jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified Jan 7, 2020
jpayne@69: 
jpayne@69: Description:  Shrinks sketches to a smaller fixed length.
jpayne@69: 
jpayne@69: Please read bbmap/docs/guides/BBSketchGuide.txt for more information.
jpayne@69: 
jpayne@69: Usage:       subsketch.sh in=file.sketch out=sub.sketch size=1000 autosize=f
jpayne@69: Bulk usage:  subsketch.sh in=big#.sketch out=small#.sketch sizemult=0.5
jpayne@69: 
jpayne@69: Standard parameters:
jpayne@69: in=<file>       Input sketch file containing one or more sketches.
jpayne@69: out=<file>      Output sketch file.
jpayne@69: size=10000      Size of sketches to generate, if autosize=f.
jpayne@69: autosize=t      Autosize sketches based on genome size.
jpayne@69: sizemult=1      Adjust default sketch autosize by this factor.
jpayne@69: blacklist=      Apply a blacklist to the sketch before resizing.
jpayne@69: files=31        If the output filename contains a # symbol,
jpayne@69:                 spread the output across this many files, replacing
jpayne@69:                 the # with a number.
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 out-of-memory
jpayne@69:                 exception occurs.  Requires Java 8u92+.
jpayne@69: -da             Disable assertions.
jpayne@69: 
jpayne@69: For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
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 [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 3200m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: sendsketch() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP sketch.SubSketch $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: sendsketch "$@"