#!/bin/bash
declare -A MCR
ln -s ../bowtie2_005/sort_uniq.bam A1.bam
ln -s ../bowtie2_006/sort_uniq.bam B1.bam
ln -s ../bowtie2_009/sort_uniq.bam A2.bam
ln -s ../bowtie2_010/sort_uniq.bam B2.bam
ln -s ../bowtie2_013/sort_uniq.bam A4.bam
ln -s ../bowtie2_014/sort_uniq.bam B4.bam
MCR[ A1.bam ]=10281393
MCR[ B1.bam ]=2731870 
MCR[ A2.bam ]=11369366
MCR[ B2.bam ]=8497753 
MCR[ A4.bam ]=16936642
MCR[ B4.bam ]=13632318


let min=9999999999;
for i in *bam
do
if [ ${MCR[ $i ]} -le $min ]; then let min=${MCR[ $i ]}; fi
done
echo "Sampling to smallest library containing" $min " reads"

for i in *bam
do
sc=$(echo "scale=15; $min/${MCR[ $i ]}" | bc) 
echo $i ${MCR[ $i ]} $sc
/data/results/tools/proton/tophat2unstranded-bigwig1.sh $i /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mmu.mm9.genome
#/data/results/tools/proton/tophat2stranded-sampled-bigwig1.sh $i /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/hsa.hg19.genome $sc
done