THREADs=8

for FN in ITRC27-BrEU-wt3.bam ITRC28-BrEU-wt4.bam ITRC29-GRO-DENTC-wt1a.bam 
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run379/www/$FN ../$FN"
fi
done


for FN in ITRC30-GRO-DENTC-wt1b.bam ITRC31-GRO-USP22-DENTC-ko1.bam ITRC32-GRO-USP22-DENTC-ko2.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run380/www/$FN ../$FN"
fi
done


for FN in ITRC33-GRO-USP22-DENTC-ko3.bam ITRC34-EU-wt1.bam ITRC35-EU-wt2.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run381/www/$FN ../$FN"
fi
done


for FN in ITRC36-EU-USP22-ko1.bam  ITRC37-EU-USP22-ko2.bam ITRC38-EU-DENTC-wt2.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run382/www/$FN ../$FN"
fi
done

for FN in ITRC39-EU-DENTC-wt3.bam ITRC40-EU-USP22-DENTC-ko4.bam ITRC41-EU-USP22-DENTC-ko5.bam
do 
if [ ! -f $FN ]; then
sem -j $THREADs --id merging "samtools merge $FN  ../../../run383/www/$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