--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbsplitpairs.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,82 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified February 17, 2015
+
+Description:  Separates paired reads into files of 'good' pairs and 'good' singletons by removing 'bad' reads that are shorter than a min length.
+Designed to handle situations where reads become too short to be useful after trimming.  This program also optionally performs quality trimming.
+
+Usage:        bbsplitpairs.sh in=<input file> out=<pair output file> outs=<singleton output file> minlen=<minimum read length, an integer>
+
+Input may be fasta or fastq, compressed or uncompressed.
+
+Optional parameters (and their defaults)
+
+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.
+outsingle=<file>    (outs) Write singleton reads here.
+
+overwrite=t         (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.
+interleaved=auto    (int) If true, forces fastq input to be paired and interleaved.
+qtrim=f             Trim read ends to remove bases with quality below trimq.
+                    Values: rl (trim both ends), f (neither end), r (right end only), l (left end only).
+trimq=6             Trim quality threshold.
+minlen=20           (ml) Reads shorter than this after trimming will be discarded.
+ziplevel=2          (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
+fixinterleaving=f   (fint) Fixes corrupted interleaved files by examining pair names.  Only use on files with broken interleaving.
+repair=f            (rp) Fixes arbitrarily corrupted paired reads by examining read names.  High memory.
+ain=f               (allowidenticalnames) When detecting pair names, allows identical names, instead of requiring /1 and /2 or 1: and 2:
+
+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="-Xmx200m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+splitpairs() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+splitpairs "$@"