--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/msa.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,88 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified February 5, 2020
+
+Description:  Aligns a query sequence to reference sequences.
+Outputs the best matching position per reference sequence.
+If there are multiple queries, only the best-matching query will be used.
+MSA in this context stands for MultiStateAligner, not Multiple Sequence Alignment.
+
+Usage:
+msa.sh in=<file> out=<file> literal=<literal,literal,...>
+or
+msa.sh in=<file> out=<file> ref=<lfile>
+
+Parameters:
+in=<file>       File containing reads.
+out=<file>      Sam output file.
+literal=        A sequence of bases to match, or a comma-delimited list.
+ref=<file>      A fasta file of bases to match.  Please set either ref
+                or literal, not both.
+rcomp=t         Also look for reverse-complements of the sequences.
+addr=f          Add r_ prefix to reverse-complemented alignments.
+replicate=f     Make copies of sequences with undefined bases for every
+                possible combination.  For example, ATN would expand to
+                ATA, ATC, ATG, and ATT.
+cutoff=0        Ignore alignments with identity below this (range 0-1).
+swap=f          Swap the reference and query; e.g., report read alignments
+                to the reference instead of reference alignments to the reads.
+
+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/"
+
+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 [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 2000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+msa() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.FindPrimers $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+msa "$@"