count_pos () { RETVAL=`awk '/^'$2'/ && ('${FIELD[S_HEND]}' == "'$3'") \
genometools-1.6.1+ds/scripts/hop.sh-336- && ('${FIELD[S_CHAR]}' == "'$4'")' $1 | wc -l`; }
genometools-1.6.1+ds/scripts/hop.sh:337: nof_seq_long () { RETVAL=`grep "^$2--$2" $1 | awk '{ print $2 }'`
genometools-1.6.1+ds/scripts/hop.sh-338- if [ "$RETVAL" == "" ]; then RETVAL=0; fi; }
genometools-1.6.1+ds/scripts/hop.sh-339- OUTFILE=$2
genometools-1.6.1+ds/scripts/hop.sh:340: MAX_READ_LEN=`grep 'maximum length' $3 | awk '{ print $4 }'`
genometools-1.6.1+ds/scripts/hop.sh:341: NOFSEQ=`grep 'sequences' $3 | awk '{ print $2 }'`
genometools-1.6.1+ds/scripts/hop.sh-342- nof_seq_long $3 1; S=$RETVAL
genometools-1.6.1+ds/scripts/hop.sh:343: P=`echo "$S / $NOFSEQ" | bc -l`
genometools-1.6.1+ds/scripts/hop.sh-344- rm -f $OUTFILE
##############################################
genometools-1.6.1+ds/scripts/hop.sh-371- S=$[$RETVAL+$S]
genometools-1.6.1+ds/scripts/hop.sh:372: P=`echo "(1.0 - ($S / $NOFSEQ)) * 100" | bc -l`
genometools-1.6.1+ds/scripts/hop.sh-373- count_all_pos $1 I $i; I=$RETVAL
##############################################
genometools-1.6.1+ds/scripts/hop.sh-390- grep -v '^#' $1 | awk '{ print '${FIELD[S_ID]}' }' | sort | uniq -c > $MAP~tmpfile
genometools-1.6.1+ds/scripts/hop.sh:391: echo "# edited reads: `cat $MAP~tmpfile | wc -l`" >> $1
genometools-1.6.1+ds/scripts/hop.sh-392- t=0
genometools-1.6.1+ds/scripts/hop.sh-393- for ((i=1;i<10;i++)); do
genometools-1.6.1+ds/scripts/hop.sh:394: c=`awk ' $1 == '$i $MAP~tmpfile | wc -l`
genometools-1.6.1+ds/scripts/hop.sh-395- if [ $c == 0 ]; then
##############################################
genometools-1.6.1+ds/scripts/hop.sh-545- diff $SMAP.eds $MAP.eds > $EDSDIFF
genometools-1.6.1+ds/scripts/hop.sh:546: CORR=`cat $MAP.eds | wc -l`
genometools-1.6.1+ds/scripts/hop.sh:547: ERR=`cat $SMAP.eds | wc -l`
genometools-1.6.1+ds/scripts/hop.sh:548: FN=`grep '^<' $EDSDIFF | wc -l`
genometools-1.6.1+ds/scripts/hop.sh:549: FP=`grep '^>' $EDSDIFF | wc -l`
genometools-1.6.1+ds/scripts/hop.sh-550- TP=$[$CORR-$FP]
genometools-1.6.1+ds/scripts/hop.sh:551: GENOMEDESC=`head -n 1 $GENOME`
genometools-1.6.1+ds/scripts/hop.sh:552: SGENOMEDESC=`head -n 1 $SGENOME`
genometools-1.6.1+ds/scripts/hop.sh-553- echo "==== Computing evaluation statistics..."
##############################################
genometools-1.6.1+ds/scripts/hop.sh-596- echo "- false negatives: $FN" | tee -a $INFO
genometools-1.6.1+ds/scripts/hop.sh:597: SN=`echo "$TP * 100 / ($TP + $FN)" | bc -l`
genometools-1.6.1+ds/scripts/hop.sh:598: PR=`echo "$TP * 100 / ($TP + $FP)" | bc -l`
genometools-1.6.1+ds/scripts/hop.sh-599- printf -- "- sensitivity: %.2f %%\n" $SN | tee -a $INFO
##############################################
genometools-1.6.1+ds/scripts/pre-commit-10- then
genometools-1.6.1+ds/scripts/pre-commit:11: APIS=`echo "$1" | grep -F "_api.h"`
genometools-1.6.1+ds/scripts/pre-commit-12- if [ ${#APIS} -ne 0 ]; then
##############################################
genometools-1.6.1+ds/scripts/run-se-da.sh-25-
genometools-1.6.1+ds/scripts/run-se-da.sh:26:reference=`basename $referencefile`
genometools-1.6.1+ds/scripts/run-se-da.sh-27-seedlength=14
##############################################
genometools-1.6.1+ds/scripts/run-se-da.sh-45-then
genometools-1.6.1+ds/scripts/run-se-da.sh:46: query=`basename $queryfile`
genometools-1.6.1+ds/scripts/run-se-da.sh-47- scripts/convert2myersformat.rb ${queryfile} > ${query}.fasta
##############################################
genometools-1.6.1+ds/scripts/rdj-parsetranscript.rb-129- @operation[i+1] ||= ".to_f" unless @noautofloat
genometools-1.6.1+ds/scripts/rdj-parsetranscript.rb:130: value = eval("$#{i+1}#{@operation[i+1]}")
genometools-1.6.1+ds/scripts/rdj-parsetranscript.rb-131- warn_if_not_nil(var, value)
##############################################
genometools-1.6.1+ds/scripts/sktest-match.sh-50-#then
genometools-1.6.1+ds/scripts/sktest-match.sh:51: #for inputfile in `ls testdata/*.fna` ${AT} ${U8} ${ATK} `ls ${GTTESTDATA}/DNA-mix/Grumbach.fna/*.fna`
genometools-1.6.1+ds/scripts/sktest-match.sh-52- #do
##############################################
genometools-1.6.1+ds/scripts/runmkfm_dw.sh-84-do
genometools-1.6.1+ds/scripts/runmkfm_dw.sh:85: indexname=`basename ${rfile}`
genometools-1.6.1+ds/scripts/runmkfm_dw.sh-86- needconstruction1 ${rfile} \
##############################################
genometools-1.6.1+ds/scripts/shulength.sh-23- echo "failure: cmp -s result.pairwise result.multi"
genometools-1.6.1+ds/scripts/shulength.sh:24: # echo "`tail -1 ${file1}`x`tail -1 ${file2}`y" | ${WOTD} | dot -Tpdf > dot.pdf
genometools-1.6.1+ds/scripts/shulength.sh-25- # mkvtree -db ${file1} ${file2} -dna -suf -lcp -tis -indexname mkv-tmp
##############################################
genometools-1.6.1+ds/scripts/itertestcases.sh-19- apply ${filepath}
genometools-1.6.1+ds/scripts/itertestcases.sh:20: testnum=`expr ${testnum} + 1`
genometools-1.6.1+ds/scripts/itertestcases.sh-21-done
##############################################
genometools-1.6.1+ds/scripts/skclean.sh-20-do
genometools-1.6.1+ds/scripts/skclean.sh:21: headfile="obj/src/match/`basename ${filename} .c`"
genometools-1.6.1+ds/scripts/skclean.sh-22- rm -f ${headfile}.o ${headfile}.d ${headfile}.splint
##############################################
genometools-1.6.1+ds/scripts/skclean.sh-24-
genometools-1.6.1+ds/scripts/skclean.sh:25:for filename in `ls ${SKTOOLS} src/ltr/*.c`
genometools-1.6.1+ds/scripts/skclean.sh-26-do
genometools-1.6.1+ds/scripts/skclean.sh:27: headfile="obj/src/ltr/`basename ${filename} .c`"
genometools-1.6.1+ds/scripts/skclean.sh-28- rm -f ${headfile}.o ${headfile}.d ${headfile}.splint
##############################################
genometools-1.6.1+ds/scripts/skclean.sh-32-
genometools-1.6.1+ds/scripts/skclean.sh:33:for filename in `ls ${SKTOOLS}`
genometools-1.6.1+ds/scripts/skclean.sh-34-do
genometools-1.6.1+ds/scripts/skclean.sh:35: headfile="obj/src/tools/`basename ${filename} .c`"
genometools-1.6.1+ds/scripts/skclean.sh-36- rm -f ${headfile}.o ${headfile}.d ${headfile}.splint
##############################################
genometools-1.6.1+ds/scripts/checkmaxpairs.sh-60- fi
genometools-1.6.1+ds/scripts/checkmaxpairs.sh:61: resultfile="${GTTESTDATA}/repfind-result/`basename ${filename}`.result"
genometools-1.6.1+ds/scripts/checkmaxpairs.sh-62- checkerror "cmp -s ${resultfile} result.mp"
##############################################
genometools-1.6.1+ds/scripts/sfx-big.sh-11-
genometools-1.6.1+ds/scripts/sfx-big.sh:12:for filename in `ls ${DATA}/fib*.fas.gz`
genometools-1.6.1+ds/scripts/sfx-big.sh-13-do
##############################################
genometools-1.6.1+ds/scripts/makeprimetable.sh-3-PRIMES=/projects/gi/primegen/primes
genometools-1.6.1+ds/scripts/makeprimetable.sh:4:OUTFILE=`dirname $0`/../src/extended/md5set_primes_table.h
genometools-1.6.1+ds/scripts/makeprimetable.sh-5-
##############################################
genometools-1.6.1+ds/scripts/makeprimetable.sh-35-
genometools-1.6.1+ds/scripts/makeprimetable.sh:36:LARGEST_PRIME=`tail -n 1 $OUTFILE`
genometools-1.6.1+ds/scripts/makeprimetable.sh-37-# remove trailing comma:
##############################################
genometools-1.6.1+ds/scripts/makeprimetable.sh-39-
genometools-1.6.1+ds/scripts/makeprimetable.sh:40:NOFPRIMES=`cat $OUTFILE | wc -l`
genometools-1.6.1+ds/scripts/makeprimetable.sh-41-
##############################################
genometools-1.6.1+ds/scripts/vmnameclash.sh-5- extractsyms.sh lib/libgenometools.a lib/libgtunstable.a | sort -u > GTNAMES
genometools-1.6.1+ds/scripts/vmnameclash.sh:6: common=`comm -1 -2 GTNAMES ${WORKVSTREE}/src/VMNAMES | wc -l`
genometools-1.6.1+ds/scripts/vmnameclash.sh-7- if test $common -gt 0
##############################################
genometools-1.6.1+ds/scripts/esq-in-bytes.sh-11-
genometools-1.6.1+ds/scripts/esq-in-bytes.sh:12:for dbseq in `${GTDIR}/scripts/findfasta.rb`
genometools-1.6.1+ds/scripts/esq-in-bytes.sh-13-do
genometools-1.6.1+ds/scripts/esq-in-bytes.sh-14- ${GTDIR}/bin/gt encseq encode -indexname db $dbseq
genometools-1.6.1+ds/scripts/esq-in-bytes.sh:15: for queryseq in `${GTDIR}/scripts/findfasta.rb`
genometools-1.6.1+ds/scripts/esq-in-bytes.sh-16- do
##############################################
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-23-
genometools-1.6.1+ds/scripts/sim-read-mapping.sh:24:minlength=`expr ${readlength} \* 80`
genometools-1.6.1+ds/scripts/sim-read-mapping.sh:25:minlength=`expr ${minlength} \/ 100`
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-26-$gt_bin/gt encseq encode -indexname reference -sds no -md5 no -des no ${inputfile}
##############################################
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-61- #grep '^#' tmp.matches
genometools-1.6.1+ds/scripts/sim-read-mapping.sh:62: sensitivity=`./collect-mappings.rb ${numreads} tmp.matches | grep -v '^#'`
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-63- printf "\t${sensitivity}" >> $outfile_nw_m
##############################################
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-66- $gt_bin/gt seed_extend ${common} -weakends -bias-parameters > tmp.matches
genometools-1.6.1+ds/scripts/sim-read-mapping.sh:67: sensitivity=`./collect-mappings.rb ${numreads} tmp.matches | grep -v '^#'`
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-68- printf "\t${sensitivity}" >> $outfile_w_m
##############################################
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-71- $gt_bin/gt seed_extend ${common} > tmp.matches
genometools-1.6.1+ds/scripts/sim-read-mapping.sh:72: sensitivity=`./collect-mappings.rb ${numreads} tmp.matches | grep -v '^#'`
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-73- printf "\t${sensitivity}" >> $outfile_nw_nm
##############################################
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-76- $gt_bin/gt seed_extend ${common} -weakends > tmp.matches
genometools-1.6.1+ds/scripts/sim-read-mapping.sh:77: sensitivity=`./collect-mappings.rb ${numreads} tmp.matches | grep -v '^#'`
genometools-1.6.1+ds/scripts/sim-read-mapping.sh-78- printf "\t${sensitivity}" >> $outfile_w_nm
##############################################
genometools-1.6.1+ds/scripts/build_dists.sh-16- CPPFLAGS='-fno-stack-protector -U_FORTIFY_SOURCE -D_GNU_SOURCE' dist > $TMPFILE
genometools-1.6.1+ds/scripts/build_dists.sh:17:DISTRIBUTION=`tail -n 1 $TMPFILE`
genometools-1.6.1+ds/scripts/build_dists.sh-18-cp -f $DISTRIBUTION $DISTDIR
##############################################
genometools-1.6.1+ds/scripts/build_dists.sh-28- amalgamation=yes cairo=no DISTSUFFIX=-barebone dist > $TMPFILE
genometools-1.6.1+ds/scripts/build_dists.sh:29:DISTRIBUTION=`tail -n 1 $TMPFILE`
genometools-1.6.1+ds/scripts/build_dists.sh-30-cp -f $DISTRIBUTION $DISTDIR
##############################################
genometools-1.6.1+ds/scripts/build_dists.sh-40- amalgamation=yes DISTSUFFIX=-complete dist > $TMPFILE
genometools-1.6.1+ds/scripts/build_dists.sh:41:DISTRIBUTION=`tail -n 1 $TMPFILE`
genometools-1.6.1+ds/scripts/build_dists.sh-42-cp -f $DISTRIBUTION $DISTDIR
##############################################
genometools-1.6.1+ds/scripts/build_dists.sh-65- dist > $TMPFILE
genometools-1.6.1+ds/scripts/build_dists.sh:66:DISTRIBUTION=`tail -n 1 $TMPFILE`
genometools-1.6.1+ds/scripts/build_dists.sh-67-cp -f $DISTRIBUTION $DISTDIR
##############################################
genometools-1.6.1+ds/scripts/build_dists.sh-92- dist > $TMPFILE
genometools-1.6.1+ds/scripts/build_dists.sh:93:DISTRIBUTION=`tail -n 1 $TMPFILE`
genometools-1.6.1+ds/scripts/build_dists.sh-94-cp -f $DISTRIBUTION $DISTDIR
##############################################
genometools-1.6.1+ds/scripts/build_dists.sh-121- dist > $TMPFILE
genometools-1.6.1+ds/scripts/build_dists.sh:122:DISTRIBUTION=`tail -n 1 $TMPFILE`
genometools-1.6.1+ds/scripts/build_dists.sh-123-cp -f $DISTRIBUTION $DISTDIR
##############################################
genometools-1.6.1+ds/scripts/build_dists.sh-150- dist > $TMPFILE
genometools-1.6.1+ds/scripts/build_dists.sh:151:DISTRIBUTION=`tail -n 1 $TMPFILE`
genometools-1.6.1+ds/scripts/build_dists.sh-152-cp -f $DISTRIBUTION $DISTDIR
##############################################
genometools-1.6.1+ds/scripts/all-vs-all.sh-6-
genometools-1.6.1+ds/scripts/all-vs-all.sh:7:for reference in `${GTDIR}/scripts/findfasta.rb -n -e ${excludelist}`
genometools-1.6.1+ds/scripts/all-vs-all.sh-8-do
genometools-1.6.1+ds/scripts/all-vs-all.sh-9- bin/gt encseq encode -indexname ref-index ${reference}
genometools-1.6.1+ds/scripts/all-vs-all.sh:10: for query in `${GTDIR}/scripts/findfasta.rb -n -e ${excludelist}`
genometools-1.6.1+ds/scripts/all-vs-all.sh-11- do
##############################################
genometools-1.6.1+ds/scripts/create_html-4-do
genometools-1.6.1+ds/scripts/create_html:5: SHORTNAME=`echo $FILE | cut -f 4 -d '/' | cut -f 1 -d '.'`
genometools-1.6.1+ds/scripts/create_html-6- echo -n '.'
##############################################
genometools-1.6.1+ds/scripts/rununique-test.sh-56- then
genometools-1.6.1+ds/scripts/rununique-test.sh:57: numofrfiles=`expr ${numofrfiles} + 1`
genometools-1.6.1+ds/scripts/rununique-test.sh-58- else
##############################################
genometools-1.6.1+ds/scripts/rununique-test.sh-93- indexlist="${indexlist} ${IDIR}/midx${fn}"
genometools-1.6.1+ds/scripts/rununique-test.sh:94: fn=`expr ${fn} + 1`
genometools-1.6.1+ds/scripts/rununique-test.sh-95- done
##############################################
genometools-1.6.1+ds/scripts/prepend_all-20-then
genometools-1.6.1+ds/scripts/prepend_all:21: echo "Usage: `basename $0` preprend_file file [...]" >&2
genometools-1.6.1+ds/scripts/prepend_all-22- echo "Prepend \"preprend_file\" to each \"file\" and replace it afterwards." >&2
##############################################
genometools-1.6.1+ds/scripts/prepend_all-39- else
genometools-1.6.1+ds/scripts/prepend_all:40: echo "`basename $0`: cat command failed, removing tmpfile"
genometools-1.6.1+ds/scripts/prepend_all-41- rm -f $TMPFILE
##############################################
genometools-1.6.1+ds/scripts/rdj-spacepeak.sh-32- /usr/bin/time $@ &
genometools-1.6.1+ds/scripts/rdj-spacepeak.sh:33: tpid=`pgrep -P ${ppid} -n -f time`
genometools-1.6.1+ds/scripts/rdj-spacepeak.sh-34- if [[ ${tpid} -ne "" ]]; then
genometools-1.6.1+ds/scripts/rdj-spacepeak.sh:35: pid=`pgrep -P ${tpid} -n -f $1` # $! may work here but not later
genometools-1.6.1+ds/scripts/rdj-spacepeak.sh-36- fi
##############################################
genometools-1.6.1+ds/scripts/rdj-spacepeak.sh-49- savedtpid=${tpid}
genometools-1.6.1+ds/scripts/rdj-spacepeak.sh:50: tpid=`pgrep -P ${ppid} -n -f time`
genometools-1.6.1+ds/scripts/rdj-spacepeak.sh-51- done
##############################################
genometools-1.6.1+ds/scripts/extract-seqs.sh-12-do
genometools-1.6.1+ds/scripts/extract-seqs.sh:13: env -i bin/gt seq -width 70 -showseqnum `expr ${seqnum} + 1` ${inputfile}
genometools-1.6.1+ds/scripts/extract-seqs.sh-14-done
##############################################
genometools-1.6.1+ds/scripts/runmkfm.sh-77-do
genometools-1.6.1+ds/scripts/runmkfm.sh:78: indexname=`basename ${rfile}`
genometools-1.6.1+ds/scripts/runmkfm.sh-79- needconstruction1 ${rfile} \
##############################################
genometools-1.6.1+ds/scripts/calltestcase.sh-9-
genometools-1.6.1+ds/scripts/calltestcase.sh:10:TMPFILE=`mktemp ${TMPDIR}/TMP.XXXXXX` || exit 1
genometools-1.6.1+ds/scripts/calltestcase.sh-11-if test $# -eq 0
##############################################
genometools-1.6.1+ds/scripts/calltestcase.sh-21-
genometools-1.6.1+ds/scripts/calltestcase.sh:22:for keyword in `cat ${TMPFILE}`
genometools-1.6.1+ds/scripts/calltestcase.sh-23-do
##############################################
genometools-1.6.1+ds/scripts/calltestcase.sh-31-
genometools-1.6.1+ds/scripts/calltestcase.sh:32:for keyword in `cat ${TMPFILE}`
genometools-1.6.1+ds/scripts/calltestcase.sh-33-do
##############################################
genometools-1.6.1+ds/scripts/runmaxpairs.sh-66- fi
genometools-1.6.1+ds/scripts/runmaxpairs.sh:67: resultfile="`basename ${filename}`.result"
genometools-1.6.1+ds/scripts/runmaxpairs.sh-68- cp result.vm ${resultfile}
##############################################
genometools-1.6.1+ds/scripts/esa-compressed.sh-4-
genometools-1.6.1+ds/scripts/esa-compressed.sh:5:for filename in `${GTDIR}/scripts/findfasta.rb`
genometools-1.6.1+ds/scripts/esa-compressed.sh-6-do
##############################################
genometools-1.6.1+ds/scripts/single-read-mapping.sh-21-env -i bin/gt encseq encode -indexname reference-idx ${inputfile}
genometools-1.6.1+ds/scripts/single-read-mapping.sh:22:minlength=`expr ${readlength} \* ${mincoverage}`
genometools-1.6.1+ds/scripts/single-read-mapping.sh:23:minlength=`expr ${minlength} \/ 100`
genometools-1.6.1+ds/scripts/single-read-mapping.sh-24-common="-v -ii reference-idx -qii query-idx --no-reverse -outfmt fstperquery -l ${minlength} -minidentity ${minidentity} -seedlength ${seedlength}"
##############################################
genometools-1.6.1+ds/scripts/gff3tidy_all-19-then
genometools-1.6.1+ds/scripts/gff3tidy_all:20: echo "Usage: `basename $0` file [...]" >&2
genometools-1.6.1+ds/scripts/gff3tidy_all-21- echo "Apply \"gt gff3 -tidy\" to each \"file\" and replace it afterwards." >&2
##############################################
genometools-1.6.1+ds/scripts/gff3tidy_all-35- else
genometools-1.6.1+ds/scripts/gff3tidy_all:36: echo "`basename $0`: gt gff3 -tidy command failed, removing tmpfile"
genometools-1.6.1+ds/scripts/gff3tidy_all-37- rm -f $TMPFILE
##############################################
genometools-1.6.1+ds/scripts/esa-sfxthreaded.sh-4-
genometools-1.6.1+ds/scripts/esa-sfxthreaded.sh:5:for filename in `${GTDIR}/scripts/findfasta.rb`
genometools-1.6.1+ds/scripts/esa-sfxthreaded.sh-6-do
##############################################
genometools-1.6.1+ds/scripts/runmerge.sh-25- indexlist="${indexlist} ${INDEXDIR}/midx${num}"
genometools-1.6.1+ds/scripts/runmerge.sh:26: num=`expr ${num} + 1`
genometools-1.6.1+ds/scripts/runmerge.sh-27-done
##############################################
genometools-1.6.1+ds/scripts/gprof-run.sh-1-#!/bin/sh
genometools-1.6.1+ds/scripts/gprof-run.sh:2:Yeast=`ls ${GTTESTDATA}/ltrharvest/s_cer/chr[01][0-9].*.gz`
genometools-1.6.1+ds/scripts/gprof-run.sh-3-bin/gt packedindex mkindex -sprank -tis -dna -pl -bsize 10 -locfreq 32 -dir rev\
##############################################
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh-110-function __get_lognumber {
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh:111: _LOGNUM=`cat $LOGSDIR/.NEXT`
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh:112: __NEXTFREE=`echo $_LOGNUM + 1 | bc`
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh-113- echo $__NEXTFREE > $LOGSDIR/.NEXT
##############################################
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh-210-function __append_version_sga {
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh:211: echo "# version: `$SGA --version | head -n 1`" | tee -a $_LOG
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh-212-}
##############################################
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh-215-function __append_version_edena {
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh:216: echo "# version: `$EDENA -v | head -n 1`" | tee -a $_LOG
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh-217-}
##############################################
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh-554-function runnext {
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh:555: crr=`echo $0 | grep "run(\d)" -P -o | cut -c4`
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh:556: nxt=`echo $crr + 1 | bc`
genometools-1.6.1+ds/scripts/rdj-runbenchmark.sh-557- if [[ -e ./run$nxt ]]; then ./run$nxt; fi
##############################################
genometools-1.6.1+ds/src/match/triangular_def.h-32-
genometools-1.6.1+ds/src/match/triangular_def.h:33:/* The _ADDR(N,I,J) macros give the position of cell [i,j] in an (upper)
genometools-1.6.1+ds/src/match/triangular_def.h-34- triangular matrix. It only works if J >= I. */
genometools-1.6.1+ds/src/match/triangular_def.h:35:#define GT_STRICT_TRIANGULAR_ADDR(N,I,J) (((I)*((N<<1)-3-(I)))>>1)+(J)-1
genometools-1.6.1+ds/src/match/triangular_def.h:36:#define GT_TRIANGULAR_ADDR(N,I,J) (((I)*((N<<1)-1-(I)))>>1)+(J)
genometools-1.6.1+ds/src/match/triangular_def.h-37-
genometools-1.6.1+ds/src/match/triangular_def.h:38:/* The _SADDR(N,I,J) macros give the position of cell [i,j] in a
genometools-1.6.1+ds/src/match/triangular_def.h-39- simmetrical matrix. I and J may be any positive integer < N. */
genometools-1.6.1+ds/src/match/triangular_def.h:40:#define GT_STRICT_TRIANGULAR_SADDR(N,I,J)\
genometools-1.6.1+ds/src/match/triangular_def.h:41: (J>=I) ? GT_STRICT_TRIANGULAR_ADDR(N,I,J) : GT_STRICT_TRIANGULAR_ADDR(N,J,I)
genometools-1.6.1+ds/src/match/triangular_def.h:42:#define GT_TRIANGULAR_SADDR(N,I,J)\
genometools-1.6.1+ds/src/match/triangular_def.h:43: (J>=I) ? GT_TRIANGULAR_ADDR(N,I,J) : GT_TRIANGULAR_ADDR(N,J,I)
genometools-1.6.1+ds/src/match/triangular_def.h-44-
##############################################
genometools-1.6.1+ds/src/match/randomcodes-hpcorrect.c-34- ((SDATA)->pw_scores[\
genometools-1.6.1+ds/src/match/randomcodes-hpcorrect.c:35: GT_STRICT_TRIANGULAR_SADDR((SDATA)->hmers_alloc,(I),(J))])
genometools-1.6.1+ds/src/match/randomcodes-hpcorrect.c-36-
##############################################
genometools-1.6.1+ds/testsuite/gt_sketch_include.rb-105-Test do
genometools-1.6.1+ds/testsuite/gt_sketch_include.rb:106: m = `#{$bin}gt sketch -help`.match(/graphics format\s+choose from ([^ ]+)/m)
genometools-1.6.1+ds/testsuite/gt_sketch_include.rb-107- raise TestFailedError if m.nil?
##############################################
genometools-1.6.1+ds/testsuite/gt_suffixerator_include.rb-520-# conditional tests
genometools-1.6.1+ds/testsuite/gt_suffixerator_include.rb:521:if !`#{$bin}/gt suffixerator -help`.match(/memlimit/).nil? then
genometools-1.6.1+ds/testsuite/gt_suffixerator_include.rb-522- if $gttestdata then
##############################################
genometools-1.6.1+ds/testsuite/gt_suffixerator_include.rb-531- :maxtime => 600
genometools-1.6.1+ds/testsuite/gt_suffixerator_include.rb:532: out = `env GT_MEM_BOOKKEEPING=on GT_ENV_OPTIONS=-spacepeak #{$bin}/gt suffixerator -v -suf -ii dmel`
genometools-1.6.1+ds/testsuite/gt_suffixerator_include.rb-533- if m = out.match(/space peak in megabytes: ([.0-9]+) /) then
##############################################
genometools-1.6.1+ds/testsuite/gt_readjoiner_include.rb-1237- "#{' -mirrored' unless singlestrand} -indexname i"
genometools-1.6.1+ds/testsuite/gt_readjoiner_include.rb:1238: is64bit = Kernel.system("#{$bin}gt -64bit")
genometools-1.6.1+ds/testsuite/gt_readjoiner_include.rb-1239- sizeofint = is64bit ? 8 : 4
##############################################
genometools-1.6.1+ds/testsuite/gt_encseq2spm_include.rb-31- "#{$bin}/gt encseq2spm -ii sfx -l 45 -memlimit 2MB",:retval => 1
genometools-1.6.1+ds/testsuite/gt_encseq2spm_include.rb:32: if not Kernel.system("#{$bin}gt -64bit")
genometools-1.6.1+ds/testsuite/gt_encseq2spm_include.rb-33- run_test "#{$bin}/gt suffixerator -db #{readset} " + \
##############################################
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb-339-Test do
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb:340: is64 = Kernel.system("#{$bin}gt -64bit")
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb-341- if is64 then
##############################################
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb-354-Test do
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb:355: is64 = Kernel.system("#{$bin}gt -64bit")
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb-356- if !is64 then
##############################################
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb-388-Test do
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb:389: is64 = Kernel.system("#{$bin}gt -64bit")
genometools-1.6.1+ds/testsuite/gt_encseq_include.rb-390- if is64 then
##############################################
genometools-1.6.1+ds/testsuite/gt_csr_include.rb-15- run_test "#$bin/gt compreads decompress -file test"
genometools-1.6.1+ds/testsuite/gt_csr_include.rb:16: `grep -v @ #$testdata/#{file} > original`
genometools-1.6.1+ds/testsuite/gt_csr_include.rb-17- `grep -v @ test.fastq > test_out`
##############################################
genometools-1.6.1+ds/testsuite/gt_csr_include.rb-39- run_test "#$bin/gt compreads decompress -file test"
genometools-1.6.1+ds/testsuite/gt_csr_include.rb:40: `grep -v -e '^@' #$testdata/#{file} > original`
genometools-1.6.1+ds/testsuite/gt_csr_include.rb-41- `grep -v '^@' test.fastq > test_out`
##############################################
genometools-1.6.1+ds/gtdata/obo_files/so-xp.obo-118-name: scRNA_primary_transcript
genometools-1.6.1+ds/gtdata/obo_files/so-xp.obo:119:def: "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
genometools-1.6.1+ds/gtdata/obo_files/so-xp.obo-120-synonym: "scRNA primary transcript" EXACT []
##############################################
genometools-1.6.1+ds/gtdata/obo_files/so.obo-118-name: scRNA_primary_transcript
genometools-1.6.1+ds/gtdata/obo_files/so.obo:119:def: "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
genometools-1.6.1+ds/gtdata/obo_files/so.obo-120-synonym: "scRNA primary transcript" EXACT []
##############################################
genometools-1.6.1+ds/debian/patches/reproducible-15- echo '#define GT_CONFIG_H' ;\
genometools-1.6.1+ds/debian/patches/reproducible:16: echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
genometools-1.6.1+ds/debian/patches/reproducible-17-- echo '#define GT_CFLAGS "$(EXP_CFLAGS) $(GT_CFLAGS)"' ;\
##############################################
genometools-1.6.1+ds/debian/rules-29-ifeq ($(shell faketime 'last friday' date > /dev/null 2> /dev/null; echo $$?),0)
genometools-1.6.1+ds/debian/rules:30: FAKETIME:=faketime -f "`TZ=UTC date -d @$(SOURCE_DATE_EPOCH) +'%Y-%m-%d %H:%M:%S'`"
genometools-1.6.1+ds/debian/rules-31-endif
##############################################
genometools-1.6.1+ds/debian/strip-nondeterminism/a2x-7-if faketime 'last friday' date > /dev/null 2> /dev/null; then
genometools-1.6.1+ds/debian/strip-nondeterminism/a2x:8: exec faketime -f "`TZ=UTC date -d @$SOURCE_DATE_EPOCH +'%Y-%m-%d %H:%M:%S'`" \
genometools-1.6.1+ds/debian/strip-nondeterminism/a2x-9- /usr/bin/a2x "$@"
##############################################
genometools-1.6.1+ds/debian/strip-nondeterminism/pdflatex-11-if faketime 'last friday' date > /dev/null 2> /dev/null; then
genometools-1.6.1+ds/debian/strip-nondeterminism/pdflatex:12: exec faketime -f "`TZ=UTC date -d @$SOURCE_DATE_EPOCH +'%Y-%m-%d %H:%M:%S'`" \
genometools-1.6.1+ds/debian/strip-nondeterminism/pdflatex-13- /usr/bin/pdflatex "$@"
##############################################
genometools-1.6.1+ds/.pc/reproducible/Makefile-701- | cut -d'(' -f1 >> $@.src
genometools-1.6.1+ds/.pc/reproducible/Makefile:702: $(V_DO)for L in `cat $@.src`; do \
genometools-1.6.1+ds/.pc/reproducible/Makefile-703- printf "\t\t$$L;\n" >> $@; \
##############################################
genometools-1.6.1+ds/.pc/reproducible/Makefile-713- echo '#define GT_CONFIG_H' ;\
genometools-1.6.1+ds/.pc/reproducible/Makefile:714: echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
genometools-1.6.1+ds/.pc/reproducible/Makefile-715- echo '#define GT_CFLAGS "$(EXP_CFLAGS) $(GT_CFLAGS)"' ;\
##############################################
genometools-1.6.1+ds/.pc/reproducible/Makefile-861-
genometools-1.6.1+ds/.pc/reproducible/Makefile:862:VERSION:="`cat $(CURDIR)/VERSION`"
genometools-1.6.1+ds/.pc/reproducible/Makefile-863-SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
##############################################
genometools-1.6.1+ds/.pc/reproducible/Makefile-1221- src/examples/gtkviewer.c \
genometools-1.6.1+ds/.pc/reproducible/Makefile:1222: -lcairo `$(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags --libs gtk+-2.0` \
genometools-1.6.1+ds/.pc/reproducible/Makefile-1223- -lgenometools
##############################################
genometools-1.6.1+ds/.pc/adding_soname/Makefile-702- | cut -d'(' -f1 >> $@.src
genometools-1.6.1+ds/.pc/adding_soname/Makefile:703: $(V_DO)for L in `cat $@.src`; do \
genometools-1.6.1+ds/.pc/adding_soname/Makefile-704- printf "\t\t$$L;\n" >> $@; \
##############################################
genometools-1.6.1+ds/.pc/adding_soname/Makefile-714- echo '#define GT_CONFIG_H' ;\
genometools-1.6.1+ds/.pc/adding_soname/Makefile:715: echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
genometools-1.6.1+ds/.pc/adding_soname/Makefile-716- echo '#define GT_CFLAGS "$(subst $(shell pwd),.,$(EXP_CFLAGS)) $(subst $(shell pwd),.,$(GT_CFLAGS))"' ;\
##############################################
genometools-1.6.1+ds/.pc/adding_soname/Makefile-862-
genometools-1.6.1+ds/.pc/adding_soname/Makefile:863:VERSION:="`cat $(CURDIR)/VERSION`"
genometools-1.6.1+ds/.pc/adding_soname/Makefile-864-SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
##############################################
genometools-1.6.1+ds/.pc/adding_soname/Makefile-1222- src/examples/gtkviewer.c \
genometools-1.6.1+ds/.pc/adding_soname/Makefile:1223: -lcairo `$(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags --libs gtk+-2.0` \
genometools-1.6.1+ds/.pc/adding_soname/Makefile-1224- -lgenometools
##############################################
genometools-1.6.1+ds/.pc/libbam-fix/Makefile-704- | cut -d'(' -f1 >> $@.src
genometools-1.6.1+ds/.pc/libbam-fix/Makefile:705: $(V_DO)for L in `cat $@.src`; do \
genometools-1.6.1+ds/.pc/libbam-fix/Makefile-706- printf "\t\t$$L;\n" >> $@; \
##############################################
genometools-1.6.1+ds/.pc/libbam-fix/Makefile-716- echo '#define GT_CONFIG_H' ;\
genometools-1.6.1+ds/.pc/libbam-fix/Makefile:717: echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
genometools-1.6.1+ds/.pc/libbam-fix/Makefile-718- echo '#define GT_CFLAGS "$(subst $(shell pwd),.,$(EXP_CFLAGS)) $(subst $(shell pwd),.,$(GT_CFLAGS))"' ;\
##############################################
genometools-1.6.1+ds/.pc/libbam-fix/Makefile-864-
genometools-1.6.1+ds/.pc/libbam-fix/Makefile:865:VERSION:="`cat $(CURDIR)/VERSION`"
genometools-1.6.1+ds/.pc/libbam-fix/Makefile-866-SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
##############################################
genometools-1.6.1+ds/.pc/libbam-fix/Makefile-1225- src/examples/gtkviewer.c \
genometools-1.6.1+ds/.pc/libbam-fix/Makefile:1226: -lcairo `$(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags --libs gtk+-2.0` \
genometools-1.6.1+ds/.pc/libbam-fix/Makefile-1227- -lgenometools
##############################################
genometools-1.6.1+ds/.pc/use-mx32/Makefile-718- | cut -d'(' -f1 >> $@.src
genometools-1.6.1+ds/.pc/use-mx32/Makefile:719: $(V_DO)for L in `cat $@.src`; do \
genometools-1.6.1+ds/.pc/use-mx32/Makefile-720- printf "\t\t$$L;\n" >> $@; \
##############################################
genometools-1.6.1+ds/.pc/use-mx32/Makefile-730- echo '#define GT_CONFIG_H' ;\
genometools-1.6.1+ds/.pc/use-mx32/Makefile:731: echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
genometools-1.6.1+ds/.pc/use-mx32/Makefile-732- echo '#define GT_CFLAGS "$(subst $(shell pwd),.,$(EXP_CFLAGS)) $(subst $(shell pwd),.,$(GT_CFLAGS))"' ;\
##############################################
genometools-1.6.1+ds/.pc/use-mx32/Makefile-878-
genometools-1.6.1+ds/.pc/use-mx32/Makefile:879:VERSION:="`cat $(CURDIR)/VERSION`"
genometools-1.6.1+ds/.pc/use-mx32/Makefile-880-SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
##############################################
genometools-1.6.1+ds/.pc/use-mx32/Makefile-1239- src/examples/gtkviewer.c \
genometools-1.6.1+ds/.pc/use-mx32/Makefile:1240: -lcairo `$(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags --libs gtk+-2.0` \
genometools-1.6.1+ds/.pc/use-mx32/Makefile-1241- -lgenometools
##############################################
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile-720- | cut -d'(' -f1 >> $@.src
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile:721: $(V_DO)for L in `cat $@.src`; do \
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile-722- printf "\t\t$$L;\n" >> $@; \
##############################################
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile-732- echo '#define GT_CONFIG_H' ;\
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile:733: echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile-734- echo '#define GT_CFLAGS "$(subst $(shell pwd),.,$(EXP_CFLAGS)) $(subst $(shell pwd),.,$(GT_CFLAGS))"' ;\
##############################################
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile-880-
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile:881:VERSION:="`cat $(CURDIR)/VERSION`"
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile-882-SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
##############################################
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile-1241- src/examples/gtkviewer.c \
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile:1242: -lcairo `$(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags --libs gtk+-2.0` \
genometools-1.6.1+ds/.pc/ignore-m32-m64.patch/Makefile-1243- -lgenometools
##############################################
genometools-1.6.1+ds/Makefile-704- | cut -d'(' -f1 >> $@.src
genometools-1.6.1+ds/Makefile:705: $(V_DO)for L in `cat $@.src`; do \
genometools-1.6.1+ds/Makefile-706- printf "\t\t$$L;\n" >> $@; \
##############################################
genometools-1.6.1+ds/Makefile-716- echo '#define GT_CONFIG_H' ;\
genometools-1.6.1+ds/Makefile:717: echo '#define GT_CC "'`$(CC) --version | head -n 1`\" ;\
genometools-1.6.1+ds/Makefile-718- echo '#define GT_CFLAGS "$(subst $(shell pwd),.,$(EXP_CFLAGS)) $(subst $(shell pwd),.,$(GT_CFLAGS))"' ;\
##############################################
genometools-1.6.1+ds/Makefile-864-
genometools-1.6.1+ds/Makefile:865:VERSION:="`cat $(CURDIR)/VERSION`"
genometools-1.6.1+ds/Makefile-866-SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
##############################################
genometools-1.6.1+ds/Makefile-1225- src/examples/gtkviewer.c \
genometools-1.6.1+ds/Makefile:1226: -lcairo `$(OVERRIDE_PC_PATH) pkg-config --silence-errors --cflags --libs gtk+-2.0` \
genometools-1.6.1+ds/Makefile-1227- -lgenometools