--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/kmercountmulti.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,84 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified February 20, 2020
+
+Description:  Estimates cardinality of unique kmers in sequence data.
+Processes multiple kmer lengths simultaneously to produce a histogram.
+
+Usage:  kmercountmulti.sh in=<file> sweep=<20,100,8> out=<histogram output>
+
+Parameters:
+in=<file>           (in1) Input file, or comma-delimited list of files.
+in2=<file>          Optional second file for paired reads.
+out=<file>          Histogram output.  Default is stdout.
+k=                  Comma-delimited list of kmer lengths to use.
+sweep=min,max,incr  Use incremented kmer values from min to max. For example,
+                    sweep=20,26,2 is equivalent to k=20,22,24,26.
+buckets=2048        Use this many buckets for counting; higher decreases
+                    variance, for large datasets.  Must be a power of 2.
+seed=-1             Use this seed for hash functions.  
+                    A negative number forces a random seed.
+minprob=0           Set to a value between 0 and 1 to exclude kmers with a 
+                    lower probability of being correct.
+hashes=1            Use this many hash functions.  More hashes yield greater
+                    accuracy, but H hashes takes H times as long.
+stdev=f             Print standard deviations.
+
+Shortcuts:
+The # symbol will be substituted for 1 and 2.
+For example:
+kmercountmulti.sh in=read#.fq
+...is equivalent to:
+kmercountmulti.sh in1=read1.fq in2=read2.fq
+
+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="-Xmx500m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+function kmercountmulti() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.KmerCountMulti $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+kmercountmulti "$@"