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