1#!/usr/local/bin/bash 2 3usage(){ 4echo " 5Written by Brian Bushnell 6Last modified Jan 7, 2020 7 8Description: Shrinks sketches to a smaller fixed length. 9 10Please read bbmap/docs/guides/BBSketchGuide.txt for more information. 11 12Usage: subsketch.sh in=file.sketch out=sub.sketch size=1000 autosize=f 13Bulk usage: subsketch.sh in=big#.sketch out=small#.sketch sizemult=0.5 14 15Standard parameters: 16in=<file> Input sketch file containing one or more sketches. 17out=<file> Output sketch file. 18size=10000 Size of sketches to generate, if autosize=f. 19autosize=t Autosize sketches based on genome size. 20sizemult=1 Adjust default sketch autosize by this factor. 21blacklist= Apply a blacklist to the sketch before resizing. 22files=31 If the output filename contains a # symbol, 23 spread the output across this many files, replacing 24 the # with a number. 25 26Java Parameters: 27-Xmx This will set Java's memory usage, overriding autodetection. 28 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. 29 The max is typically 85% of physical memory. 30-eoom This flag will cause the process to exit if an out-of-memory 31 exception occurs. Requires Java 8u92+. 32-da Disable assertions. 33 34For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt. 35Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 36" 37} 38 39#This block allows symlinked shellscripts to correctly set classpath. 40pushd . > /dev/null 41DIR="${BASH_SOURCE[0]}" 42while [ -h "$DIR" ]; do 43 cd "$(dirname "$DIR")" 44 DIR="$(readlink "$(basename "$DIR")")" 45done 46cd "$(dirname "$DIR")" 47DIR="$(pwd)/" 48popd > /dev/null 49 50#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" 51CP="$DIR""current/" 52 53z="-Xmx4g" 54z2="-Xms4g" 55set=0 56 57if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then 58 usage 59 exit 60fi 61 62calcXmx () { 63 source "$DIR""/calcmem.sh" 64 setEnvironment 65 parseXmx "$@" 66 if [[ $set == 1 ]]; then 67 return 68 fi 69 freeRam 3200m 84 70 z="-Xmx${RAM}m" 71 z2="-Xms${RAM}m" 72} 73calcXmx "$@" 74 75sendsketch() { 76 local CMD="java $EA $EOOM $z -cp $CP sketch.SubSketch $@" 77# echo $CMD >&2 78 eval $CMD 79} 80 81sendsketch "$@" 82