jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified April 30, 2019
jpayne@69: 
jpayne@69: Description:  Performs set operations on VCF files:
jpayne@69: Union, intersection, and subtraction.
jpayne@69: 
jpayne@69: Usage:  comparevcf.sh in=<file,file,...> out=<file>
jpayne@69: 
jpayne@69: I/O parameters:
jpayne@69: in=<file>       Input; must be at least 2 files.
jpayne@69: out=<file>      Output file.
jpayne@69: ref=<file>      Reference file; optional.  Usually not needed.
jpayne@69: shist=<file>    (scorehist) Output for variant score histogram.
jpayne@69: overwrite=f     (ow) Set to false to force the program to abort rather than
jpayne@69: bgzip=f         Use bgzip for gzip compression.
jpayne@69: 
jpayne@69: Processing Mode (choose one only):
jpayne@69: subtract=t      Subtract all other files from the first file.
jpayne@69: union=f         Make a union of all files.
jpayne@69: intersection=f  Make an intersection of all files.
jpayne@69: 
jpayne@69: Processing Parameters:
jpayne@69: addsamples=t    Include all samples in the output lines. (TODO)
jpayne@69: splitalleles=f  Split multi-allelic lines into multiple lines.
jpayne@69: splitsubs=f     Split multi-base substitutions into SNPs.
jpayne@69: canonize=t      Trim variations down to a canonical representation.
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
jpayne@69:                 specify 200 megs. The max is typically 85% of physical memory.
jpayne@69: -eoom           This flag will cause the process to exit if an out-of-memory
jpayne@69:                 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 [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 4000m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: comparevcf() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 -cp $CP var2.CompareVCF $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: comparevcf "$@"