THREADs=8


for FN in ITC290-Pho-wt3.bam ITC293-Pho-DENwt2.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run366/www/$FN ../../../run367/www/$FN ../$FN"
fi
done



for FN in ITC294-Pho-AlSm1.bam  ITC295-Pho-AlSm2.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run366/www/$FN ../$FN"
fi
done

for FN in ITC296-Pho-DENAlSm3.bam ITC297-Pho-DENAlSm4.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN ../../../run367/www/$FN ../$FN"
fi
done

for FN in ITC298-PolII-Untrwt3.bam ITC299-PolII-Untrwt4.bam ITC300-PolII-Untrko1.bam ITC301-PolII-Untrko3.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run369/www/$FN ../../../run384/www/$FN ../$FN"
fi
done


for FN in ITC302-PolII-DENTCPwt1.bam ITC303-PolII-DENTCPwt3.bam ITC304-PolII-DENTCPko2.bam ITC305-PolII-DENTCPko4.bam 
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN ../../../run368/www/$FN ../$FN"
fi
done


sem --id merging --wait

for FN in *bam
do
if [ ! -f ${FN%.*}.flagstat.txt ]; then
sem -j $THREADs "samtools flagstat $FN > ${FN%.*}.flagstat.txt"
fi
done