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dont append when splitting and clean-up gen-vcfs #180

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dont append when splitting and clean-up gen-vcfs #180

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a5fd36a
dont append when splitting and clean-up gen-vcfs
brentp Mar 22, 2017
db68c32
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brentp Mar 23, 2017
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dont append when splitting and clean-up gen-vcfs
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@brentp
brentp committed Mar 23, 2017
commit a5fd36a7f54572dc0e84460ccbb719183b762ee2
2 changes: 1 addition & 1 deletion scripts/lumpy_smooth
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Original file line number Diff line number Diff line change
Expand Up @@ -270,7 +270,7 @@ fi
export -f BAM_PREP
echo -en $BAMS | xargs -I{} -P $THREADS bash -c "BAM_PREP {}"

export GLOBAL_LUMPY="$LUMPY_HOME/bin/lumpy -mw 4 -t $(mktemp) -tt 0 -P $EXCLUDE "
export GLOBAL_LUMPY="$LUMPY_HOME/bin/lumpy -mw 4 -t $(mktemp) -tt 0 $EXCLUDE "

for SAMPLE_CSV in ${OPTS[@]:$((OPTIND - 1))}; do
SAMPLE_ARRAY=(${SAMPLE_CSV//,/ })
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45 changes: 24 additions & 21 deletions scripts/par-svtyper.sh
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Expand Up @@ -20,27 +20,29 @@ export -f svtpar

genvcfs() {
set -euo pipefail
bams=$1
nth=0
tmpvcf=$TMPDIR/tmp.$$.$nth.vcf
echo -e "$header" > $tmpvcf
k=0
lines=$1
vcf=$2
set +e
header="$(less $vcf | head -2000 | grep ^#)"
set -e
# run this once to force the calculation of the bam stats.
# this avoids a race condition.
svtpar <(echo -e "$header")
while read -r line || [[ -n "$line" ]]; do
k=$((k + 1))
echo -e "$line" >> $tmpvcf
if [[ "$k" -eq "$LINES" ]]; then
# echo the bam and the vcf so they can be sent to svtyper.
echo "$tmpvcf"
nth=$((nth + 1))
tmpvcf=$TMPDIR/tmp.$$.$nth.vcf
echo -e "$header" > $tmpvcf
k=0;
fi
done < "$vcf"
echo "$tmpvcf"

zless "$vcf" | awk -vtmp=$TMPDIR -vtmpvcf="$TMPDIR/0.tmp.$$.vcf" -vpid=$$ -v header="$header" -vLINES=$lines 'BEGIN{nth=1;} !((NR - 1) % LINES) {
# we print the tmpvcf and move onto the next.
if(NR > 1) {
print tmpvcf;
}
tmpvcf=tmp"/"nth".tmp."pid".vcf.gz"
print header > tmpvcf;
nth+=1;
}
{
print $0 > tmpvcf;
}
END {
print tmpvcf;
}'
}

vcfsort() {
Expand All @@ -56,7 +58,7 @@ fi
export mypid=$$

cleanup() {
rm -f $TMPDIR/tmp.$mypid.*.vcf
rm -f $TMPDIR/*.$mypid.vcf*
rm -f $TMPDIR/tmp.$mypid.*.lib
}

Expand All @@ -78,7 +80,8 @@ type gargs >/dev/null 2>&1 || {
psvtyper() {
set -euo pipefail
export header=$(head -2000 $vcf | grep ^#)
genvcfs $bams | gargs -p $THREADS "svtpar {}" | vcfsort
svtpar <(echo -e "$header")
genvcfs $LINES $vcf | gargs -p $THREADS "svtpar {}" | vcfsort
}

mkdir -p $TMPDIR
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