#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified April 11, 2019

Description:  Compresses or decompresses files based on extensions.
This only exists because the syntax and default behavior of many
compression utilities is unintuitive; it is just a wrapper, and
relies on existing executables in the command line (pigz, lbzip, etc.)
Does not delete the input file.
Does not untar files.

Usage:  unzip.sh in=<file> out=<file>

Parameters:
in=<file>       Input file.
out=<file>      Output file for good reads.
zl=             Set the compression level; 0-9 or 11.

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

#This block allows symlinked shellscripts to correctly set classpath.
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/"

z="-Xmx200m"
EA="-ea"
EOOM=""
set=0

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

calcXmx () {
	source "$DIR""/calcmem.sh"
	parseXmx "$@"
}
calcXmx "$@"

filtersam() {
	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 unload PrgEnv-intel
		module load PrgEnv-gnu/7.1
		module load samtools/1.4
		module load pigz
	fi
	local CMD="java $EA $EOOM $z -cp $CP jgi.A_SampleByteFile $@"
#	echo $CMD >&2
	eval $CMD
}

filtersam "$@"
