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bwaQsStepTwoCountReads.sh
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bwaQsStepTwoCountReads.sh
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if [ $# -lt 1 ]; then
echo $0 QThreshold
exit
fi
Qt=$1
source ~/.bashrc
source ./initvars.sh
source $configDir/bwa.config.sh
source $tophatshvar
cd ..
#Qt=${qThresholds[1]}
procDir=processed_Q$Qt
qinfix=q$Qt.SAM
cd $samseDirOutCoyote
#samples=( R2 R3 R4 R5 )
#procDir=processed_Q10
#qinfix=q10.SAM
saveIFS=$IFS
IFS=`echo -en ","`
declare -a samples=($Samples)
IFS=$saveIFS
rootdir=`pwd`
allsampleconfig=$rootdir/allsamples.config
echo $configDir
echo $procDir $qinfix
echo $allsampleconfig
echo ${samples[@]}
#exit
rm $allsampleconfig
nsamples=${#samples[@]}
for((sample_i=0;sample_i<$nsamples;sample_i++)) do
sample=${samples[$sample_i]}
logout=$rootdir/$sample
totalReadsThisSample=0
totalReadsMappedThisSample=0
totalReadsUnmappedThisSample=0
totalReadsMappedPassQThisSample=0
#if [ ! -d $i ]; then
# echo $i is not directory, continue
#fi
echo "processing sample $sample"
cd $sample
cd $procDir
for part_out in *.part.stdout; do
source $part_out
cat $part_out
totalReadsThisSample=`expr $totalReadsThisSample + $totalReads`
totalReadsMappedThisSample=`expr $totalReadsMappedThisSample + $totalReadsMapped`
totalReadsUnmappedThisSample=`expr $totalReadsUnmappedThisSample + $totalReadsUnmapped`
totalReadsMappedPassQThisSample=`expr $totalReadsMappedPassQThisSample + $totalReadsPassQ`
done
cd ..
cd ..
echo "sample=$sample" > ${logout}.config
echo "totalReads=$totalReadsThisSample" >> ${logout}.config
echo "totalReadsMapped=$totalReadsMappedThisSample" >> ${logout}.config
echo "totalReadsUnmapped=$totalReadsUnmappedThisSample" >> ${logout}.config
echo "totalReadsPassQ=$totalReadsMappedPassQThisSample" >> ${logout}.config
echo "samples[$sample_i]=\"$sample\"" >> $allsampleconfig
echo "totalReadss[$sample_i]=$totalReadsThisSample" >> $allsampleconfig
echo "totalReadsMappeds[$sample_i]=$totalReadsMappedThisSample" >> $allsampleconfig
echo "totalReadsUnmappeds[$sample_i]=$totalReadsUnmappedThisSample" >> $allsampleconfig
echo "totalReadsPassQs[$sample_i]=$totalReadsMappedPassQThisSample" >> $allsampleconfig
done
echo "numSamples=$nsamples" >> $allsampleconfig