#!/bin/bash
#samtoroc in=<infile>

usage(){
echo "
Written by Brian Bushnell
Last modified May 23, 2014

Description:  Creates a ROC curve from a sam file of synthetic reads with headers generated by RandomReads3.java

Usage:        samtoroc.sh in=<sam file> reads=<number of reads in input fastq>

Parameters:
in=<file>     Specify the input sam file, or stdin.
thresh=20     Max deviation from correct location to be considered 'loosely correct'.
blasr=f       Set to 't' for BLASR output; fixes extra information added to read names.
ssaha2=f      Set to 't' for SSAHA2 or SMALT output; fixes incorrect soft-clipped read locations.
bitset=t      Track read ID's to detect secondary alignments.
              Necessary for mappers that incorrectly output multiple primary alignments per read.

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

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

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

samtoroc() {
	if [[ $NERSC_HOST == genepool ]]; then
		module unload oracle-jdk
		module unload samtools
		module load oracle-jdk/1.7_64bit
		module load samtools
	fi
	local CMD="java $EA $z -cp $CP align2.MakeRocCurve $@"
#	echo $CMD >&2
	eval $CMD
}

samtoroc "$@"
