jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified December 19, 2018
jpayne@69: 
jpayne@69: Description:  Calls peaks from a 2-column (x, y) tab-delimited histogram.
jpayne@69: 
jpayne@69: Usage:        callpeaks.sh in=<histogram file> out=<output file>
jpayne@69: 
jpayne@69: Peak-calling parameters:
jpayne@69: in=<file>           'in=stdin.fq' will pipe from standard in.
jpayne@69: out=<file>          Write the peaks to this file.  Default is stdout.
jpayne@69: minHeight=2         (h) Ignore peaks shorter than this.
jpayne@69: minVolume=5         (v) Ignore peaks with less area than this.
jpayne@69: minWidth=3          (w) Ignore peaks narrower than this.
jpayne@69: minPeak=2           (minp) Ignore peaks with an X-value below this. 
jpayne@69:                     Useful when low-count kmers are filtered).
jpayne@69: maxPeak=BIG         (maxp) Ignore peaks with an X-value above this.
jpayne@69: maxPeakCount=10     (maxpc) Print up to this many peaks (prioritizing height).
jpayne@69: countColumn=1       (col) For multi-column input, this column, zero-based, 
jpayne@69:                     contains the counts.
jpayne@69: ploidy=-1           Specify ploidy; otherwise it will be autodetected.
jpayne@69: logscale=f          Transform to log-scale prior to peak-calling.  Useful
jpayne@69:                     for kmer-frequency histograms.
jpayne@69: 
jpayne@69: Smoothing parameters:
jpayne@69: smoothradius=0      Integer radius of triangle filter.  Set above zero to 
jpayne@69:                     smooth data prior to peak-calling.  Higher values are 
jpayne@69:                     smoother.
jpayne@69: smoothprogressive=f Set to true to widen the filter as the x-coordinate
jpayne@69:                     increases.  Useful for kmer-frequency histograms.
jpayne@69: maxradius=10        Maximum radius of progressive smoothing function.
jpayne@69: progressivemult=2   Increment radius each time depth increases by this factor.
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="-Xmx200m"
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: stats() {
jpayne@69: 	local CMD="java $EA $EOOM -Xmx120m -cp $CP jgi.CallPeaks $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: stats "$@"