#!/bin/bash
#shuffle in=<infile> out=<outfile>

usage(){
echo "
Written by Brian Bushnell
Last modified November 19, 2015

Description:  Reorders reads randomly, keeping pairs together.

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


Standard parameters:
in=<file>           The 'in=' flag is needed if the input file is not the first parameter.  'in=stdin' will pipe from standard in.
in2=<file>          Use this if 2nd read of pairs are in a different file.
out=<file>          The 'out=' flag is needed if the output file is not the second parameter.  'out=stdout' will pipe to standard out.
out2=<file>         Use this to write 2nd read of pairs to a different file.
overwrite=t         (ow) Set to false to force the program to abort rather than overwrite an existing file.
ziplevel=2          (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
interleaved=auto    (int) Set to t or f to override interleaving autodetection.

Processing parameters:
shuffle             Randomly reorders reads (default).
name                Sort reads by name.
coordinate          Sort reads by mapping location.
sequence            Sort reads by sequence.


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.

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="-Xmx2g"
z2="-Xms2g"
EA="-ea"
set=0

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

calcXmx () {
	source "$DIR""/calcmem.sh"
	parseXmx "$@"
	if [[ $set == 1 ]]; then
		return
	fi
	freeRam 2000m 84
	z="-Xmx${RAM}m"
	z2="-Xms${RAM}m"
}
calcXmx "$@"

shuffle() {
	if [[ $NERSC_HOST == genepool ]]; then
		module unload oracle-jdk
		module load oracle-jdk/1.7_64bit
		module load pigz
	fi
	local CMD="java $EA $z -cp $CP jgi.Shuffle $@"
	echo $CMD >&2
	eval $CMD
}

shuffle "$@"
