#!/bin/bash

function usage(){
echo "
Written by Brian Bushnell
Last modified June 15, 2017

Description:  Splits sam reads into 6 output files depending on mapping.

Usage:        splitsam6way.sh <input> <r1plus> <r1minus> <r1unmapped> <r2plus> <r2minus> <r2unmapped>

Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}

pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
  cd "$(dirname "$DIR")"
  DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null

#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"
EA="-ea"
EOOM=""
set=0

if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
	usage
	exit
fi

function split() {
	if [[ $SHIFTER_RUNTIME == 1 ]]; then
		#Ignore NERSC_HOST
		shifter=1
	elif [[ $NERSC_HOST == genepool ]]; then
		module unload oracle-jdk
		module load oracle-jdk/1.8_144_64bit
		module load samtools/1.4
		module load pigz
	elif [[ $NERSC_HOST == denovo ]]; then
		module unload java
		module load java/1.8.0_144
		module load PrgEnv-gnu/7.1
		module load samtools/1.4
		module load pigz
	elif [[ $NERSC_HOST == cori ]]; then
		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
		module unload java
		module load java/1.8.0_144
		module load PrgEnv-gnu/7.1
		module load samtools/1.4
		module load pigz
	fi
	local CMD="java $EA $EOOM -Xmx128m -Xms128m -cp $CP jgi.SplitSam6Way $@"
	echo $CMD >&2
	eval $CMD
}

split "$@"
