--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/mutate.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,100 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified August 6, 2019
+
+Description:  Creates a mutant version of a genome.
+
+Usage:  mutate.sh in=<input file> out=<output file> id=<identity>
+
+I/O parameters:
+in=<file>       Input genome.
+out=<file>      Output mutant genome.
+vcf=<file>      Output VCF file showing variations added.
+overwrite=f     (ow) Set to false to force the program to abort rather than
+                overwrite an existing file.
+ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression
+                level; lower compression is faster.
+
+Processing parameters:
+subrate=0       Substitution rate, 0 to 1.     
+indelrate=0     Indel rate, 0 to 1.
+maxindel=1      Max indel length.
+indelspacing=10 Minimum distance between subsequent indels.
+id=1            Target identity, 0 to 1; 1 means 100%.
+                If this is used it will override subrate and indelrate;
+                99% of the mutations will be substitutions, and 1% indels.
+fraction=1      Genome fraction, 0 to 1; 1 means 100%.  A lower fraction
+                will randomly select that fraction on a per-sequence basis,
+                possibly incurring one chimeric junction per sequence.
+                Not compatible with VCF output.
+period=-1       If positive, place exactly one mutation every X bases.
+prefix=         Set this flag to rename the new contigs with this prefix
+                and a number.
+amino=f         Treat the input as amino acid sequence.
+ploidy=1        Set the ploidy.  ploidy>1 allows heterozygous mutations.
+                This will create one copy of each input sequence per ploidy.
+hetrate=0.5     If polyploid, fraction of mutations that are heterozygous.
+nohomopolymers=f  If true, prevent indels in homopolymers that lead to
+                ambiguous variant calls.  For example, inserting A between
+                AC or deleting T from TTTT.  This is mainly for grading 
+                purposes.  It does not fully solve the problem, but greatly
+                improves concordance (reducing disagreements by 70%).
+
+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${RAM}m"
+}
+calcXmx "$@"
+
+mutate() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.MutateGenome $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+mutate "$@"