#!/bin/bash


bams='results/05-filter_qual_bos_qual25'
ref='reference/Rank6_Signatures_sorted.bed'
out='results/05-filter_qual_bos_qual25/multibamc'

mkdir -p $out
declare -a my_array=("HIGH1_Aligned.sortedByCoord.out.bam HIGH2_Aligned.sortedByCoord.out.bam HIGH3_Aligned.sortedByCoord.out.bam LOW1_Aligned.sortedByCoord.out.bam LOW2_Aligned.sortedByCoord.out.bam LOW3_Aligned.sortedByCoord.out.bam")



multiBamCov -f 0.1 -bams $bams/HIGH1_Aligned.sortedByCoord.out.bam $bams/HIGH2_Aligned.sortedByCoord.out.bam $bams/HIGH3_Aligned.sortedByCoord.out.bam $bams/LOW1_Aligned.sortedByCoord.out.bam $bams/LOW2_Aligned.sortedByCoord.out.bam $bams/LOW3_Aligned.sortedByCoord.out.bam \
        -bed $ref > $out/'All_multibamcov.txt';