--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/crosscontaminate.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,93 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified February 17, 2015
+
+Description:  Generates synthetic cross-contaminated files from clean files.
+Intended for use with synthetic reads generated by SynthMDA or RandomReads.
+
+Usage:        crosscontaminate.sh in=<file,file,...> out=<file,file,...>
+
+Input parameters:
+in=<file,file,...>  Clean input reads.
+innamefile=<file>   A file containing the names of input files, 
+                    one name per line.
+interleaved=auto    (int) t/f overrides interleaved autodetection.
+qin=auto            Input quality offset: 33 (Sanger), 64, or auto.
+reads=-1            If positive, quit after processing X reads or pairs.
+
+Processing Parameters:
+minsinks=1          Min contamination destinations from one source.
+maxsinks=8          Max contamination destinations from one source.
+minprob=0.000005    Min allowed contamination rate (geometric distribution).
+maxprob=0.025       Max allowed contamination rate.
+
+Output parameters:
+out=<file,file,...> Contaminated output reads.
+outnamefile=<file>  A file containing the names of output files, 
+                    one name per line.
+overwrite=t         (ow) Grant permission to overwrite files.
+#showspeed=t        (ss) 'f' suppresses display of processing speed.
+ziplevel=2          (zl) Compression level; 1 (min) through 9 (max).
+threads=auto        (t) Set number of threads to use; default is number of 
+                    logical processors.
+qout=auto           Output quality offset: 33 (Sanger), 64, or auto.
+shuffle=f           Shuffle contents of output files.
+shufflethreads=3    Use this many threads for shuffling (uses more memory).
+
+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 [[ $set == 1 ]]; then
+	return
+	fi
+	freeRam 4000m 42
+	z="-Xmx${RAM}m"
+}
+calcXmx "$@"
+
+crosscontaminate() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.CrossContaminate $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+crosscontaminate "$@"