jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified Jan 29, 2020
jpayne@69: 
jpayne@69: Description:  Adds, removes, or replaces SSU sequence of existing sketches.
jpayne@69: Sketches and SSU fasta files must be annotated with TaxIDs.
jpayne@69: 
jpayne@69: Usage:           addssu.sh in=a.sketch out=b.sketch 16S=16S.fa 18S=18S.fa
jpayne@69: 
jpayne@69: Standard parameters:
jpayne@69: in=<file>       Input sketch file.
jpayne@69: out=<file>      Output sketch file.
jpayne@69: 
jpayne@69: Additional files (optional):
jpayne@69: 16S=<file>      A fasta file of 16S sequences.  These should be renamed
jpayne@69:                 so that they start with tid|# where # is the taxID.
jpayne@69:                 Should not contain organelle rRNA.
jpayne@69: 18S=<file>      A fasta file of 18S sequences.  These should be renamed
jpayne@69:                 so that they start with tid|# where # is the taxID.
jpayne@69:                 Should not contain organelle rRNA.
jpayne@69: tree=auto       Path to TaxTree, if performing prok/euk-specific operations.
jpayne@69: 
jpayne@69: Processing parameters:
jpayne@69: preferSSUMap=f
jpayne@69: preferSSUMapEuks=f
jpayne@69: preferSSUMapProks=f
jpayne@69: SSUMapOnly=f
jpayne@69: SSUMapOnlyEuks=f
jpayne@69: SSUMapOnlyProks=f
jpayne@69: clear16S=f
jpayne@69: clear18S=f
jpayne@69: clear16SEuks=f
jpayne@69: clear18SEuks=f
jpayne@69: clear16SProks=f
jpayne@69: clear18SProks=f
jpayne@69: 
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: -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.AddSSU $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: sendsketch "$@"