--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/repair.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,90 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified November 9, 2016
+
+Description:  Re-pairs reads that became disordered or had some mates eliminated.
+Please read bbmap/docs/guides/RepairGuide.txt for more information.
+
+Usage:  repair.sh in=<input file> out=<pair output> outs=<singleton output>
+
+Input may be fasta, fastq, or sam, compressed or uncompressed.
+
+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.
+outs=<file>     (outsingle) 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.
+ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression
+                level; lower compression is faster.
+fint=f          (fixinterleaving) Fixes corrupted interleaved files using read
+                names.  Only use on files with broken interleaving - correctly
+                interleaved files from which some reads were removed.
+repair=t        (rp) Fixes arbitrarily corrupted paired reads by using read 
+                names.  Uses much more memory than 'fint' mode.
+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="-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${RAM}m"
+}
+calcXmx "$@"
+
+repair() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles rp $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+repair "$@"