runBamstat.sh.bak

if [ $# -eq 4 ]; then

BAMFILE=$1
STATSDIR=$2
DISTANCE=$3
MAPQ=$4

echo Saving stats on `pwd`/$BAMFILE to `pwd`/$STATSDIR

mkdir $STATSDIR
cd $STATSDIR

/shr/home/cc472/code/bamstat/bamstat -b -i ../$BAMFILE

sort -k2,2 -k5,5 -k3n,3n translocPairs.txt > translocPairs.sorted.txt
/shr/home/ah644/code/mgh/cluster/readPairCluster -u -d $DISTANCE -s 3 -q $MAPQ -r translocPairs.sorted.txt > translocClusters_d${DISTANCE}_q${MAPQ}.txt

sort -k2,2 -k5,5 -k3n,3n inversionPairs.txt > inversionPairs.sorted.txt
/shr/home/ah644/code/mgh/cluster/readPairCluster -u -d $DISTANCE -s 3 -q $MAPQ -r inversionPairs.sorted.txt > inversionClusters_d${DISTANCE}_q${MAPQ}.txt

sort -k2,2 -k5,5 -k3n,3n deletionPairs.txt > deletionPairs.sorted.txt
/shr/home/ah644/code/mgh/cluster/readPairCluster -u -d $DISTANCE -s 3 -q $MAPQ -r deletionPairs.sorted.txt > deletionClusters_d${DISTANCE}_q${MAPQ}.txt

MAPQ=20

/shr/home/ah644/code/mgh/cluster/readPairCluster -u -d $DISTANCE -s 3 -q $MAPQ -r translocPairs.sorted.txt > translocClusters_d${DISTANCE}_q${MAPQ}.txt
/shr/home/ah644/code/mgh/cluster/readPairCluster -u -d $DISTANCE -s 3 -q $MAPQ -r inversionPairs.sorted.txt > inversionClusters_d${DISTANCE}_q${MAPQ}.txt
/shr/home/ah644/code/mgh/cluster/readPairCluster -u -d $DISTANCE -s 3 -q $MAPQ -r deletionPairs.sorted.txt > deletionClusters_d${DISTANCE}_q${MAPQ}.txt



else
 echo "usage:"
 echo "  runStats.sh [bamfilename] [statsOuputDir] [distance] [mapQ]"
 echo ""
fi