--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbcountunique.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,93 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified August 1, 2016
+
+Description:  Generates a kmer uniqueness histogram, binned by file position.
+There are 3 columns for single reads, 6 columns for paired:
+count        number of reads or pairs processed
+r1_first     percent unique 1st kmer of read 1
+r1_rand      percent unique random kmer of read 1
+r2_first     percent unique 1st kmer of read 2
+r2_rand      percent unique random kmer of read 2
+pair         percent unique concatenated kmer from read 1 and 2
+
+Please read bbmap/docs/guides/CalcUniquenessGuide.txt for more information.
+
+Usage:	bbcountunique.sh in=<input> out=<output>
+
+Input parameters:
+in2=null            Second input file for paired reads
+interleaved=auto    Set true/false to override autodetection of the input file as paired interleaved.
+samplerate=1        Set to below 1 to sample a fraction of input reads.
+reads=-1            Only process this number of reads, then quit (-1 means all)
+
+Output parameters:
+out=<file>          File for output stats
+
+Processing parameters:
+k=25                Kmer length (range 1-31).
+interval=25000      Print one line to the histogram per this many reads.
+cumulative=f        Show cumulative numbers rather than per-interval numbers.
+percent=t           Show percentages of unique reads.
+count=f             Show raw counts of unique reads.
+printlastbin=f      (plb) Print a line for the final undersized bin.
+minprob=0           Ignore kmers with a probability of correctness below this (based on q-scores).
+
+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="-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${RAM}m"
+}
+calcXmx "$@"
+
+bbcountunique() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.CalcUniqueness $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+bbcountunique "$@"