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|
set -euo pipefail
export vcf=$1
export bams=$2
export LINES=250
svtpar() {
set -euo pipefail
subvcf=$1
lib=$TMPDIR/tmp.$mypid.$(echo $bams | md5sum | awk '{ print $1 }').lib
svtyper -B $bams -i $subvcf -l $lib
# vcf is a temporary file so clean it up.
# but for the first time, it's and fd from the header so the rm will fail.
set +e
tail -1 $subvcf 2>/dev/null | awk '{ print "svtyped through:" $1":"$2 }' > /dev/stderr
rm -f $subvcf >/dev/null 2>&1
}
export -f svtpar
genvcfs() {
set -euo pipefail
bams=$1
nth=0
tmpvcf=$TMPDIR/tmp.$$.$nth.vcf
echo -e "$header" > $tmpvcf
k=0
# run this once to force the calculation of the bam stats.
# this avoids a race condition.
svtpar <(echo -e "$header")
while read -r line || [[ -n "$line" ]]; do
k=$((k + 1))
echo -e "$line" >> $tmpvcf
if [[ "$k" -eq "$LINES" ]]; then
# echo the bam and the vcf so they can be sent to svtyper.
echo "$tmpvcf"
nth=$((nth + 1))
tmpvcf=$TMPDIR/tmp.$$.$nth.vcf
echo -e "$header" > $tmpvcf
k=0;
fi
done < "$vcf"
echo "$tmpvcf"
}
vcfsort() {
awk 'BEGIN{x=0;} $0 ~/^#/{ if(x==0) {print;} if($1 == "#CHROM"){x=1}; next;} {x=1; print $0 | "LC_ALL=C sort --buffer-size 2G -k1,1 -k2,2n" }'
}
export -f genvcfs
if [[ -z ${TMPDIR+x} ]]; then
export TMPDIR=/tmp/
fi
export mypid=$$
cleanup() {
rm -f $TMPDIR/tmp.$mypid.*.vcf
rm -f $TMPDIR/tmp.$mypid.*.lib
}
trap cleanup EXIT
# add gargs to path
export PATH=$PATH:.
# get gargs if it doesn't exist
type gargs >/dev/null 2>&1 || {
if [ "$(uname)" == "Darwin" ]; then
wget -O gargs https://github.com/brentp/gargs/releases/download/v0.3.5/gargs_darwin
else
wget -O gargs https://github.com/brentp/gargs/releases/download/v0.3.5/gargs_linux
fi
chmod +x ./gargs
}
psvtyper() {
set -euo pipefail
export header=$(head -2000 $vcf | grep ^#)
genvcfs $bams | gargs -p $THREADS "svtpar {}" | vcfsort
}
mkdir -p $TMPDIR
export -f psvtyper
psvtyper
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