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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
abacas-1.3.1/abacas-377- {
abacas-1.3.1/abacas:378: @running = `$command --maxmatch -l $seed -p $choice $reference $query_file &> /dev/null`;
abacas-1.3.1/abacas:379: @deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
abacas-1.3.1/abacas-380- if ($is_circular == 1)
abacas-1.3.1/abacas-381- {
abacas-1.3.1/abacas:382: @coordsRes = `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
abacas-1.3.1/abacas-383- }
##############################################
abacas-1.3.1/abacas-385- {
abacas-1.3.1/abacas:386: @coordsRes = `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
abacas-1.3.1/abacas-387-
##############################################
abacas-1.3.1/abacas-391- {
abacas-1.3.1/abacas:392: @running = `$command -p $choice $reference $query_file &> /dev/null`;
abacas-1.3.1/abacas:393: @deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
abacas-1.3.1/abacas:394: if ($is_circular ==1) {@coordsRes = `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;}
abacas-1.3.1/abacas:395: else { @coordsRes = `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;}
abacas-1.3.1/abacas-396- }
##############################################
abacas-1.3.1/abacas-402- {
abacas-1.3.1/abacas:403: @running = `$command --maxmatch -l $seed -x 1 -p $choice $reference $query_file &> /dev/null`;
abacas-1.3.1/abacas:404: @deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
abacas-1.3.1/abacas-405- if ($is_circular == 1)
abacas-1.3.1/abacas-406- {
abacas-1.3.1/abacas:407: @coordsRes= `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
abacas-1.3.1/abacas-408- }
##############################################
abacas-1.3.1/abacas-410- {
abacas-1.3.1/abacas:411: @coordsRes= `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
abacas-1.3.1/abacas-412- }
##############################################
abacas-1.3.1/abacas-415- {
abacas-1.3.1/abacas:416: @running = `$command -l $seed -p $choice $reference $query_file &> /dev/null`;
abacas-1.3.1/abacas:417: @deltaRes = `$run_df -q $choice.delta >$choice.filtered.delta`;
abacas-1.3.1/abacas-418- if ($is_circular == 1) {
abacas-1.3.1/abacas:419: @coordsRes= `$run_st -c -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
abacas-1.3.1/abacas-420- }
##############################################
abacas-1.3.1/abacas-422- {
abacas-1.3.1/abacas:423: @coordsRes= `$run_st -i $min_id -v $min_cov -V $diff_cov -l $min_len -R -u unused_contigs.out $choice.filtered.delta > $choice.tiling`;
abacas-1.3.1/abacas-424- }
##############################################
abacas-1.3.1/abacas-434- my $ask = 'which';
abacas-1.3.1/abacas:435: my @check_prog = `$ask $prog`;
abacas-1.3.1/abacas-436- my $path_toPass;
##############################################
abacas-1.3.1/abacas-457- }
abacas-1.3.1/abacas:458: my @final_check = `$ask $command`;
abacas-1.3.1/abacas-459- if (exists $final_check[0] && $final_check[0] =~ /$prog$/)
##############################################
abacas-1.3.1/abacas-576- my $call ="show-coords -H -T -q $deltaName > $deltaName.coords ";
abacas-1.3.1/abacas:577: !system(" $call") or die "Problems doing the show-coords comparison: $call $!\n";
abacas-1.3.1/abacas-578-
##############################################
abacas-1.3.1/abacas-770- my $call = "$path_prog --maxmatch -c 100 -b 40 -p $name.repeats -l 25 $reference $reference &> /dev/null ";
abacas-1.3.1/abacas:771: !system("$call") or die "Problems doing the nucmer comparison: $call $!\n";
abacas-1.3.1/abacas-772- $call ="$path_coords -r -c -l $name.repeats.delta > $name.repeats.coords ";
abacas-1.3.1/abacas:773: !system(" $call") or die "Problems doing the show-coords comparison: $call $!\n";
abacas-1.3.1/abacas-774-
##############################################
abacas-1.3.1/abacas-1281-# my @formating = `
abacas-1.3.1/abacas:1282: !system("$formatdb $new_reference_file") or die "ERROR: Could not find 'formatdb' for blast\n";
abacas-1.3.1/abacas-1283- my $blast_opt = 'blastall -m 9 -p tblastx -d ';
##############################################
abacas-1.3.1/abacas-1285-# my @bigger_b = `
abacas-1.3.1/abacas:1286: !system("$blast_opt $new_reference_file -i $contigs_inBin -o blast.out") or die "ERROR: Could not find 'blastall' , please install blast in your working path (other dir==0)\n$blast_opt $new_reference_file -i $contigs_inBin -o blast.out\n \n";
abacas-1.3.1/abacas-1287- }
##############################################
abacas-1.3.1/abacas-1447-
abacas-1.3.1/abacas:1448: my @Pr3_output = `$pr3_path -format_output <data`;
abacas-1.3.1/abacas-1449- #print $positions[$i], "\t", $i, " ", $path_toPass, " ", $rf, $exc1, " ",$exc2, "\n";
##############################################
abacas-1.3.1/abacas-1527-
abacas-1.3.1/abacas:1528: my @Rrun = `$path_toPass $options -p R $rf $rq &> /dev/null`;
abacas-1.3.1/abacas-1529- print ".";
##############################################
abacas-1.3.1/abacas-1540- close (RP);
abacas-1.3.1/abacas:1541: my @Lrun = `$path_toPass $options -p L $rf $lq &> /dev/null`;
abacas-1.3.1/abacas-1542- print ".";
##############################################
abacas-1.3.1/debian/get-orig-source-4-
abacas-1.3.1/debian/get-orig-source:5:PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
abacas-1.3.1/debian/get-orig-source-6-
##############################################
abacas-1.3.1/debian/get-orig-source-8- # if called manually run uscan to obtain file and version number
abacas-1.3.1/debian/get-orig-source:9: # VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
abacas-1.3.1/debian/get-orig-source-10- VERSION=`uscan --verbose --force-download | \
##############################################
abacas-1.3.1/debian/get-orig-source-15- # If called by uscan
abacas-1.3.1/debian/get-orig-source:16: VERSION=`echo $@ | sed 's?^.*--upstream-version \([0-9.]\+\) .*abacas.*?\1?'`
abacas-1.3.1/debian/get-orig-source-17- if echo "$VERSION" | grep -q "upstream-version" ; then
##############################################
abacas-1.3.1/debian/get-orig-source-23-#if [ "$VERSION" = "" ] ; then
abacas-1.3.1/debian/get-orig-source:24:# VERSION=`ls ../${PKG}.*.pl | sed "s/.*$PKG\.\(.*\)\.pl/\1/"`
abacas-1.3.1/debian/get-orig-source-25-#fi