--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/kcompress.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,103 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified July 16, 2018
+
+Description:  Compresses sequence data into a fasta file containing each kmer
+exactly once.  Allows arbitrary kmer set operations via multiple passes.
+
+Usage:  kcompress.sh in=<reads> out=<contigs> min=<1> max=<2147483647>
+
+Input parameters:
+in=<file>           Primary input file for reads to use as kmer data.
+in2=<file>          Second input file for paired data.
+reads=-1            Only process this number of reads, then quit (-1 means all).
+
+Output parameters:
+out=<file>          Write contigs (in contig mode).
+showstats=t         Print assembly statistics after writing contigs.
+fuse=0              Fuse output sequences into chunks at least this long,
+                    padded with 1 N between sequences.
+
+Prefiltering parameters:
+prefilter=0         If set to a positive integer, use a countmin sketch
+                    to ignore kmers with depth of that value or lower.
+prehashes=2         Number of hashes for prefilter.
+prefiltersize=0.2   (pff) Fraction of memory to use for prefilter.
+minprobprefilter=t  (mpp) Use minprob for the prefilter.
+prepasses=1         Use this many prefiltering passes; higher be more thorough
+                    if the filter is very full.  Set to 'auto' to iteratively 
+                    prefilter until the remaining kmers will fit in memory.
+
+Hashing parameters:
+k=31                Kmer length (1 to 31).
+prealloc=t          Pre-allocate memory rather than dynamically growing; 
+                    faster and more memory-efficient.  A float fraction (0-1)
+                    may be specified; default is 1.
+minprob=0.5         Ignore kmers with overall probability of correctness below this.
+minprobmain=t       (mpm) Use minprob for the primary kmer counts.
+threads=X           Spawn X threads (default is number of logical processors).
+
+Assembly parameters:
+mincount=1          (min) Only retain kmers that occur at least this many times.
+maxcount=BIG        (max) Only retain kmers that occur at most this many times.
+requiresamecount    (rsc) Only build contigs from kmers with exactly the same count.
+rcomp=t             Store forward and reverse kmers together.  Setting this to
+                    false will only use forward kmers.
+
+
+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.
+"
+}
+
+#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="-Xmx14g"
+z2="-Xms14g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 15000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+kcompress() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.KmerCompressor $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+kcompress "$@"