#!/bin/bash

READDIR="/home/reads/" # Directory all reads are stored in
GENOME="/home/ref_chr_17" # reference genome 
INDEX="chr17.fa.ormind" # Genome index

for file in $READDIR*.1.fastq; do prefix=${file%%.fastq}; prefix=${prefix##$READDIR}; java -Xmx4000M -jar omixon-toolkit-cmd.jar -config orm.properties -orm.referenceUrl $GENOME -orm.outputUrl ./$prefix.sam -orm.inputUrl $READDIR$prefix.fastq -orm.mate.mode false -toolkit.useAllProcessors true -orm.index.loadUrl $INDEX -toolkit.tmpDir ./ -orm.alignment.maxindel 65; done

