THREADs=8
FN=ITC274-PolII-wt3.bam
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run365/www/$FN   ../../../run364/www/$FN ../$FN"
fi

for FN in ITC275-PolII-wt4.bam ITC276-PolII-DENwt1.bam ITC277-PolII-DENwt2.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run365/www/$FN ../$FN"
fi
done


for FN in ITC278-PolII-AlSm1.bam ITC279-PolII-AlSm2.bam ITC280-PolII-DENAlSm3.bam ITC281-PolII-DENAlSm4.bam
do
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN ../../../run364/www/$FN  ../../../run389/wwwIT/$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