jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified February 20, 2020
jpayne@69: 
jpayne@69: Description:  Estimates cardinality of unique kmers in sequence data.
jpayne@69: Processes multiple kmer lengths simultaneously to produce a histogram.
jpayne@69: 
jpayne@69: Usage:  kmercountmulti.sh in=<file> sweep=<20,100,8> out=<histogram output>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>           (in1) Input file, or comma-delimited list of files.
jpayne@69: in2=<file>          Optional second file for paired reads.
jpayne@69: out=<file>          Histogram output.  Default is stdout.
jpayne@69: k=                  Comma-delimited list of kmer lengths to use.
jpayne@69: sweep=min,max,incr  Use incremented kmer values from min to max. For example,
jpayne@69:                     sweep=20,26,2 is equivalent to k=20,22,24,26.
jpayne@69: buckets=2048        Use this many buckets for counting; higher decreases
jpayne@69:                     variance, for large datasets.  Must be a power of 2.
jpayne@69: seed=-1             Use this seed for hash functions.  
jpayne@69:                     A negative number forces a random seed.
jpayne@69: minprob=0           Set to a value between 0 and 1 to exclude kmers with a 
jpayne@69:                     lower probability of being correct.
jpayne@69: hashes=1            Use this many hash functions.  More hashes yield greater
jpayne@69:                     accuracy, but H hashes takes H times as long.
jpayne@69: stdev=f             Print standard deviations.
jpayne@69: 
jpayne@69: Shortcuts:
jpayne@69: The # symbol will be substituted for 1 and 2.
jpayne@69: For example:
jpayne@69: kmercountmulti.sh in=read#.fq
jpayne@69: ...is equivalent to:
jpayne@69: kmercountmulti.sh in1=read1.fq in2=read2.fq
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
jpayne@69:                     out-of-memory exception occurs.  Requires Java 8u92+.
jpayne@69: -da                 Disable assertions.
jpayne@69: 
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="-Xmx500m"
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 "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: function kmercountmulti() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.KmerCountMulti $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: kmercountmulti "$@"