jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell and Jonathan Rood
jpayne@69: Last modified September 15, 2015
jpayne@69: 
jpayne@69: Dedupe2 is identical to Dedupe except it supports hashing unlimited kmer
jpayne@69: prefixes and suffixes per sequence.  Dedupe supports at most 2 of each,
jpayne@69: but uses slightly more memory.  You can manually set the number of kmers to
jpayne@69: hash per read with the numaffixmaps (nam) flag.  Dedupe will automatically
jpayne@69: call Dedupe2 if necessary (if nam=3 or higher) so this script is no longer
jpayne@69: necessary.
jpayne@69: 
jpayne@69: For documentation, please consult dedupe.sh; syntax is identical.
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: JNI="-Djava.library.path=""$DIR""jni/"
jpayne@69: JNI=""
jpayne@69: 
jpayne@69: z="-Xmx1g"
jpayne@69: z2="-Xms1g"
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: dedupe() {
jpayne@69: 	local CMD="java $JNI $EA $EOOM $z $z2 -cp $CP jgi.Dedupe2 $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: dedupe "$@"