! /bin/bash

$ -l mem=30G,time=50::

$ -j y

$ -N bam2fq

$ -cwd

source ~/.bashrc

in_dir=/ifs/data/dipg_cbttc_bam
out_dir=/ifs/data/dipg_cbttc_fastq

mkdir $out_dir

for fullpath in "$in_dir"/*

do
filename="{fullpath:0:{#filename}}" # Substring from 0 thru pos of filename
base="{filename:${#base} + 1}"

echo dir
echo ext

java -Xmx2g -jar /ifs/scratch/picard.jar SamToFastq I={out_dir}/{out_dir}/${base}_R2.fastq

samtools bam2fq {out_dir}/${base}.fastq

done