#!/bin/bash

READDIR="/home/reads/" # Directory all reads are stored in
GENOME="/home/ref_chr_17" # reference genome 

for file in $READDIR*.1.fastq; do prefix=${file%%.1.fastq}; prefix=${prefix##$READDIR}; java -Xmx4000M -jar omixon-letter-space-toolkit.jar -config orm.properties -orm.referenceUrl $GENOME -orm.outputUrl ./$prefix.sam -orm.inputUrl $READDIR$prefix.1.fastq,$READDIR$prefix.2.fastq -orm.mate.mode true -toolkit.useAllProcessors true -toolkit.tmpDir ./ -orm.alignment.maxindel 65 -orm.mate.orientation FR; done

