#! /bin/bash

# Copyright (c) 2013, Ian Reid, Concordia University Centre for Structural and Functional Genomics
# All rights reserved.

set -o errexit
SIMUL=$1
GENOME_FA=$2

[[ -e $SIMUL.true_mappings.by_name.bam ]] && chmod u+w $SIMUL.true_mappings.by_name.bam
samtools fillmd -uS $SIMUL.true_mappings.sam $GENOME_FA | samtools sort -n -m 20000000000 - $SIMUL.true_mappings.by_name
bam2fastq -o $SIMUL#.fastq $SIMUL.true_mappings.by_name.bam
echo "Read simulation is done."