File: inefficient-merger-for-testing

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python-pairix 0.3.8-1
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#!/bin/bash

outdir=$1; shift
outprefix=$1; shift
type=$1; shift

[ -d $outdir ] || mkdir -p $outdir

rm -f $outdir/$outprefix.pairs
touch $outdir/$outprefix.pairs
for input_pair in $@
do
  gunzip -c $input_pair >> $outdir/$outprefix.pairs
done


if [ "$type" == "pairs" ]; then
 sort -k2,2 -k4,4 -k3,3g -k5,5g $outdir/$outprefix.pairs | bin/bgzip -fc > $outdir/$outprefix.bsorted.pairs.gz
 bin/pairix -f $outdir/$outprefix.bsorted.pairs.gz
elif [ "$type" == "merged_nodups" ]; then
 sort -t' ' -k2,2 -k6,6 -k3,3g -k7,7g $outdir/$outprefix.pairs | bin/bgzip -fc > $outdir/$outprefix.bsorted.pairs.gz
 bin/pairix -f -p merged_nodups $outdir/$outprefix.bsorted.pairs.gz
elif [ "$type" == "old_merged_nodups" ]; then
 sort -t' ' -k3,3 -k7,7 -k4,4g -k8,8g $outdir/$outprefix.pairs | bin/bgzip -fc > $outdir/$outprefix.bsorted.pairs.gz
 bin/pairix -f -p old_merged_nodups $outdir/$outprefix.bsorted.pairs.gz
fi