--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/kmerlimit2.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,86 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified July 31, 2018
+
+Description:  Subsamples reads to reach a target unique kmer limit.
+
+Differences between versions:
+kmerlimit.sh uses 1 pass and outputs all reads until a limit is hit,
+meaning the input reads should be in random order with respect to sequence.
+kmerlimit2.sh uses 2 passes and randomly subsamples from the file, so
+it works with reads in any order.
+
+Usage:  kmerlimit2.sh in=<input file> out=<output file> limit=<number>
+
+Standard parameters:
+in=<file>       Primary input, or read 1 input.
+in2=<file>      Read 2 input if reads are in two files.
+out=<file>      Primary output, or read 1 output.
+out2=<file>     Read 2 output if reads are in two files.
+overwrite=t     (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:
+k=31            Kmer length, 1-32.
+limit=          The number of unique kmers to produce.
+mincount=1      Ignore kmers seen fewer than this many times.
+minqual=0       Ignore bases with quality below this.
+minprob=0.2     Ignore kmers with correctness probability below this.
+trials=25       Simulation trials.
+seed=-1         Set to a positive number for deterministic output.
+maxlen=50m      Max length of a temp array used in simulation.
+
+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="-Xmx1000m"
+z2="-Xms1000m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+kmerlimit2() {
+	local CMD="java $EA $EOOM $z -cp $CP sketch.KmerLimit2 $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+kmerlimit2 "$@"