--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/plotflowcell.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,93 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified August 9, 2018
+
+Description:  Generates statistics about flowcell positions.
+
+Usage:	plotflowcell.sh in=<input> out=<output>
+
+Input parameters:
+in=<file>           Primary input file.
+in2=<file>          Second input file for paired reads in two files.
+indump=<file>       Specify an already-made dump file to use instead of
+                    analyzing the input reads.
+reads=-1            Process this number of reads, then quit (-1 means all).
+interleaved=auto    Set true/false to override autodetection of the
+                    input file as paired interleaved.
+
+Output parameters:
+out=<file>          Output file for filtered reads.
+dump=<file>         Write a summary of quality information by coordinates.
+
+Tile parameters:
+xsize=500           Initial width of micro-tiles.
+ysize=500           Initial height of micro-tiles.
+size=               Allows setting xsize and ysize tot he same value.
+target=800          Iteratively increase the size of micro-tiles until they
+                    contain an average of at least this number of reads.
+
+Other parameters:
+trimq=-1            If set to a positive number, trim reads to that quality
+                    level instead of filtering them.
+qtrim=r             If trimq is positive, to quality trimming on this end
+                    of the reads.  Values are r, l, and rl for right,
+                    left, and both ends.
+
+Java Parameters:
+-Xmx                This will set Java's memory usage, overriding autodetection.
+                    -Xmx20g will specify 20 GB of RAM; -Xmx200m will specify 
+                    200 MB.  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/"
+
+z="-Xmx8g"
+z2="-Xms8g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+	return
+	fi
+	freeRam 3200m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+plotflowcell() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP hiseq.PlotFlowCell $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+plotflowcell "$@"