#!/bin/bash
PATH=/data/results/tools/bedtools/bedtools2/bin:$PATH; export PATH
declare -A MCR


MCR[ ITC144-InputP14.bam ]=20552489
MCR[ ITC145-InputP60.bam ]=14440615
MCR[ ITC154-Med12P60.bam ]=12247160

let min=9999999999;
for i in *bam
do
if [ ${MCR[ $i ]} -le $min ]; then let min=${MCR[ $i ]}; fi
done
let min=14766791
echo "Sampling to smallest library containing" $min " reads"

for i in ITC144-InputP14.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
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh $i /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai $sc
done

/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC145-InputP60.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1.0
/data/results/tools/proton/tophat2unstranded-sampled-bigwig1.sh ITC154-Med12P60.bam /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai 1.0