#files that will be subsampled
bam_names=*pooled.sorted.bam
for bam_name in $bam_names
do
	fname=`basename $bam_name`
	echo "this is the fname"
	echo $fname
	bname=${fname%\.bam}
	timepoint=${fname%\-rep0-id_-pooled.sorted.bam}
	
	
	scaling_factor=`cat scaling_factors_for_pooled.tab | grep -w $timepoint | cut -f2`
	scaling_factor_dec=`echo $scaling_factor | sed s/0.//g`
	
	echo "bname"
	echo $bname
	echo "timepoint"
	echo $timepoint
	echo "scaling factor"
	echo $scaling_factor_dec
	
	echo "samtools command"
	echo "samtools view -b -s 10.$scaling_factor_dec $fname > ${bname}.sorted.subsampled.bam "
	samtools view -b -s 10.$scaling_factor_dec $fname > ${bname}.sorted.subsampled.bam 
	
done