#!/bin/bash

function usage(){
echo "
Written by Brian Bushnell
Last modified June 16, 2016

Description:  Splits a sequence file evenly into multiple files.

Usage:  partition.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> ways=<number>

in2 and out2 are for paired reads and are optional.
If input is paired and out2 is not specified, data will be written interleaved.
Output filenames MUST contain a '%' symbol.  This will be replaced by a number.

Parameters and their defaults:

in=<file>           Input file.
out=<file>          Output file pattern.
ways=-1             The number of output files to create; must be positive.

ow=f                (overwrite) Overwrites files that already exist.
app=f               (append) Append to files that already exist.
zl=4                (ziplevel) Set compression level, 1 (low) to 9 (max).
int=f               (interleaved) Determines whether INPUT file is considered interleaved.

Java Parameters:
-Xmx                This will be passed to Java to set memory usage, overriding the program's automatic memory detection.
                    -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.  The max is typically 85% of physical memory.
-eoom               This flag will cause the process to exit if an out-of-memory exception occurs.  Requires Java 8u92+.
-da                 Disable assertions.

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/"

z="-Xmx400m"
EA="-ea"
EOOM=""
set=0

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

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

function partition() {
	if [[ $NERSC_HOST == genepool ]]; then
		module unload oracle-jdk
		module load oracle-jdk/1.8_144_64bit
		module load pigz
		module load samtools/1.4
	fi
	local CMD="java $EA $EOOM $z -cp $CP jgi.PartitionReads $@"
	echo $CMD >&2
	eval $CMD
}

partition "$@"
