--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/synthmda.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,86 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified October 22, 2015
+
+Description:  Generates synthetic reads following an MDA-amplified single cell's coverage distribution.
+
+Usage:  synthmda.sh in=<reference> out=<reads out file>
+
+Input may be fasta or fastq, compressed or uncompressed.
+
+Parameters:
+reads=12000000      Generate this many reads.
+paired=t            Generate paired reads.
+length=150          Reads should be this long.
+minlen=4000         Min length of MDA contig.
+maxlen=150000       Max length of MDA contig.
+cycles=9            Number of MDA cycles; higher is more spiky.
+initialratio=1.3    Fraction of genome initially replicated; 
+                    lower is more spiky.
+ratio=1.7           Fraction of genome replicated per cycle.
+refout=null         Write MDA'd genome to this file.
+perfect=0           This fraction of reads will be error-free.
+amp=200             'amp' flag sent to RandomReads (higher is more spiky).
+build=7             Index MDA'd genome in this location.
+prefix=null         Generated reads will start with this prefix.
+overwrite=t         (ow) Set to false to force the program to abort rather 
+                    than overwrite an existing file.
+
+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 [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 4000m 80
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+synthmda() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.SynthMDA $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+synthmda "$@"