#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified November 9, 2016

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.
int=auto        (interleaved) 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 set Java's memory usage, overriding autodetection.
                -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.
"
}

#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="-Xmx2g"
z2="-Xms2g"
set=0

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

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

shuffle() {
	local CMD="java $EA $EOOM $z $z2 -cp $CP sort.Shuffle $@"
	echo $CMD >&2
	eval $CMD
}

shuffle "$@"
