--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/makecontaminatedgenomes.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,81 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified August 29, 2017
+
+Description:  Generates synthetic contaminated partial genomes from clean genomes.
+Output is formatted as (prefix)_bases1_fname1_bases2_fname2_counter_(suffix).
+
+Usage:        makecontaminatedgenomes.sh in=<file> out=<pattern>
+
+I/O parameters:
+in=<file>       A file containing one input file path per line.
+out=<pattern>   A file name containing a # symbol (or other regex).
+                The regex will be replaced by source filenames.
+
+Processing Parameters:
+count=1         Number of output files to make.
+seed=-1         RNG seed; negative for a random seed.
+exp1=1          Exponent for genome 1 size fraction.
+exp2=1          Exponent for genome 2 size fraction.
+subrate=0       Rate to add substitutions to new genomes (0-1).
+indelrate=0     Rate to add substitutions to new genomes (0-1).
+regex=#         Use this substitution regex for replacement.
+delimiter=_     Use this delimiter in the new file names.
+
+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 "$@"
+
+makecontaminatedgenomes() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.MakeContaminatedGenomes $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+makecontaminatedgenomes "$@"