jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified February 17, 2015
jpayne@69: 
jpayne@69: Description:  Generates synthetic cross-contaminated files from clean files.
jpayne@69: Intended for use with synthetic reads generated by SynthMDA or RandomReads.
jpayne@69: 
jpayne@69: Usage:        crosscontaminate.sh in=<file,file,...> out=<file,file,...>
jpayne@69: 
jpayne@69: Input parameters:
jpayne@69: in=<file,file,...>  Clean input reads.
jpayne@69: innamefile=<file>   A file containing the names of input files, 
jpayne@69:                     one name per line.
jpayne@69: interleaved=auto    (int) t/f overrides interleaved autodetection.
jpayne@69: qin=auto            Input quality offset: 33 (Sanger), 64, or auto.
jpayne@69: reads=-1            If positive, quit after processing X reads or pairs.
jpayne@69: 
jpayne@69: Processing Parameters:
jpayne@69: minsinks=1          Min contamination destinations from one source.
jpayne@69: maxsinks=8          Max contamination destinations from one source.
jpayne@69: minprob=0.000005    Min allowed contamination rate (geometric distribution).
jpayne@69: maxprob=0.025       Max allowed contamination rate.
jpayne@69: 
jpayne@69: Output parameters:
jpayne@69: out=<file,file,...> Contaminated output reads.
jpayne@69: outnamefile=<file>  A file containing the names of output files, 
jpayne@69:                     one name per line.
jpayne@69: overwrite=t         (ow) Grant permission to overwrite files.
jpayne@69: #showspeed=t        (ss) 'f' suppresses display of processing speed.
jpayne@69: ziplevel=2          (zl) Compression level; 1 (min) through 9 (max).
jpayne@69: threads=auto        (t) Set number of threads to use; default is number of 
jpayne@69:                     logical processors.
jpayne@69: qout=auto           Output quality offset: 33 (Sanger), 64, or auto.
jpayne@69: shuffle=f           Shuffle contents of output files.
jpayne@69: shufflethreads=3    Use this many threads for shuffling (uses more memory).
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 [[ $set == 1 ]]; then
jpayne@69: 	return
jpayne@69: 	fi
jpayne@69: 	freeRam 4000m 42
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: crosscontaminate() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.CrossContaminate $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: crosscontaminate "$@"