--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/comparessu.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,89 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified December 4, 2019
+
+Description:  Aligns SSUs to each other and reports identity.
+This requires sequences annotated with a taxID in their header.
+
+Usage:  comparessu.sh in=<input file> out=<output file>
+
+Input may be fasta or fastq, compressed or uncompressed.
+
+Standard parameters:
+in=<file>       Input sequences.
+out=<file>      Output data.
+t=              Set the number of threads; default is logical processors.
+overwrite=f     (ow) Set to false to force the program to abort rather than
+                overwrite an existing file.
+showspeed=t     (ss) Set to 'f' to suppress display of processing speed.
+ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression
+                level; lower compression is faster.
+reads=-1        If positive, quit after this many sequences.
+
+Processing parameters:
+ata=f           Do an all-to-all comparison.  Otherwise, each sequence will
+                only be compared to one other randomly-selected sequence
+                per taxonomic level.
+minlen=0        Ignore sequences shorter than this.
+maxlen=BIG      Ignore sequences longer than this.
+maxns=-1        If positive, ignore sequences with more than this many Ns.
+
+
+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="-Xmx4g"
+z2="-Xms4g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 4000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+comparessu() {
+	local CMD="java $EA $EOOM $z -cp $CP sketch.CompareSSU $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+comparessu "$@"