--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/callpeaks.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,76 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified December 19, 2018
+
+Description:  Calls peaks from a 2-column (x, y) tab-delimited histogram.
+
+Usage:        callpeaks.sh in=<histogram file> out=<output file>
+
+Peak-calling parameters:
+in=<file>           'in=stdin.fq' will pipe from standard in.
+out=<file>          Write the peaks to this file.  Default is stdout.
+minHeight=2         (h) Ignore peaks shorter than this.
+minVolume=5         (v) Ignore peaks with less area than this.
+minWidth=3          (w) Ignore peaks narrower than this.
+minPeak=2           (minp) Ignore peaks with an X-value below this. 
+                    Useful when low-count kmers are filtered).
+maxPeak=BIG         (maxp) Ignore peaks with an X-value above this.
+maxPeakCount=10     (maxpc) Print up to this many peaks (prioritizing height).
+countColumn=1       (col) For multi-column input, this column, zero-based, 
+                    contains the counts.
+ploidy=-1           Specify ploidy; otherwise it will be autodetected.
+logscale=f          Transform to log-scale prior to peak-calling.  Useful
+                    for kmer-frequency histograms.
+
+Smoothing parameters:
+smoothradius=0      Integer radius of triangle filter.  Set above zero to 
+                    smooth data prior to peak-calling.  Higher values are 
+                    smoother.
+smoothprogressive=f Set to true to widen the filter as the x-coordinate
+                    increases.  Useful for kmer-frequency histograms.
+maxradius=10        Maximum radius of progressive smoothing function.
+progressivemult=2   Increment radius each time depth increases by this factor.
+
+Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
+"
+}
+
+#This block allows symlinked shellscripts to correctly set classpath.
+pushd . > /dev/null
+DIR="${BASH_SOURCE[0]}"
+while [ -h "$DIR" ]; do
+  cd "$(dirname "$DIR")"
+  DIR="$(readlink "$(basename "$DIR")")"
+done
+cd "$(dirname "$DIR")"
+DIR="$(pwd)/"
+popd > /dev/null
+
+#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
+CP="$DIR""current/"
+
+z="-Xmx200m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+stats() {
+	local CMD="java $EA $EOOM -Xmx120m -cp $CP jgi.CallPeaks $@"
+#	echo $CMD >&2
+	eval $CMD
+}
+
+stats "$@"