===========================================================
.___ __ __
_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
vmatch-2.3.1+dfsg/src/Emulate/repfind.pl-37- my $inputfile = $argv[$argcount-1];
vmatch-2.3.1+dfsg/src/Emulate/repfind.pl:38: my $indexname = `basename $inputfile`;
vmatch-2.3.1+dfsg/src/Emulate/repfind.pl-39- chomp($indexname);
##############################################
vmatch-2.3.1+dfsg/src/Emulate/repfind.pl-127- my @args = split(' ',$argstring);
vmatch-2.3.1+dfsg/src/Emulate/repfind.pl:128: my($retcode) = system($argstring);
vmatch-2.3.1+dfsg/src/Emulate/repfind.pl-129- $retcode = $? >> 8;
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/Allwhatsthere.sh-7-do
vmatch-2.3.1+dfsg/src/Mkvtree/Allwhatsthere.sh:8: indexname=`basename ${filename} .prj`
vmatch-2.3.1+dfsg/src/Mkvtree/Allwhatsthere.sh-9- ./allwhatsthere.x ${indexname}
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh-155-
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh:156: plen=`expr $plen + 1`
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh-157- done
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh-166-
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh:167: plen=`expr $plen + 1`
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh-168- done
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh-177-
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh:178: plen=`expr $plen + 1`
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh-179- done
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh-192- checkerror
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh:193: plen=`expr $plen + 1`
vmatch-2.3.1+dfsg/src/Mkvtree/Checkall.sh-194- done
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-25-
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:26:#define ADDR(I) ((Uint) ((I) - mkvaux->sortedsuffixes))
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-27-#define COMPAREOFFSET (UCHAR_MAX + 1)
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-254- (Showuint) __LINE__,\
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:255: (Showuint) ADDR(L),\
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:256: (Showuint) ADDR(R),\
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-257- (Showuint) (D))
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-264- DEBUG3(3,"# POPMKVstack(%lu,%lu,%lu)\n",\
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:265: (Showuint) ADDR(L),\
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:266: (Showuint) ADDR(R),\
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-267- (Showuint) (D))
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-677- DEBUG3(3,"# inssort(%lu,%lu,%lu)=",
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:678: (Showuint) ADDR(left),
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:679: (Showuint) ADDR(right),
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-680- (Showuint) depth);
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-731- DEBUG4(3,"# bentleysedgewick(%lu,%lu,%lu,base=%lu)\n",
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:732: (Showuint) ADDR(l),
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:733: (Showuint) ADDR(r),
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-734- (Showuint) d,
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:735: (Showuint) ADDR(lcpbase));
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-736-
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-739- {
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:740: printf("addunsortedrange(%lu,%lu)\n",(Showuint) ADDR(l),
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:741: (Showuint) ADDR(r));
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-742- addunsortedrange(rmnsufinfo,maxdepth->uintvalue,l,r);
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-818- DEBUG2(3,"# left=%lu,right=%lu,",
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:819: (Showuint) ADDR(left),
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:820: (Showuint) ADDR(right));
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-821- DEBUG2(3,"a=%lu,b=%lu,",
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:822: (Showuint) ADDR(pa),
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:823: (Showuint) ADDR(pb));
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-824- DEBUG2(3,"c=%lu,d=%lu\n",
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:825: (Showuint) ADDR(pc),
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:826: (Showuint) ADDR(pd));
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-827- if((w = (Sint) (pd-pc)) > 0)
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-981- lcpschecked += checklcpsubtab(mkvaux,virtualtree,
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:982: ADDR(left),(Uint) (right-left));
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-983-#endif
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-1040- lcpschecked += checklcpsubtab(mkvaux,virtualtree,
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c:1041: ADDR(left),(Uint) (right-left));
vmatch-2.3.1+dfsg/src/Mkvtree/bese.c-1042-#endif
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/longsort.c-113- (Showuint) __LINE__,\
vmatch-2.3.1+dfsg/src/Mkvtree/longsort.c:114: (Showuint) ADDR(L),\
vmatch-2.3.1+dfsg/src/Mkvtree/longsort.c:115: (Showuint) ADDR(R),\
vmatch-2.3.1+dfsg/src/Mkvtree/longsort.c-116- (Showuint) (D))
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/longsort.c-123- DEBUG3(3,"# POPMKVstack(%lu,%lu,%lu)\n",\
vmatch-2.3.1+dfsg/src/Mkvtree/longsort.c:124: (Showuint) ADDR(L),\
vmatch-2.3.1+dfsg/src/Mkvtree/longsort.c:125: (Showuint) ADDR(R),\
vmatch-2.3.1+dfsg/src/Mkvtree/longsort.c-126- (Showuint) (D))
##############################################
vmatch-2.3.1+dfsg/src/Mkvtree/makeseqset.sh-18-setenv VMINP "/home/kwimmenauer/Vmatchinput"
vmatch-2.3.1+dfsg/src/Mkvtree/makeseqset.sh:19:setenv ATK "\${VMINP}/`basename ${ATK}`"
vmatch-2.3.1+dfsg/src/Mkvtree/makeseqset.sh:20:setenv AT "\${VMINP}/`basename ${AT}`"
vmatch-2.3.1+dfsg/src/Mkvtree/makeseqset.sh:21:setenv SWK "\${VMINP}/`basename ${SWK}`"
vmatch-2.3.1+dfsg/src/Mkvtree/makeseqset.sh:22:setenv SW "\${VMINP}/`basename ${SW}`"
vmatch-2.3.1+dfsg/src/Mkvtree/makeseqset.sh:23:setenv SWS "\${VMINP}/`basename ${SWS}`"
vmatch-2.3.1+dfsg/src/Mkvtree/makeseqset.sh:24:setenv U8GB "\${VMINP}/`basename ${U8GB}`"
vmatch-2.3.1+dfsg/src/Mkvtree/makeseqset.sh-25-ENDOFECHO
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Apmcheck.sh-60-
vmatch-2.3.1+dfsg/src/Vmatch/Apmcheck.sh:61:echo "number of matches is `wc -l ${OUTONLINE}.vms`"
vmatch-2.3.1+dfsg/src/Vmatch/Apmcheck.sh-62-
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Checkmstat.sh-26- checkerror
vmatch-2.3.1+dfsg/src/Vmatch/Checkmstat.sh:27: headlen=`expr ${headlen} + 10`
vmatch-2.3.1+dfsg/src/Vmatch/Checkmstat.sh-28- done
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Cmpmatchcl.sh-24-
vmatch-2.3.1+dfsg/src/Vmatch/Cmpmatchcl.sh:25:indexname=`basename $database`
vmatch-2.3.1+dfsg/src/Vmatch/Cmpmatchcl.sh-26-if test -f ${indexname}.prj
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Cnt.sh-18-
vmatch-2.3.1+dfsg/src/Vmatch/Cnt.sh:19:if test -f "`basename $1`.bwt"
vmatch-2.3.1+dfsg/src/Vmatch/Cnt.sh-20-then
vmatch-2.3.1+dfsg/src/Vmatch/Cnt.sh:21: echo "`basename $1.bwt` exists"
vmatch-2.3.1+dfsg/src/Vmatch/Cnt.sh-22-else
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Cnt.sh-30-
vmatch-2.3.1+dfsg/src/Vmatch/Cnt.sh:31:indexname=`basename $1`
vmatch-2.3.1+dfsg/src/Vmatch/Cnt.sh-32-cmd="./vmatch.x -d -i -l $2 $indexname"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Complete.sh-18-
vmatch-2.3.1+dfsg/src/Vmatch/Complete.sh:19:if test -f "`basename $2`.prj"
vmatch-2.3.1+dfsg/src/Vmatch/Complete.sh-20-then
vmatch-2.3.1+dfsg/src/Vmatch/Complete.sh:21: echo "`basename $2`.prj exists"
vmatch-2.3.1+dfsg/src/Vmatch/Complete.sh-22-else
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Complete.sh-27-
vmatch-2.3.1+dfsg/src/Vmatch/Complete.sh:28:indexname=`basename $2`
vmatch-2.3.1+dfsg/src/Vmatch/Complete.sh-29-
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Hamcheck.sh-47-
vmatch-2.3.1+dfsg/src/Vmatch/Hamcheck.sh:48:echo "number of matches is `wc -l ${OUTONLINE}.sort`"
vmatch-2.3.1+dfsg/src/Vmatch/Hamcheck.sh-49-
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterapmcheck.sh-32-
vmatch-2.3.1+dfsg/src/Vmatch/Iterapmcheck.sh:33:for pattern in `../Mkvtree/vsubseqselect.x -minlength 17 -maxlength 32 -snum ${numofpatterns} apmindex | grep -v '^#'`
vmatch-2.3.1+dfsg/src/Vmatch/Iterapmcheck.sh-34-do
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh-21-echo "----------$0-------------"
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh:22:seqs="`ls ${ATK} ${ATK2}` ${VAC} ${CNN} ${Y3}"
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh-23-
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh-25-filename2="${SWK2}"
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh:26:echo "`basename $filename1` `basename $filename2`"
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh-27-cmd="./Map.sh protein $filename1 $filename2 -l 5"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh-39- then
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh:40: echo "`basename $filename1` `basename $filename2`"
vmatch-2.3.1+dfsg/src/Vmatch/Itermap.sh-41- cmd="./Map.sh dna $filename1 $filename2 -l 18"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Itermum.sh-12-GRUMBACH=../testdata/Grumbach
vmatch-2.3.1+dfsg/src/Vmatch/Itermum.sh:13:seqs=`ls ${GRUMBACH}/[a-z]*.fna`
vmatch-2.3.1+dfsg/src/Vmatch/Itermum.sh-14-
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Itermum.sh-21- then
vmatch-2.3.1+dfsg/src/Vmatch/Itermum.sh:22: echo "`basename $filenameA` `basename $filenameB` $leastlength"
vmatch-2.3.1+dfsg/src/Vmatch/Itermum.sh-23- cmd="./Mum.sh $filenameA $filenameB $leastlength"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-16-echo "----------$0-------------"
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh:17:for filename in `ls ../testdata/at1MB ${GRUMBACHSEQ}/*.seq`
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-18-do
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-30- checkerror
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh:31: cmd="./Qonl.sh `basename ${filename}` ${U8} 20 0"
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-32- ${cmd}
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-33- checkerror
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh:34: cmd="./Qonl.sh `basename ${filename}` ${U8} 20 0 palindromic"
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-35- ${cmd}
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-36- checkerror
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh:37: cmd="./Qonl.sh `basename ${filename}` ${U8} 30 -1"
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-38- ${cmd}
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-39- checkerror
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh:40: cmd="./Qonl.sh `basename ${filename}` ${U8} 30 -1 palindromic"
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-41- ${cmd}
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-42- checkerror
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh:43: cmd="./Qonl.sh `basename ${filename}` ${U8} 30 1"
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-44- ${cmd}
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-45- checkerror
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh:46: cmd="./Qonl.sh `basename ${filename}` ${U8} 30 1 palindromic"
vmatch-2.3.1+dfsg/src/Vmatch/Iterqonl.sh-47- ${cmd}
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterquery.sh-31-do
vmatch-2.3.1+dfsg/src/Vmatch/Iterquery.sh:32: dist=`expr $i \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/Iterquery.sh-33- cmd="./Query.sh dna 60 $dist"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterqueryms.sh-79-
vmatch-2.3.1+dfsg/src/Vmatch/Iterqueryms.sh:80: howmany=`expr $howmany + 2`
vmatch-2.3.1+dfsg/src/Vmatch/Iterqueryms.sh-81-done
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterrep.sh-22-do
vmatch-2.3.1+dfsg/src/Vmatch/Iterrep.sh:23: patternlist=`onePE.rand.x R100000acgt $number $plength` || exit 1
vmatch-2.3.1+dfsg/src/Vmatch/Iterrep.sh-24- for p in ${patternlist}
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterrep.sh-66- done
vmatch-2.3.1+dfsg/src/Vmatch/Iterrep.sh:67: plength=`expr $plength + 1`
vmatch-2.3.1+dfsg/src/Vmatch/Iterrep.sh-68-done
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterrepms.sh-79-
vmatch-2.3.1+dfsg/src/Vmatch/Iterrepms.sh:80: howmany=`expr $howmany + 1`
vmatch-2.3.1+dfsg/src/Vmatch/Iterrepms.sh-81-done
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterunique.sh-13-
vmatch-2.3.1+dfsg/src/Vmatch/Iterunique.sh:14:seqs=`ls ${GRUMBACH}/[a-z]*.fna`
vmatch-2.3.1+dfsg/src/Vmatch/Iterunique.sh-15-AT=../testdata/at1MB
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Iterunique.sh-19-do
vmatch-2.3.1+dfsg/src/Vmatch/Iterunique.sh:20: echo "`basename $filename`"
vmatch-2.3.1+dfsg/src/Vmatch/Iterunique.sh-21- cmd="./UniqueDB.sh 200 20 0 $filename "
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh-13-echo "----------$0-------------"
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh:14:for filename in `ls ${IKEDA}/*.seq`
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh-15-do
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh-18- do
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh:19: l=`expr $d \* 10`
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh:20: l=`expr $l + 24`
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh-21- if test $d -ne 0
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh-22- then
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh:23: dist=`expr $d \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/Large.sh-24- cmd="Rep.sh $filename $l $dist"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Map.sh-41-
vmatch-2.3.1+dfsg/src/Vmatch/Map.sh:42:cmd="./vmatch.x $* -q $file2 `basename $file1`"
vmatch-2.3.1+dfsg/src/Vmatch/Map.sh-43-${cmd} > shitlebrit
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Map.sh-52-
vmatch-2.3.1+dfsg/src/Vmatch/Map.sh:53:cmd="./vmatch.x $* -q `basename $file2` `basename $file1`"
vmatch-2.3.1+dfsg/src/Vmatch/Map.sh-54-${cmd} > shitlebrit
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Qonl.sh-37-then
vmatch-2.3.1+dfsg/src/Vmatch/Qonl.sh:38: hval=`expr $dval \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/Qonl.sh-39- dstring="-h $hval"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh-55-
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh:56:if test -f `basename ${database}`.prj
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh-57-then
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh-66-then
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh:67: hval=`expr $3 \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh-68- dist="-h $hval -allmax"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh-77-
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh:78:indexname=`basename ${database}`
vmatch-2.3.1+dfsg/src/Vmatch/Query.sh-79-cmd="./vmatch.x -l $2 ${dist} ${allindex}"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Queryms.sh-36-
vmatch-2.3.1+dfsg/src/Vmatch/Queryms.sh:37:if test -f "`basename ${db}`.bwt"
vmatch-2.3.1+dfsg/src/Vmatch/Queryms.sh-38-then
vmatch-2.3.1+dfsg/src/Vmatch/Queryms.sh:39: echo "`basename ${db}.bwt` exists"
vmatch-2.3.1+dfsg/src/Vmatch/Queryms.sh-40-else
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Queryms.sh-47-then
vmatch-2.3.1+dfsg/src/Vmatch/Queryms.sh:48: hval=`expr $dval \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/Queryms.sh-49- vmdist="-h $hval -allmax"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Regexp.sh-14- numofregexp=$1
vmatch-2.3.1+dfsg/src/Vmatch/Regexp.sh:15: numoflines=`expr ${numofregexp} + ${numofregexp}`
vmatch-2.3.1+dfsg/src/Vmatch/Regexp.sh-16- head -n ${numoflines} Regexp.fas > Regexp.tmp
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Rep.sh-39-then
vmatch-2.3.1+dfsg/src/Vmatch/Rep.sh:40: hval=`expr $3 \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/Rep.sh-41- dist="-h $hval -allmax"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Rep.sh-50-
vmatch-2.3.1+dfsg/src/Vmatch/Rep.sh:51:indexname=`basename $1`
vmatch-2.3.1+dfsg/src/Vmatch/Rep.sh-52-formatopts="-absolute -noscore -noidentity"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Repms.sh-29-fi
vmatch-2.3.1+dfsg/src/Vmatch/Repms.sh:30:if test -f "`basename $1`.bwt"
vmatch-2.3.1+dfsg/src/Vmatch/Repms.sh-31-then
vmatch-2.3.1+dfsg/src/Vmatch/Repms.sh:32: echo "`basename $1.bwt` exists"
vmatch-2.3.1+dfsg/src/Vmatch/Repms.sh-33-else
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Repms.sh-40-then
vmatch-2.3.1+dfsg/src/Vmatch/Repms.sh:41: hval=`expr $3 \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/Repms.sh-42- vmdist="-h $hval -allmax"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/UniqueDB.sh-24-then
vmatch-2.3.1+dfsg/src/Vmatch/UniqueDB.sh:25: hval=`expr $3 \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/UniqueDB.sh-26- dist="-h $hval -allmax"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/UniqueQ1.sh-26-then
vmatch-2.3.1+dfsg/src/Vmatch/UniqueQ1.sh:27: hval=`expr $distval \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/UniqueQ1.sh-28- dist="-h $hval"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/UniqueQ2.sh-26-then
vmatch-2.3.1+dfsg/src/Vmatch/UniqueQ2.sh:27: hval=`expr $distval \* -1`
vmatch-2.3.1+dfsg/src/Vmatch/UniqueQ2.sh-28- dist="-h $hval"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Vstmstats.sh-19-textfile=$2
vmatch-2.3.1+dfsg/src/Vmatch/Vstmstats.sh:20:indexname=`basename ${patternfile}`
vmatch-2.3.1+dfsg/src/Vmatch/Vstmstats.sh-21-if test -f "${indexname}.prj"
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh-13-echo "----------$0-------------"
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh:14:seqs=`ls ${GRUMBACH}/[m-z]*.fna`
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh-15-
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh-30- vmoptions="$mode $xdropmode $xdropbelow -leastscore $leastscore"
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh:31: cmd="./vmatch.x ${vmoptions} `basename ${filename}`"
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh-32- ${cmd} > tmp.match
##############################################
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh-38-
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh:39: cmd="./vmatch.x -s ${vmoptions} `basename ${filename}`"
vmatch-2.3.1+dfsg/src/Vmatch/Xdrop.sh-40- ${cmd} > /dev/null
##############################################
vmatch-2.3.1+dfsg/src/bin/Checkmergebig.sh-46- indexlist="${indexlist} merindex${idxnum}"
vmatch-2.3.1+dfsg/src/bin/Checkmergebig.sh:47: idxnum=`expr $idxnum + 1`
vmatch-2.3.1+dfsg/src/bin/Checkmergebig.sh-48-done
##############################################
vmatch-2.3.1+dfsg/src/bin/Checkmergeesa.sh-58-do
vmatch-2.3.1+dfsg/src/bin/Checkmergeesa.sh:59: indexname=`echo ${filename} | sed -e 's/tmp/idx/'`
vmatch-2.3.1+dfsg/src/bin/Checkmergeesa.sh-60- indexlist="${indexlist} ${indexname}"
##############################################
vmatch-2.3.1+dfsg/src/bin/Indexname.sh-29-
vmatch-2.3.1+dfsg/src/bin/Indexname.sh:30:firstfile=`echo $1 | sed -e 's/^-//'`
vmatch-2.3.1+dfsg/src/bin/Indexname.sh:31:indexname="${indexdir}/`basename ${firstfile}`"
vmatch-2.3.1+dfsg/src/bin/Indexname.sh-32-shift
vmatch-2.3.1+dfsg/src/bin/Indexname.sh-33-
vmatch-2.3.1+dfsg/src/bin/Indexname.sh:34:for filename in `echo $* | tr ' ' '\n'`
vmatch-2.3.1+dfsg/src/bin/Indexname.sh-35-do
vmatch-2.3.1+dfsg/src/bin/Indexname.sh:36: filename=`echo $filename | sed -e 's/^-//'`
vmatch-2.3.1+dfsg/src/bin/Indexname.sh:37: indexname="${indexname}-`basename ${filename}`"
vmatch-2.3.1+dfsg/src/bin/Indexname.sh-38-done
##############################################
vmatch-2.3.1+dfsg/src/bin/Itersed.sh-9-case "${directory}" in
vmatch-2.3.1+dfsg/src/bin/Itersed.sh:10: "kurtz") FILELIST="`ls ${directory}/*.[ch] ${directory}/*.gen`";;
vmatch-2.3.1+dfsg/src/bin/Itersed.sh:11: "Vmatch") FILELIST="`ls ${directory}/*.[ch] ${directory}/*.gen`";;
vmatch-2.3.1+dfsg/src/bin/Itersed.sh:12: *) FILELIST="`ls ${directory}/*.[ch]`";;
vmatch-2.3.1+dfsg/src/bin/Itersed.sh-13-esac
##############################################
vmatch-2.3.1+dfsg/src/bin/Itersubseq.sh-18-indexname=$1
vmatch-2.3.1+dfsg/src/bin/Itersubseq.sh:19:numofsequences=`grep 'numofsequences=' ${indexname}.prj | sed -e 's/numofsequences=//'`
vmatch-2.3.1+dfsg/src/bin/Itersubseq.sh-20-seqnum=0
##############################################
vmatch-2.3.1+dfsg/src/bin/Itersubseq.sh-25- checkerror
vmatch-2.3.1+dfsg/src/bin/Itersubseq.sh:26: seqnum=`expr ${seqnum} + 1`
vmatch-2.3.1+dfsg/src/bin/Itersubseq.sh-27-done
##############################################
vmatch-2.3.1+dfsg/src/bin/Makeindex.sh-23-
vmatch-2.3.1+dfsg/src/bin/Makeindex.sh:24:if test -f `basename ${ATindex}.prj`
vmatch-2.3.1+dfsg/src/bin/Makeindex.sh-25-then
##############################################
vmatch-2.3.1+dfsg/src/bin/Makeindex.sh-32-
vmatch-2.3.1+dfsg/src/bin/Makeindex.sh:33:if test -f `basename ${SWindex}.prj`
vmatch-2.3.1+dfsg/src/bin/Makeindex.sh-34-then
##############################################
vmatch-2.3.1+dfsg/src/bin/bininstall.sh-40- checkerror
vmatch-2.3.1+dfsg/src/bin/bininstall.sh:41: destfile="`basename ${binaryfile} .x`"
vmatch-2.3.1+dfsg/src/bin/bininstall.sh-42- echo "install ${binaryfile} in ${installpath}/${destfile}"
##############################################
vmatch-2.3.1+dfsg/src/bin/checkforSELECTheaders.sh-6-then
vmatch-2.3.1+dfsg/src/bin/checkforSELECTheaders.sh:7: numofheader=`ls ${selpath}/*.h | wc -l`
vmatch-2.3.1+dfsg/src/bin/checkforSELECTheaders.sh-8- if test ${numofheader} -ne ${mustnumofheader}
##############################################
vmatch-2.3.1+dfsg/src/bin/cmpCal.sh-34-then
vmatch-2.3.1+dfsg/src/bin/cmpCal.sh:35: for filename in `ls ${VSTREEDATA}/DNA/*/*.seq`
vmatch-2.3.1+dfsg/src/bin/cmpCal.sh-36- do
##############################################
vmatch-2.3.1+dfsg/src/bin/cmpCal.sh-47- do
vmatch-2.3.1+dfsg/src/bin/cmpCal.sh:48: for filename in `ls $DIR/$pat`
vmatch-2.3.1+dfsg/src/bin/cmpCal.sh-49- do
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-37-
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:38:me=`echo "$0" | sed -e 's,.*/,,'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-39-
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-106-: ${TMPDIR=/tmp} ;
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:107: { tmp=`(umask 077 && mktemp -d -q "$TMPDIR/cgXXXXXX") 2>/dev/null` && test -n "$tmp" && test -d "$tmp" ; } ||
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-108- { test -n "$RANDOM" && tmp=$TMPDIR/cg$$-$RANDOM && (umask 077 && mkdir $tmp) ; } ||
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-191- *)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:192: release=`echo ${UNAME_RELEASE}|sed -e 's/[-_].*/\./'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-193- ;;
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-240- if test $UNAME_RELEASE = "V4.0"; then
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:241: UNAME_RELEASE=`/usr/sbin/sizer -v | awk '{print $3}'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-242- fi
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-246- # types through head -n 1, so we only detect the type of CPU 0.
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:247: ALPHA_CPU_TYPE=`/usr/sbin/psrinfo -v | sed -n -e 's/^ The alpha \(.*\) processor.*$/\1/p' | head -n 1`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-248- case "$ALPHA_CPU_TYPE" in
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-283- # 1.2 uses "1.2" for uname -r.
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:284: echo ${UNAME_MACHINE}-dec-osf`echo ${UNAME_RELEASE} | sed -e 's/^[VTX]//' | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-285- exit 0 ;;
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-334- sun4H:SunOS:5.*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:335: echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-336- exit 0 ;;
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-337- sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:338: echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-339- exit 0 ;;
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-340- i86pc:SunOS:5.*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:341: echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-342- exit 0 ;;
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-346- # it's likely to be more like Solaris than SunOS4.
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:347: echo sparc-sun-solaris3`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-348- exit 0 ;;
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-355- # Japanese Language versions have a version number like `4.1.3-JL'.
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:356: echo sparc-sun-sunos`echo ${UNAME_RELEASE}|sed -e 's/-/_/'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-357- exit 0 ;;
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-361- sun*:*:4.2BSD:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:362: UNAME_RELEASE=`(sed 1q /etc/motd | awk '{print substr($5,1,3)}') 2>/dev/null`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-363- test "x${UNAME_RELEASE}" = "x" && UNAME_RELEASE=3
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-440- $CC_FOR_BUILD -o $dummy $dummy.c \
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:441: && $dummy `echo "${UNAME_RELEASE}" | sed -n 's/\([0-9]*\).*/\1/p'` \
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-442- && exit 0
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-495- *:IRIX*:*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:496: echo mips-sgi-irix`echo ${UNAME_RELEASE}|sed -e 's/-/_/g'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-497- exit 0 ;;
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-534- *:AIX:*:[45])
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:535: IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-536- if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-569- 9000/[34678]??:HP-UX:*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:570: HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-571- case "${UNAME_MACHINE}" in
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-623-EOF
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:624: (CCOPTS= $CC_FOR_BUILD -o $dummy $dummy.c 2>/dev/null) && HP_ARCH=`$dummy`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-625- test -z "$HP_ARCH" && HP_ARCH=hppa
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-641- ia64:HP-UX:*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:642: HPUX_REV=`echo ${UNAME_RELEASE}|sed -e 's/[^.]*.[0B]*//'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-643- echo ia64-hp-hpux${HPUX_REV}
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-741- FUJITSU_SYS=`uname -p | tr 'ABCDEFGHIJKLMNOPQRSTUVWXYZ' 'abcdefghijklmnopqrstuvwxyz' | sed -e 's/\///'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:742: FUJITSU_REL=`echo ${UNAME_RELEASE} | sed -e 's/ /_/'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-743- echo "${FUJITSU_PROC}-fujitsu-${FUJITSU_SYS}${FUJITSU_REL}"
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-764-EOF
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:765: eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-766- # GNU/FreeBSD systems have a "k" prefix to indicate we are using
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-768- case ${LIBC} in gnu) kernel_only='k' ;; esac
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:769: echo ${UNAME_MACHINE}-unknown-${kernel_only}freebsd`echo ${UNAME_RELEASE}|sed -e 's/[-(].*//'`${LIBC:+-$LIBC}
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-770- exit 0 ;;
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-798- prep*:SunOS:5.*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:799: echo powerpcle-unknown-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-800- exit 0 ;;
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-801- *:GNU:*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:802: echo `echo ${UNAME_MACHINE}|sed -e 's,[-/].*$,,'`-unknown-gnu`echo ${UNAME_RELEASE}|sed -e 's,/.*$,,'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-803- exit 0 ;;
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-834-EOF
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:835: eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-836- test x"${CPU}" != x && echo "${CPU}-unknown-linux-gnu" && exit 0
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-853-EOF
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:854: eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^CPU=`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-855- test x"${CPU}" != x && echo "${CPU}-unknown-linux-gnu" && exit 0
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-951-EOF
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:952: eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep ^LIBC=`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-953- test x"${LIBC}" != x && echo "${UNAME_MACHINE}-pc-linux-${LIBC}" && exit 0
##############################################
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-987- i*86:*:4.*:* | i*86:SYSTEM_V:4.*:*)
vmatch-2.3.1+dfsg/src/bin/config-guess.sh:988: UNAME_REL=`echo ${UNAME_RELEASE} | sed 's/\/MP$//'`
vmatch-2.3.1+dfsg/src/bin/config-guess.sh-989- if grep Novell /usr/include/link.h >/dev/null 2>/dev/null; then
##############################################
vmatch-2.3.1+dfsg/src/bin/expandinc.pl-47- {
vmatch-2.3.1+dfsg/src/bin/expandinc.pl:48: if($line =~ /^include (.*)$/)
vmatch-2.3.1+dfsg/src/bin/expandinc.pl-49- {
##############################################
vmatch-2.3.1+dfsg/src/bin/install.sh-103-
vmatch-2.3.1+dfsg/src/bin/install.sh:104: -t=*) transformarg=`echo $1 | sed 's/-t=//'`
vmatch-2.3.1+dfsg/src/bin/install.sh-105- shift
##############################################
vmatch-2.3.1+dfsg/src/bin/install.sh-107-
vmatch-2.3.1+dfsg/src/bin/install.sh:108: -b=*) transformbasename=`echo $1 | sed 's/-b=//'`
vmatch-2.3.1+dfsg/src/bin/install.sh-109- shift
##############################################
vmatch-2.3.1+dfsg/src/bin/install.sh-169- then
vmatch-2.3.1+dfsg/src/bin/install.sh:170: dst=$dst/`basename "$src"`
vmatch-2.3.1+dfsg/src/bin/install.sh-171- else
##############################################
vmatch-2.3.1+dfsg/src/bin/install.sh-176-## this sed command emulates the dirname command
vmatch-2.3.1+dfsg/src/bin/install.sh:177:dstdir=`echo "$dst" | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
vmatch-2.3.1+dfsg/src/bin/install.sh-178-
##############################################
vmatch-2.3.1+dfsg/src/bin/install.sh-190-IFS='%'
vmatch-2.3.1+dfsg/src/bin/install.sh:191:set - `echo "$dstdir" | sed -e 's@/@%@g' -e 's@^%@/@'`
vmatch-2.3.1+dfsg/src/bin/install.sh-192-IFS=$oIFS
##############################################
vmatch-2.3.1+dfsg/src/bin/install.sh-224- then
vmatch-2.3.1+dfsg/src/bin/install.sh:225: dstfile=`basename "$dst"`
vmatch-2.3.1+dfsg/src/bin/install.sh-226- else
##############################################
vmatch-2.3.1+dfsg/src/bin/install.sh-234- then
vmatch-2.3.1+dfsg/src/bin/install.sh:235: dstfile=`basename "$dst"`
vmatch-2.3.1+dfsg/src/bin/install.sh-236- else
##############################################
vmatch-2.3.1+dfsg/src/bin/libinstall.sh-17-
vmatch-2.3.1+dfsg/src/bin/libinstall.sh:18:for archive in `ls ${libdir}/*.a`
vmatch-2.3.1+dfsg/src/bin/libinstall.sh-19-do
##############################################
vmatch-2.3.1+dfsg/src/bin/libinstall.sh-23- checkerror
vmatch-2.3.1+dfsg/src/bin/libinstall.sh:24: echo "install `basename ${archive}` in ${installpath}"
vmatch-2.3.1+dfsg/src/bin/libinstall.sh-25- cmd="cp -f $archive ${installpath}"
##############################################
vmatch-2.3.1+dfsg/src/bin/libinstall.sh-27- checkerror
vmatch-2.3.1+dfsg/src/bin/libinstall.sh:28: basefile=`basename ${archive}`
vmatch-2.3.1+dfsg/src/bin/libinstall.sh-29- chmod g+r ${installpath}/${basefile}
##############################################
vmatch-2.3.1+dfsg/src/bin/linkvm.sh-17-execdir=$1
vmatch-2.3.1+dfsg/src/bin/linkvm.sh:18:execfiles=`find ${execdir} -maxdepth 1 -type f ! -name '*\.*' -print`
vmatch-2.3.1+dfsg/src/bin/linkvm.sh-19-for filename in ${execfiles}
vmatch-2.3.1+dfsg/src/bin/linkvm.sh-20-do
vmatch-2.3.1+dfsg/src/bin/linkvm.sh:21: bname=`basename ${filename}`
vmatch-2.3.1+dfsg/src/bin/linkvm.sh-22- cmd="ln -s ${filename} ${bname}.x"
##############################################
vmatch-2.3.1+dfsg/src/bin/makeauto.sh-20-tar xvzf $gzpath
vmatch-2.3.1+dfsg/src/bin/makeauto.sh:21:subdir=`basename ${gzpath} .tar.gz`
vmatch-2.3.1+dfsg/src/bin/makeauto.sh-22-
vmatch-2.3.1+dfsg/src/bin/makeauto.sh-23-# required for library installation path
vmatch-2.3.1+dfsg/src/bin/makeauto.sh:24:PATHEND=`grep 'PATHEND=' ${WORKVSTREESRC}/Makedef | sed -e 's/PATHEND=//'`
vmatch-2.3.1+dfsg/src/bin/makeauto.sh-25-
##############################################
vmatch-2.3.1+dfsg/src/bin/makedep.pl-23-
vmatch-2.3.1+dfsg/src/bin/makedep.pl:24:my($retcode) = system($argstring);
vmatch-2.3.1+dfsg/src/bin/makedep.pl-25-$retcode = $? >> 8;
##############################################
vmatch-2.3.1+dfsg/src/bin/makedep.pl-45-
vmatch-2.3.1+dfsg/src/bin/makedep.pl:46:$retcode = system($gcccall);
vmatch-2.3.1+dfsg/src/bin/makedep.pl-47-$retcode = $? >> 8;
##############################################
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh-9-len=10
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh:10:filelen=`expr 10000 \* $1`
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh-11-oneFE.rand.x acgt $filelen
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh:12:seqs=`onePE.rand.x R${filelen}acgt $1 20`
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh-13-for seq in $seqs
##############################################
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh-15- printf ">seq%s\n%*.*s\n" $i $len $len $seq
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh:16: len=`expr $len + 1`
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh:17: i=`expr $i + 1`
vmatch-2.3.1+dfsg/src/bin/mkrandfast.sh-18- if test $len -gt 20
##############################################
vmatch-2.3.1+dfsg/src/bin/mkvtreeall.sh-15-
vmatch-2.3.1+dfsg/src/bin/mkvtreeall.sh:16:indexname="`basename $2`"
vmatch-2.3.1+dfsg/src/bin/mkvtreeall.sh-17-
##############################################
vmatch-2.3.1+dfsg/src/bin/runVmatchprog.sh-24-else
vmatch-2.3.1+dfsg/src/bin/runVmatchprog.sh:25: execfile=`echo ${execfile} | sed -e 's/XXX$//'`
vmatch-2.3.1+dfsg/src/bin/runVmatchprog.sh:26: archi=`binarypath.sh ${execfile}`
vmatch-2.3.1+dfsg/src/bin/runVmatchprog.sh-27- cmd="${BINDIRROOT}/${archi}/${prog} $*"
##############################################
vmatch-2.3.1+dfsg/src/bin/sparcidentify.sh-23- then
vmatch-2.3.1+dfsg/src/bin/sparcidentify.sh:24: testfile="`ar t ${idfile} | head -n 1`"
vmatch-2.3.1+dfsg/src/bin/sparcidentify.sh-25- cmd="ar x ${idfile} ${testfile}"
##############################################
vmatch-2.3.1+dfsg/src/bin/sparcidentify.sh-54-fi
vmatch-2.3.1+dfsg/src/bin/sparcidentify.sh:55:filestring="`file ${testfile} | sed -e 's/,//g' -e 's/V9//' | ${AWK} '{print $3 \"-\" $6}'`"
vmatch-2.3.1+dfsg/src/bin/sparcidentify.sh-56-if test ${removetestfile} -eq 1
##############################################
vmatch-2.3.1+dfsg/src/bin/vcopy.sh-12- else
vmatch-2.3.1+dfsg/src/bin/vcopy.sh:13: cp -i `vpathkern.sh ${filename}` .
vmatch-2.3.1+dfsg/src/bin/vcopy.sh-14- fi
##############################################
vmatch-2.3.1+dfsg/src/bin/vcopyall.sh-20-do
vmatch-2.3.1+dfsg/src/bin/vcopyall.sh:21: vstreepath=`vpathkern.sh $filename`
vmatch-2.3.1+dfsg/src/bin/vcopyall.sh-22- cmp -s $vstreepath $filename
##############################################
vmatch-2.3.1+dfsg/src/bin/vgrep.sh-6-fi
vmatch-2.3.1+dfsg/src/bin/vgrep.sh:7:egrep $* -d skip `${DIRVSTREE}/src/vstree/src/bin/vstreefiles.sh`
##############################################
vmatch-2.3.1+dfsg/src/bin/vgrepsrc.sh-6-fi
vmatch-2.3.1+dfsg/src/bin/vgrepsrc.sh:7:egrep $* -d skip `${DIRVSTREE}/src/vstree/src/bin/vstreecsrc.sh`
##############################################
vmatch-2.3.1+dfsg/src/bin/vmenvvar.sh-21-
vmatch-2.3.1+dfsg/src/bin/vmenvvar.sh:22:for envvar in `cat ${TMPFILE}`
vmatch-2.3.1+dfsg/src/bin/vmenvvar.sh-23-do
vmatch-2.3.1+dfsg/src/bin/vmenvvar.sh:24: setval="`env | grep ${envvar}`"
vmatch-2.3.1+dfsg/src/bin/vmenvvar.sh-25- if test $? -eq 0
##############################################
vmatch-2.3.1+dfsg/src/bin/vpath.sh-16-FINDCALL="find ${DIRVSTREE}/src/vstree/${subdir} -name ${inputfile}"
vmatch-2.3.1+dfsg/src/bin/vpath.sh:17:numofpaths=`${FINDCALL} | grep -v SELECT | wc -l`
vmatch-2.3.1+dfsg/src/bin/vpath.sh-18-if test ${numofpaths} -eq 0
##############################################
vmatch-2.3.1+dfsg/src/bin/mklink.sh-31-cmd="make -f ${TMPFILE}"
vmatch-2.3.1+dfsg/src/bin/mklink.sh:32:CFLAGS=`${cmd}`
vmatch-2.3.1+dfsg/src/bin/mklink.sh-33-
##############################################
vmatch-2.3.1+dfsg/src/bin/vmrelease.sh-38-#define ${PROGRAM}RELEASEDATE "2007-Aug-27"
vmatch-2.3.1+dfsg/src/bin/vmrelease.sh:39:#define ${PROGRAM}VERSION "`cat ${WORKVSTREESRC}/VERSION`"
vmatch-2.3.1+dfsg/src/bin/vmrelease.sh-40-#define ${PROGRAM}COMPILEHOST "${HOSTNAME}"
##############################################
vmatch-2.3.1+dfsg/src/doc/callmkvall.pl-38- print $argstring, "\n";
vmatch-2.3.1+dfsg/src/doc/callmkvall.pl:39: my($retcode) = system($argstring);
vmatch-2.3.1+dfsg/src/doc/callmkvall.pl-40- $retcode = $? >> 8;
##############################################
vmatch-2.3.1+dfsg/src/doc/execcommand.pl-96- print STDERR "run $argstring\n";
vmatch-2.3.1+dfsg/src/doc/execcommand.pl:97: my($retcode) = system($argstring);
vmatch-2.3.1+dfsg/src/doc/execcommand.pl-98- $retcode = $? >> 8;
##############################################
vmatch-2.3.1+dfsg/src/doc/findemptyoutfiles.sh-4-do
vmatch-2.3.1+dfsg/src/doc/findemptyoutfiles.sh:5: filesize=`cat ${filename} | wc -l`
vmatch-2.3.1+dfsg/src/doc/findemptyoutfiles.sh-6- if test $filesize -eq 1
##############################################
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh-43- then
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh:44: for pathname in `cat ${specialpathfile}`
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh-45- do
##############################################
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh-54- cmd="vpathkern.sh ${filename}"
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh:55: filepath=`${cmd}`
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh-56- checkcmd
##############################################
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh-58- echo "filepath=${filepath}"
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh:59: ending=`echo ${filename} | tail -c 3`
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh-60- if test "${ending}" = ".c"
##############################################
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org-35- then
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org:36: filepath=`grep ${filename} ${specialfile}`
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org-37- if test $? -ne 0
##############################################
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org-39- cmd="vpath.sh ${filename}"
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org:40: filepath=`${cmd}`
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org-41- checkcmd
##############################################
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org-44- cmd="vpath.sh ${filename}"
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org:45: filepath=`${cmd}`
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org-46- checkcmd
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org-47- fi
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org:48: ending=`echo ${filename} | tail -c 3`
vmatch-2.3.1+dfsg/src/doc/libdoc/Geninc.sh.org-49- if test "${ending}" = ".c"
##############################################
vmatch-2.3.1+dfsg/src/kurtz/libtest/Checkflychain.sh-23-
vmatch-2.3.1+dfsg/src/kurtz/libtest/Checkflychain.sh:24:indexname=`basename ${referencefile}`
vmatch-2.3.1+dfsg/src/kurtz/libtest/Checkflychain.sh-25-tables="-tis -suf -bck -lcp -sti1"
##############################################
vmatch-2.3.1+dfsg/src/kurtz/libtest/Itercheckmini.sh-25- checkerror
vmatch-2.3.1+dfsg/src/kurtz/libtest/Itercheckmini.sh:26: leastlength=`expr ${leastlength} + 1`
vmatch-2.3.1+dfsg/src/kurtz/libtest/Itercheckmini.sh-27- done
##############################################
vmatch-2.3.1+dfsg/src/kurtz/libtest/Itercheckmini.sh-42- checkerror
vmatch-2.3.1+dfsg/src/kurtz/libtest/Itercheckmini.sh:43: leastlength=`expr ${leastlength} + 1`
vmatch-2.3.1+dfsg/src/kurtz/libtest/Itercheckmini.sh-44- done
##############################################
vmatch-2.3.1+dfsg/src/kurtz/libtest/Iterfly.sh-21-echo "----------$0-------------"
vmatch-2.3.1+dfsg/src/kurtz/libtest/Iterfly.sh:22:seqs=`ls ${GRUMBACH}/[a-z]*.fna`
vmatch-2.3.1+dfsg/src/kurtz/libtest/Iterfly.sh-23-
##############################################
vmatch-2.3.1+dfsg/src/kurtz/libtest/Iterfly.sh-29- then
vmatch-2.3.1+dfsg/src/kurtz/libtest/Iterfly.sh:30: echo "`basename $filenameA` `basename $filenameB` $leastlength"
vmatch-2.3.1+dfsg/src/kurtz/libtest/Iterfly.sh-31- cmd="Checkflychain.sh ${qvalue} ${edistvalue} $filenameA $filenameB"
##############################################
vmatch-2.3.1+dfsg/src/kurtz/libtest/checkmygzip.sh-19-
vmatch-2.3.1+dfsg/src/kurtz/libtest/checkmygzip.sh:20:for filename in `find ${directory} -type f -print`
vmatch-2.3.1+dfsg/src/kurtz/libtest/checkmygzip.sh-21-do
##############################################
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-143- DEBUG3(3,"# inssort(%lu,%lu,%lu)=",
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:144: (Showuint) ADDR(left),
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:145: (Showuint) ADDR(right),
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-146- (Showuint) depth);
##############################################
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-180- DEBUG4(3,"# bese(%lu,%lu,%lu,base=%lu)\n",
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:181: (Showuint) ADDR(l),
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:182: (Showuint) ADDR(r),
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-183- (Showuint) d,
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:184: (Showuint) ADDR(lcpbase));
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-185-*/
##############################################
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-260- DEBUG2(3,"# left=%lu,right=%lu,",
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:261: (Showuint) ADDR(left),
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:262: (Showuint) ADDR(right));
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-263- DEBUG2(3,"a=%lu,b=%lu,",
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:264: (Showuint) ADDR(pa),
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:265: (Showuint) ADDR(pb));
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-266- DEBUG2(3,"c=%lu,d=%lu\n",
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:267: (Showuint) ADDR(pc),
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c:268: (Showuint) ADDR(pd));
vmatch-2.3.1+dfsg/src/kurtz/sortstrings.c-269-*/
##############################################
vmatch-2.3.1+dfsg/src/Makefile-7-endif
vmatch-2.3.1+dfsg/src/Makefile:8:VERSION:="`cat $(CURDIR)/VERSION`"
vmatch-2.3.1+dfsg/src/Makefile-9-VMATCHDISTBASENAME:="vmatch"
##############################################
vmatch-2.3.1+dfsg/debian/patches/common-distdir.patch-8- endif
vmatch-2.3.1+dfsg/debian/patches/common-distdir.patch:9: VERSION:="`cat $(CURDIR)/VERSION`"
vmatch-2.3.1+dfsg/debian/patches/common-distdir.patch-10--SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
##############################################
vmatch-2.3.1+dfsg/debian/patches/hardening.patch-44- cmd="make -f ${TMPFILE}"
vmatch-2.3.1+dfsg/debian/patches/hardening.patch:45: CFLAGS=`${cmd}`
vmatch-2.3.1+dfsg/debian/patches/hardening.patch-46-
##############################################
vmatch-2.3.1+dfsg/debian/patches/reproducible-build.patch-26- #define ${PROGRAM}RELEASEDATE "2007-Aug-27"
vmatch-2.3.1+dfsg/debian/patches/reproducible-build.patch:27: #define ${PROGRAM}VERSION "`cat ${WORKVSTREESRC}/VERSION`"
vmatch-2.3.1+dfsg/debian/patches/reproducible-build.patch-28--#define ${PROGRAM}COMPILEHOST "`hostname`"
##############################################
vmatch-2.3.1+dfsg/.pc/no-symlink.patch/src/bin/mklink.sh-31-cmd="make -f ${TMPFILE}"
vmatch-2.3.1+dfsg/.pc/no-symlink.patch/src/bin/mklink.sh:32:CFLAGS=`${cmd}`
vmatch-2.3.1+dfsg/.pc/no-symlink.patch/src/bin/mklink.sh-33-
##############################################
vmatch-2.3.1+dfsg/.pc/common-distdir.patch/src/Makefile-7-endif
vmatch-2.3.1+dfsg/.pc/common-distdir.patch/src/Makefile:8:VERSION:="`cat $(CURDIR)/VERSION`"
vmatch-2.3.1+dfsg/.pc/common-distdir.patch/src/Makefile-9-SYSTEMNAME:="$(SYSTEM)_$(MACHINE)"
##############################################
vmatch-2.3.1+dfsg/.pc/skip-doc-installation.patch/src/Makefile-7-endif
vmatch-2.3.1+dfsg/.pc/skip-doc-installation.patch/src/Makefile:8:VERSION:="`cat $(CURDIR)/VERSION`"
vmatch-2.3.1+dfsg/.pc/skip-doc-installation.patch/src/Makefile-9-VMATCHDISTBASENAME:="vmatch"
##############################################
vmatch-2.3.1+dfsg/.pc/hardening.patch/src/bin/mklink.sh-31-cmd="make -f ${TMPFILE}"
vmatch-2.3.1+dfsg/.pc/hardening.patch/src/bin/mklink.sh:32:CFLAGS=`${cmd}`
vmatch-2.3.1+dfsg/.pc/hardening.patch/src/bin/mklink.sh-33-
##############################################
vmatch-2.3.1+dfsg/.pc/reproducible-build.patch/src/bin/vmrelease.sh-31-#define ${PROGRAM}RELEASEDATE "2007-Aug-27"
vmatch-2.3.1+dfsg/.pc/reproducible-build.patch/src/bin/vmrelease.sh:32:#define ${PROGRAM}VERSION "`cat ${WORKVSTREESRC}/VERSION`"
vmatch-2.3.1+dfsg/.pc/reproducible-build.patch/src/bin/vmrelease.sh-33-#define ${PROGRAM}COMPILEHOST "`hostname`"