--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/shuffle2.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,80 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified August 11, 2021
+
+Description:  Reorders reads randomly, keeping pairs together.
+Unlike Shuffle, Shuffle2 can write temp files to handle large datasets.
+
+Usage:  shuffle2.sh in=<file> out=<file>
+
+Standard parameters:
+in=<file>       The 'in=' flag is needed if the input file is not the first parameter.  'in=stdin' will pipe from standard in.
+in2=<file>      Use this if 2nd read of pairs are in a different file.
+out=<file>      The 'out=' flag is needed if the output file is not the second parameter.  'out=stdout' will pipe to standard out.
+out2=<file>     Use this to write 2nd read of pairs to a different file.
+overwrite=t     (ow) Set to false to force the program to abort rather than overwrite an existing file.
+ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
+int=auto        (interleaved) Set to t or f to override interleaving autodetection.
+
+Processing parameters:
+shuffle         Randomly reorders reads (default).
+seed=-1         Set to a positive number for deterministic shuffling.
+
+Java Parameters:
+-Xmx            This will set Java's memory usage, overriding autodetection.
+                -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/"
+
+z="-Xmx2g"
+z2="-Xms2g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 2000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+shuffle() {
+	local CMD="java $EA $EOOM $z -cp $CP sort.Shuffle2 $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+shuffle "$@"