jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified December 19, 2019
jpayne@69: 
jpayne@69: Description:  Merges multiple sketches into a single sketch.
jpayne@69: 
jpayne@69: Please read bbmap/docs/guides/BBSketchGuide.txt for more information.
jpayne@69: 
jpayne@69: Usage:           mergesketch.sh in=a.sketch,b.sketch out=c.sketch
jpayne@69: With wildcards:  mergesketch.sh *.sketch out=c.sketch
jpayne@69: 
jpayne@69: Standard parameters:
jpayne@69: in=<file>       Input sketches or fasta files; may be a comma-delimited
jpayne@69:                 list.  in= is optional so wildcards may be used.
jpayne@69: out=<file>      Output sketch.
jpayne@69: amino=f         Use amino acid mode.
jpayne@69: 
jpayne@69: Sketch-making parameters:
jpayne@69: mode=single     Possible modes, for fasta input:
jpayne@69:                    single: Generate one sketch per file.
jpayne@69:                    sequence: Generate one sketch per sequence.
jpayne@69: autosize=t      Produce an output sketch of whatever size the union 
jpayne@69:                 happens to be.
jpayne@69: size=           Restrict output sketch to this upper bound of size.
jpayne@69: k=32,24         Kmer length, 1-32.
jpayne@69: keyfraction=0.2 Only consider this upper fraction of keyspace.
jpayne@69: minkeycount=1   Ignore kmers that occur fewer times than this.  Values
jpayne@69:                 over 1 can be used with raw reads to avoid error kmers.
jpayne@69: depth=f         Retain kmer counts if available.
jpayne@69: 
jpayne@69: Metadata parameters: (if blank the values of the first sketch will be used)
jpayne@69: taxid=-1        Set the NCBI taxid.
jpayne@69: imgid=-1        Set the IMG id.
jpayne@69: spid=-1         Set the JGI sequencing project id.
jpayne@69: name=           Set the name (taxname).
jpayne@69: name0=          Set name0 (normally the first sequence header).
jpayne@69: fname=          Set fname (normally the file name).
jpayne@69: meta_=          Set an arbitrary metadata field.
jpayne@69:                 For example, meta_Month=March.
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.MergeSketch $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: sendsketch "$@"