--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/readlength.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,60 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified December 19, 2018
+Description:  Generates a length histogram of input reads.
+
+Usage:	readlength.sh in=<input file>
+
+in=<file>    	The 'in=' flag is needed only if the input file is not the first parameter.  'in=stdin.fq' will pipe from standard in.
+in2=<file>   	Use this if 2nd read of pairs are in a different file.
+out=<file>   	Write the histogram to this file.  Default is stdout.
+bin=10       	Set the histogram bin size.
+max=80000    	Set the max read length to track.
+round=f      	Places reads in the closest bin, rather than the highest bin of at least readlength.
+nzo=t        	(nonzeroonly) Do not print empty bins.
+reads=-1     	If nonnegative, stop after this many reads.
+
+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="-Xmx400m"
+z2="-Xms400m"
+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 $z -cp $CP jgi.MakeLengthHistogram $@"
+#	echo $CMD >&2
+	eval $CMD
+}
+
+stats "$@"