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|
#!/bin/bash
outprefix=$1
shift
INFILESTR=${@}
INFILES=(${INFILESTR// / })
NFILES=${#INFILES[@]}
if [ $NFILES -eq 1 ]
then
cp $1 $outprefix.pairs.gz
pairix -f $outprefix.pairs.gz
else
# unzipping to named pipes
arg=''
k=1
for f in $INFILESTR
do
mkfifo pp.$k
arg="$arg pp.$k"
gunzip -c $f | grep -v '^#' > pp.$k &
let "k++"
done
# header
gunzip -c ${INFILES[0]} | grep "^#" | grep -v '^#command:' > $outprefix.pairs
for f in $INFILESTR
do
gunzip -c $f | grep '^#command:' >> $outprefix.pairs
done
# merging
sort -m -k2,2 -k4,4 -k3,3g -k5,5g $arg >> $outprefix.pairs
# compressing
bgzip -f $outprefix.pairs
# indexing
pairix -f $outprefix.pairs.gz
# clean up
k=1
for f in $INFILESTR
do
rm pp.$k
let "k++"
done
fi
|
