jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified October 22, 2015
jpayne@69: 
jpayne@69: Description:  Generates synthetic reads following an MDA-amplified single cell's coverage distribution.
jpayne@69: 
jpayne@69: Usage:  synthmda.sh in=<reference> out=<reads out file>
jpayne@69: 
jpayne@69: Input may be fasta or fastq, compressed or uncompressed.
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: reads=12000000      Generate this many reads.
jpayne@69: paired=t            Generate paired reads.
jpayne@69: length=150          Reads should be this long.
jpayne@69: minlen=4000         Min length of MDA contig.
jpayne@69: maxlen=150000       Max length of MDA contig.
jpayne@69: cycles=9            Number of MDA cycles; higher is more spiky.
jpayne@69: initialratio=1.3    Fraction of genome initially replicated; 
jpayne@69:                     lower is more spiky.
jpayne@69: ratio=1.7           Fraction of genome replicated per cycle.
jpayne@69: refout=null         Write MDA'd genome to this file.
jpayne@69: perfect=0           This fraction of reads will be error-free.
jpayne@69: amp=200             'amp' flag sent to RandomReads (higher is more spiky).
jpayne@69: build=7             Index MDA'd genome in this location.
jpayne@69: prefix=null         Generated reads will start with this prefix.
jpayne@69: overwrite=t         (ow) Set to false to force the program to abort rather 
jpayne@69:                     than overwrite an existing file.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx                This will set Java's memory usage, overriding autodetection.
jpayne@69:                     -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
jpayne@69:                     The max is typically 85% of physical memory.
jpayne@69: -eoom               This flag will cause the process to exit if an
jpayne@69:                     out-of-memory exception occurs.  Requires Java 8u92+.
jpayne@69: -da                 Disable assertions.
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: 
jpayne@69: z="-Xmx4g"
jpayne@69: z2="-Xms4g"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: 	if [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 4000m 80
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: synthmda() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.SynthMDA $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: synthmda "$@"