--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbwrap.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,77 @@
+#!/bin/bash
+
+usage(){
+echo "
+Last modified February 13, 2020
+
+Description:  Wrapper for BBMap to allow multiple input and output files for the same reference.
+
+To index:                 bbwrap.sh ref=<reference fasta>
+To map:                   bbwrap.sh in=<file,file,...> out=<file,file,...>
+To map without an index:  bbwrap.sh ref=<reference fasta> in=<file,file,...> out=<file,file,...> nodisk
+To map pairs and singletons and output them into the same file:
+bbwrap.sh in1=read1.fq,singleton.fq in2=read2.fq,null out=mapped.sam append
+
+BBWrap will not work with stdin and stdout, or histogram output.
+
+Other Parameters:
+
+in=<file,file>  Input sequences to map.
+inlist=<fofn>   Alternately, input and output can be a file of filenames,
+                one line per file, using the flag inlist, outlist, outmlist,
+                in2list, etc.
+mapper=bbmap    Select mapper.  May be BBMap, BBMapPacBio, 
+                or BBMapPacBioSkimmer.
+append=f        Append to files rather than overwriting them.  
+                If append is enabled, and there is exactly one output file,
+                all output will be written to that file.
+
+***** All BBMap parameters can be used; see bbmap.sh for more details. *****
+"
+}
+
+#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 [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 3200m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+bbwrap() {
+	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBWrap build=1 overwrite=true fastareadlen=500 $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+bbwrap "$@"