--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/randomreads.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,176 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified April 1, 2019
+
+Description:  Generates random synthetic reads from a reference genome.  Read names indicate their genomic origin.
+Allows precise customization of things like insert size and synthetic mutation type, sizes, and rates.
+Read names generated by this program are used by MakeRocCure (samtoroc.sh) and GradeSamFile (gradesam.sh).
+They can also be used by BBMap (bbmap.sh) and BBMerge (bbmerge.sh) to automatically calculate
+true and false positive rates, if the flag 'parsecustom' is used.
+
+Usage:   randomreads.sh ref=<file> out=<file> length=<number> reads=<number>
+
+Basic parameters:
+out=null        Output file.  If reads are paired and a single file name is
+                given, output will be interleaved.  For paired reads in twin
+                files, set out1= and out2= 
+ref=null        Reference file.  Not needed if the reference is already indexed.
+build=1         If multiple references are indexed in the same directory,
+                each needs a unique build ID.
+midpad=300      Specifies space between scaffolds in packed index.
+reads=0         Generate this many reads (or pairs).
+coverage=-1     If positive, generate enough reads to hit this coverage
+                target, based on the genome size.
+overwrite=t     Set to false to disallow overwriting of existing files.
+replacenoref=f  Set to true to replace Ns in the reference sequence 
+                with random letters.
+simplenames=f   Set to true to generate read names that clearly indicate
+                genomic origin, without BBMap internal coordinates.
+illuminanames=f Set to true to have matching names for paired reads, 
+                rather than naming by location.
+renamebyinsert=f    Insert the insert size into the name.
+addpairnum=f    Set true to add ' 1:' and ' 2:' to the end of read names.
+addslash=f      Set true to add '/1' and '/2' to the end of read names.
+spaceslash=f    Set true to add a space before slash read pairnum.
+prefix=null     Generated reads will start with this prefix, 
+                rather than naming by location.
+seed=0          Use this to set the random number generator seed; 
+                use -1 for a random seed.
+
+Length Parameters - normally only minlength and maxlength are needed.
+minlength=150   Generate reads of up to this length.
+maxlength=150   Generate reads of at least this length.
+gaussianlength=f  Use a gaussian length distribution (for PacBio).
+                  Otherwise, the distribution is linear.
+midlength=-1    Gaussian curve peaks at this point.  Must be between
+                minlength and maxlength, in Gaussian mode.
+readlengthsd=-1 Standard deviation of the Gaussian curve.  Note that the
+                final curve is a sum of multiple curves, but this will affect
+                overall curve width.  By default this is set to 1/4 of range.
+
+Pairing parameters:
+paired=f        Set to true for paired reads.
+mininsert=      Controls minimum insert length.  Default depends on read length.
+maxinsert=      Controls maximum insert length.  Default depends on read length.
+triangle=f      Make a triangular insert size distribution.
+flat=f          Make a roughly flat insert size distribution..
+superflat=f     Make a perfectly flat insert size distribution.
+gaussian=t      Make a bell-shaped insert size distribution, with 
+                standard deviation of (maxinsert-mininsert)/6.
+samestrand=f    Generate paired reads on the same strand.
+
+Mutation parameters:
+snprate=0       Add snps to reads with this probability (0-1).
+insrate=0       Add insertions to reads with this probability (0-1).
+delrate=0       Add deletions to reads with this probability (0-1).
+subrate=0       Add contiguous substitutions to reads with this probability (0-1).
+nrate=0         Add nocalls to reads with this probability (0-1).
+
+Note: With a 'rate' of X, each read has an X chance of getting at least 
+1 mutation, X^2 chance of 2+ mutations, X^3 chance of 3+ mutations, 
+and so forth up to the maximum allowed number of mutations of that type.
+
+maxsnps=3       Add at most this many snps per read.
+maxinss=2       Add at most this many deletions per read.
+maxdels=2       Add at most this many insertions per read.
+maxsubs=2       Add at most this many contiguous substitutions per read.
+maxns=0         Add at most this many blocks of Ns per read.
+
+maxinslen=12    Max length of insertions.
+maxdellen=400   Max length of deletions.
+maxsublen=12    Max length of contiguous substitutions.
+maxnlen=1       Min length of N blocks.
+
+mininslen=1     Min length of insertions.
+mindellen=1     Min length of deletions.
+minsublen=2     Min length of contiguous substitutions.
+minnlen=1       Min length of N blocks.
+
+Illumina quality parameters:
+maxq=36         Upper bound of quality values.
+midq=28         Approximate average of quality values.
+minq=20         Lower bound of quality values.
+q=              Sets maxq, midq, and minq to the same value.
+adderrors=t     Add substitution errors based on quality values, 
+                after mutations.
+qv=4            Vary the base quality of reads by up to this much
+                to simulate tile effects.
+
+PacBio quality parameters:
+pacbio=f        Use a PacBio error model, rather than Illumina 
+                error model, and add PacBio errors after mutations.
+pbmin=0.13      Minimum rate of PacBio errors for a read.
+pbmax=0.17      Maximum rate of PacBio errors for a read.
+
+Other Parameters:
+overlap=1       Require reads to overlap scaffold end by at least this much.
+banns=f         Do not generate reads over reference Ns.
+metagenome=f    Assign scaffolds a random exponential coverage level,
+                to simulate a metagenomic or RNA coverage distribution.
+randomscaffold=f    Choose random scaffolds without respect to length.
+amp=1           Simulate highly-amplified MDA single-cell data by 
+                setting this to a higher number like 1000.
+replacenoref=f  Replace intra- and inter-scaffold Ns with random bases.
+pbadapter=      Add adapter sequence to some reads using this literal string.
+fragadapter=    Add this sequence to paired reads with insert size 
+                shorter than read length.
+fragadapter2=   Use this sequence for read 2.
+
+Java Parameters:
+-Xmx            This will set Java's memory usage, overriding the 
+                program's automatic memory detection.
+                -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.
+"
+}
+
+#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="-Xmx1g"
+z2="-Xms1g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 3200m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+randomreads() {
+	local CMD="java $EA $EOOM $z -cp $CP align2.RandomReads3 build=1 $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+randomreads "$@"