#!/bin/bash

checkExitCode() {
if [ $? -ne 0 ]; then
	echo "Error"
	exit 1;
fi
}

BASEDIR=`dirname $0`

if [ $# -lt 1 ]; then echo "Error No inputs provided" && exit 1; fi

. $BASEDIR/io.sh 1 0 1 "$@"

echo $SAMTOOLS13_HOME/samtools index -b $INPUTS1
$SAMTOOLS13_HOME/samtools index -b $INPUTS1
checkExitCode

# Rename outputs - not renaming for now since we do not need to see the output file
echo $INPUTS1 ${INPUTS1}.bai

cp ${INPUTS1}.bai $OUTPUTS1
checkExitCode