--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/plotgc.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,78 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified February 27, 2017
+
+Description:  Prints sequence gc content once per interval.
+
+Usage:  plotgc.sh in=<input file> out=<output file>
+
+Parameters:
+in=<file>       Input file. in=stdin.fa will pipe from stdin.
+out=<file>      Output file.  out=stdout will pipe to stdout.
+interval=1000   Interval length.
+offset=0        Position offset.  For 1-based indexing use offset=1.
+psb=t           (printshortbins) Print gc content for the last bin of a contig
+                even when shorter than interval.
+
+Java Parameters:
+
+-Xmx            This will set Java's memory usage, overriding automatic
+                memory detection. -Xmx20g will 
+                specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.  
+                The max is typically 85% of physical memory.
+-eoom           This flag will cause the process to exit if an out-of-memory
+                exception occurs.  Requires Java 8u92+.
+-da             Disable assertions.
+
+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/"
+JNI="-Djava.library.path=""$DIR""jni/"
+JNI=""
+
+z="-Xmx1g"
+z2="-Xms1g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 1400m 42
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+plotgc() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP driver.PlotGC $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+plotgc "$@"