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_________________ __ __ __| _/|__|/ |_
/ ___\_` __ \__ \ | | \/ __ | | \\_ __\
/ /_/ > | \// __ \| | / /_/ | | || |
\___ /|__| (____ /____/\____ | |__||__|
/_____/ \/ \/
grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pe.sh-22-
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pe.sh:23:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pe.sh:24:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pe.sh-25-
##############################################
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pe.sh-32-
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pe.sh:33:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pe.sh:34:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pe.sh-35-
##############################################
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pesr.sh-17-
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pesr.sh:18:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pesr.sh-19-
##############################################
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pesr.sh-27-
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pesr.sh:28:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pesr.sh:29:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_pesr.sh-30-
##############################################
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_sr.sh-16-
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_sr.sh:17:OUT_FILE=`basename $SR_BAM .bam`
lumpy-sv-0.3.1+dfsg/lumpy_tests/orig/bp_sr.sh-18-
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-14-
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:15:export LUMPY_HOME=`dirname $DIR`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-16-
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-19- cat << EOF
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:20: usage: `basename $0` OPTIONS bam,cnv(opt.) bam,cnv(opt.) ...
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-21-
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-119- if [ "$(uname)" == "Darwin" ]; then
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:120: ID=`$SAMTOOLS view -H $BAM | grep "^@RG" | grep -o "SM:\w*" | cut -d":" -f2 | sort -u`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-121- else
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:122: ID=`$SAMTOOLS view -H $BAM | grep "^@RG" | grep -oP "SM:[^\s]*" | cut -d":" -f2 | sort -u`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-123- fi
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-124-
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:125: RG_NUM=`echo -e $ID | wc -l`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-126- if [ "$RG_NUM" -ne "1" ]; then
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-191- if [ "$(uname)" == "Darwin" ]; then
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:192: ID=`$SAMTOOLS view -H $BAM | grep "^@RG" | grep -o "SM:\w*" | cut -d":" -f2 | sort -u`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-193- else
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:194: ID=`$SAMTOOLS view -H $BAM | grep "^@RG" | grep -oP "SM:[^\s]*" | cut -d":" -f2 | sort -u`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-195- fi
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-196-
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:197: RG_NUM=`echo -e $ID | wc -l`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-198- if [ "$RG_NUM" -ne "1" ]; then
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-235-
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:236: MEAN=`cat $OUTDIR/$ID.stats | tail -n 1| cut -f1 | cut -d":" -f2`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth:237: STD=`cat $OUTDIR/$ID.stats | tail -n 1| cut -f2 | cut -d":" -f2`
lumpy-sv-0.3.1+dfsg/scripts/lumpy_smooth-238- PE_PARAM="-pe id:$ID,bam_file:$OUTDIR/$ID.disc.bam,histo_file:$OUTDIR/$ID.histo,mean:$MEAN,stdev:$STD,read_length:$READ_LENGTH,min_non_overlap:$READ_LENGTH,discordant_z:4,back_distance:20,weight:1,min_mapping_threshold:20 "
##############################################
lumpy-sv-0.3.1+dfsg/scripts/run_histo.sh-27-
lumpy-sv-0.3.1+dfsg/scripts/run_histo.sh:28:SCRIPT_DIR=`dirname $0`
lumpy-sv-0.3.1+dfsg/scripts/run_histo.sh-29-
##############################################
lumpy-sv-0.3.1+dfsg/scripts/run_histo.sh-36-
lumpy-sv-0.3.1+dfsg/scripts/run_histo.sh:37:MEAN=`echo $OUT | cut -d" " -f1 | cut -d":" -f2`
lumpy-sv-0.3.1+dfsg/scripts/run_histo.sh:38:STDEV=`echo $OUT | cut -d" " -f2 | cut -d":" -f2`
lumpy-sv-0.3.1+dfsg/scripts/run_histo.sh-39-
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-127-# set defaults
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:128:LUMPY_DIR=`dirname $0`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-129-CONFIG="/etc/lumpy-sv/lumpyexpress.config"
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-307-then
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:308: OUTPUT=`basename "${FULL_BAM_LIST[0]}"`.vcf
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-309-fi
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:310:OUTBASE=`basename "$OUTPUT"`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-311-
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-319-then
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:320: TEMP_DIR=`mktemp -d ${OUTBASE}.XXXXXXXXXXXX`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-321-else
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-361- set +o pipefail
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:362: READ_LENGTH=`$SAMT view $EXT_OPT $FULL_BAM | head -n 10000 | gawk 'BEGIN { MAX_LEN=0 } { LEN=length($10); if (LEN>MAX_LEN) MAX_LEN=LEN } END { print MAX_LEN }'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-363- set -o pipefail
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-365- # parse the libraries in the BAM header to extract readgroups from the same library
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:366: LIB_RG_LIST=(`$PYTHON $BAMLIBS $FULL_BAM`)
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-367-
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-403- DISC_BAM=$TEMP_DIR/$OUTBASE.sample$(($i+1)).discordants.bam
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:404: DISC_SAMPLE=`$SAMT view $EXT_OPT -H $FULL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:405: RG_STRING=`echo "${LIB_RG_LIST[$j]}" | sed 's/,/,read_group:/g' | sed 's/^/read_group:/g'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:406: MEAN=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^mean" | sed 's/mean\://g'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:407: STDEV=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^stdev" | sed 's/stdev\://g'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-408- LUMPY_DISC_STRING="$LUMPY_DISC_STRING -pe bam_file:${DISC_BAM},histo_file:${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).x4.histo,mean:${MEAN},stdev:${STDEV},read_length:${READ_LENGTH},min_non_overlap:${READ_LENGTH},discordant_z:5,back_distance:10,weight:1,id:${DISC_SAMPLE},min_mapping_threshold:20,${RG_STRING}"
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-411- SPL_BAM=$TEMP_DIR/$OUTBASE.sample$(($i+1)).splitters.bam
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:412: SPL_SAMPLE=`$SAMT view $EXT_OPT -H $FULL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-413- LUMPY_SPL_STRING="$LUMPY_SPL_STRING -sr bam_file:${SPL_BAM},back_distance:10,min_mapping_threshold:20,weight:1,id:${SPL_SAMPLE},min_clip:20,${RG_STRING}"
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-461- # These elements are comma delimited strings for the readgroups for each library.
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:462: LIB_RG_LIST=(`$PYTHON $BAMLIBS ${FULL_BAM_LIST[$i]}`)
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-463-
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-475- set +o pipefail
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:476: LIB_READ_LENGTH_LIST+=(`$SAMT view $EXT_OPT ${FULL_BAM_LIST[$i]} | head -n 10000 | gawk 'BEGIN { MAX_LEN=0 } { LEN=length($10); if (LEN>MAX_LEN) MAX_LEN=LEN } END { print MAX_LEN }'`)
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-477- echo "Library read groups: ${LIB_RG_LIST[$j]}"
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-489- # construct LUMPY_SPL_STRING
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:490: SPL_SAMPLE=`$SAMT view -H $SPL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-491- LUMPY_SPL_STRING="$LUMPY_SPL_STRING -sr bam_file:${SPL_BAM},back_distance:10,min_mapping_threshold:20,weight:1,id:${SPL_SAMPLE},min_clip:20"
##############################################
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-497- DISC_BAM=${DISC_BAM_LIST[$i]}
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:498: DISC_SAMPLE=`$SAMT view -H $DISC_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:499: MEAN=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^mean" | sed 's/mean\://g'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:500: STDEV=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^stdev" | sed 's/stdev\://g'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress:501: RG_STRING=`echo "${LIB_RG_LIST[$j]}" | sed 's/,/,read_group:/g' | sed 's/^/read_group:/g'`
lumpy-sv-0.3.1+dfsg/scripts/lumpyexpress-502-
##############################################
lumpy-sv-0.3.1+dfsg/test/functional-test.sh-28-
lumpy-sv-0.3.1+dfsg/test/functional-test.sh:29:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/test/functional-test.sh:30:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/test/functional-test.sh-31-
##############################################
lumpy-sv-0.3.1+dfsg/test/functional-test.sh-39-
lumpy-sv-0.3.1+dfsg/test/functional-test.sh:40:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/functional-test.sh:41:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/functional-test.sh-42-
##############################################
lumpy-sv-0.3.1+dfsg/test/functional-test.sh-54-then
lumpy-sv-0.3.1+dfsg/test/functional-test.sh:55: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/test/functional-test.sh-56-
lumpy-sv-0.3.1+dfsg/test/functional-test.sh:57: O=`cat $OUT_DIR/$OUT_FILE.pesr.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/test/functional-test.sh-58-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh-17-
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh:18:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh:19:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh-20-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh-28-
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh:29:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh:30:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh-31-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh-41-then
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh:42: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh-43-
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh:44: O=`cat $OUT_DIR/$OUT_FILE.pe.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_pe.sh-45-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh-17-
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh:18:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh:19:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh-20-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh-28-
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh:29:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh:30:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh-31-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh-40-then
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh:41: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh-42-
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh:43: O=`cat $OUT_DIR/$OUT_FILE.pe.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_pe_pl.sh-44-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh-18-
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh:19:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh:20:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh-21-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh-29-
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh:30:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh:31:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh-32-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh-44-then
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh:45: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh-46-
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh:47: O=`cat $OUT_DIR/$OUT_FILE.pesr.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_pesr.sh-48-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh-18-
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh:19:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh:20:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh-21-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh-29-
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh:30:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh:31:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh-32-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh-43-then
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh:44: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh-45-
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh:46: O=`cat $OUT_DIR/$OUT_FILE.pesr.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_pesr_pl.sh-47-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh-17-
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh:18:OUT_DIR=`dirname $SR_BAM`
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh:19:OUT_FILE=`basename $SR_BAM .bam`
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh-20-
##############################################
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh-30-then
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh:31: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh-32-
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh:33: O=`cat $OUT_DIR/$OUT_FILE.sr.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/test/bp_sr.sh-34-
##############################################
lumpy-sv-0.3.1+dfsg/debian/createmanpages-4-
lumpy-sv-0.3.1+dfsg/debian/createmanpages:5:VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
lumpy-sv-0.3.1+dfsg/debian/createmanpages-6-NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
##############################################
lumpy-sv-0.3.1+dfsg/debian/patches/lumpyexpress.config.patch-37- # set defaults
lumpy-sv-0.3.1+dfsg/debian/patches/lumpyexpress.config.patch:38: LUMPY_DIR=`dirname $0`
lumpy-sv-0.3.1+dfsg/debian/patches/lumpyexpress.config.patch-39--CONFIG="$LUMPY_DIR/lumpyexpress.config"
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-127-# set defaults
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:128:LUMPY_DIR=`dirname $0`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-129-CONFIG="$LUMPY_DIR/lumpyexpress.config"
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-307-then
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:308: OUTPUT=`basename "${FULL_BAM_LIST[0]}"`.vcf
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-309-fi
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:310:OUTBASE=`basename "$OUTPUT"`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-311-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-319-then
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:320: TEMP_DIR=`mktemp -d ${OUTBASE}.XXXXXXXXXXXX`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-321-else
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-361- set +o pipefail
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:362: READ_LENGTH=`$SAMT view $EXT_OPT $FULL_BAM | head -n 10000 | gawk 'BEGIN { MAX_LEN=0 } { LEN=length($10); if (LEN>MAX_LEN) MAX_LEN=LEN } END { print MAX_LEN }'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-363- set -o pipefail
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-365- # parse the libraries in the BAM header to extract readgroups from the same library
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:366: LIB_RG_LIST=(`$PYTHON $BAMLIBS $FULL_BAM`)
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-367-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-403- DISC_BAM=$TEMP_DIR/$OUTBASE.sample$(($i+1)).discordants.bam
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:404: DISC_SAMPLE=`$SAMT view $EXT_OPT -H $FULL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:405: RG_STRING=`echo "${LIB_RG_LIST[$j]}" | sed 's/,/,read_group:/g' | sed 's/^/read_group:/g'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:406: MEAN=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^mean" | sed 's/mean\://g'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:407: STDEV=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^stdev" | sed 's/stdev\://g'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-408- LUMPY_DISC_STRING="$LUMPY_DISC_STRING -pe bam_file:${DISC_BAM},histo_file:${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).x4.histo,mean:${MEAN},stdev:${STDEV},read_length:${READ_LENGTH},min_non_overlap:${READ_LENGTH},discordant_z:5,back_distance:10,weight:1,id:${DISC_SAMPLE},min_mapping_threshold:20,${RG_STRING}"
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-411- SPL_BAM=$TEMP_DIR/$OUTBASE.sample$(($i+1)).splitters.bam
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:412: SPL_SAMPLE=`$SAMT view $EXT_OPT -H $FULL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-413- LUMPY_SPL_STRING="$LUMPY_SPL_STRING -sr bam_file:${SPL_BAM},back_distance:10,min_mapping_threshold:20,weight:1,id:${SPL_SAMPLE},min_clip:20,${RG_STRING}"
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-461- # These elements are comma delimited strings for the readgroups for each library.
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:462: LIB_RG_LIST=(`$PYTHON $BAMLIBS ${FULL_BAM_LIST[$i]}`)
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-463-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-475- set +o pipefail
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:476: LIB_READ_LENGTH_LIST+=(`$SAMT view $EXT_OPT ${FULL_BAM_LIST[$i]} | head -n 10000 | gawk 'BEGIN { MAX_LEN=0 } { LEN=length($10); if (LEN>MAX_LEN) MAX_LEN=LEN } END { print MAX_LEN }'`)
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-477- echo "Library read groups: ${LIB_RG_LIST[$j]}"
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-489- # construct LUMPY_SPL_STRING
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:490: SPL_SAMPLE=`$SAMT view -H $SPL_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-491- LUMPY_SPL_STRING="$LUMPY_SPL_STRING -sr bam_file:${SPL_BAM},back_distance:10,min_mapping_threshold:20,weight:1,id:${SPL_SAMPLE},min_clip:20"
##############################################
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-497- DISC_BAM=${DISC_BAM_LIST[$i]}
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:498: DISC_SAMPLE=`$SAMT view -H $DISC_BAM | grep -m 1 "^@RG" | gawk -v i=$i '{ for (j=1;j<=NF;++j) {if ($j~"^SM:") { gsub("^SM:","",$j); print $j } } }'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:499: MEAN=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^mean" | sed 's/mean\://g'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:500: STDEV=`cat ${TEMP_DIR}/$OUTBASE.sample$(($i+1)).lib$(($j+1)).insert.stats | tr '\t' '\n' | grep "^stdev" | sed 's/stdev\://g'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress:501: RG_STRING=`echo "${LIB_RG_LIST[$j]}" | sed 's/,/,read_group:/g' | sed 's/^/read_group:/g'`
lumpy-sv-0.3.1+dfsg/.pc/lumpyexpress.config.patch/scripts/lumpyexpress-502-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh-17-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh:18:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh:19:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh-20-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh-28-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh:29:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh:30:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh-31-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh-41-then
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh:42: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh-43-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh:44: O=`cat $OUT_DIR/$OUT_FILE.pe.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe.sh-45-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh-17-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh:18:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh:19:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh-20-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh-28-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh:29:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh:30:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh-31-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh-40-then
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh:41: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh-42-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh:43: O=`cat $OUT_DIR/$OUT_FILE.pe.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pe_pl.sh-44-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh-18-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh:19:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh:20:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh-21-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh-29-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh:30:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh:31:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh-32-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh-44-then
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh:45: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh-46-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh:47: O=`cat $OUT_DIR/$OUT_FILE.pesr.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr.sh-48-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh-18-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh:19:OUT_DIR=`dirname $PE_BAM`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh:20:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh-21-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh-29-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh:30:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh:31:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh-32-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh-43-then
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh:44: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh-45-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh:46: O=`cat $OUT_DIR/$OUT_FILE.pesr.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_pesr_pl.sh-47-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh-17-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh:18:OUT_DIR=`dirname $SR_BAM`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh:19:OUT_FILE=`basename $SR_BAM .bam`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh-20-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh-30-then
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh:31: EX=`cat $E | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh-32-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh:33: O=`cat $OUT_DIR/$OUT_FILE.sr.bedpe | wc -l`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/test/bp_sr.sh-34-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_pesr.sh-17-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_pesr.sh:18:OUT_FILE=`basename $PE_BAM .bam`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_pesr.sh-19-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_pesr.sh-27-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_pesr.sh:28:MEAN=`echo $MEAN_STDEV | cut -d " " -f1 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_pesr.sh:29:STDEV=`echo $MEAN_STDEV | cut -d " " -f2 | cut -d ":" -f2`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_pesr.sh-30-
##############################################
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_sr.sh-16-
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_sr.sh:17:OUT_FILE=`basename $SR_BAM .bam`
lumpy-sv-0.3.1+dfsg/.pc/fix_shebang.patch/lumpy_tests/orig/bp_sr.sh-18-