--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/kmercountexact.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,146 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified October 14, 2020
+
+Description:  Counts the number of unique kmers in a file.
+Generates a kmer frequency histogram and genome size estimate (in peaks output),
+and prints a file containing all kmers and their counts.
+Supports K=1 to infinity, though not all values are allowed.
+SEE ALSO: bbnorm.sh/khist.sh, loglog.sh, and kmercountmulti.sh.
+
+Usage:   kmercountexact.sh in=<file> khist=<file> peaks=<file>
+
+Input may be fasta or fastq, compressed or uncompressed.
+Output may be stdout or a file.  out, khist, and peaks are optional.
+
+
+Input parameters:
+in=<file>           Primary input file.
+in2=<file>          Second input file for paired reads.
+amino=f             Run in amino acid mode.
+
+Output parameters:
+out=<file>          Print kmers and their counts.  This is produces a
+                    huge file, so skip it if you only need the histogram.
+fastadump=t         Print kmers and counts as fasta versus 2-column tsv.
+mincount=1          Only print kmers with at least this depth.
+reads=-1            Only process this number of reads, then quit (-1 means all).
+dumpthreads=-1      Use this number of threads for dumping kmers (-1 means auto).
+
+Hashing parameters:
+k=31                Kmer length (1-31 is fastest).
+prealloc=t          Pre-allocate memory rather than dynamically growing; faster and more memory-efficient.  A float fraction (0-1) may be specified, default 1.
+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   Fraction of memory to use for prefilter.
+minq=6              Ignore kmers containing bases with quality below this. (TODO)
+minprob=0.0         Ignore kmers with overall probability of correctness below this.
+threads=X           Spawn X hashing threads (default is number of logical processors).
+onepass=f           If true, prefilter will be generated in same pass as kmer counts.  Much faster but counts will be lower, by up to prefilter's depth limit.
+rcomp=t             Store and count each kmer together and its reverse-complement.
+
+Histogram parameters:
+khist=<file>        Print kmer frequency histogram.
+histcolumns=2       2 columns: (depth, count).  3 columns: (depth, rawCount, count).
+histmax=100000      Maximum depth to print in histogram output.
+histheader=t        Set true to print a header line.
+nzo=t               (nonzeroonly) Only print lines for depths with a nonzero kmer count.
+gchist=f            Add an extra histogram column with the average GC%.
+
+Intersection parameters:
+ref=<file>          An input assembly of the input reads.
+intersection=<file> Output file for a 2-D histogram of read and ref kmer counts.
+refmax=6            Maximum reference kmer depth to track; read depth is controlled by 'histmax'.
+
+Smoothing parameters:
+smoothkhist=f       Smooth the output kmer histogram.
+smoothpeaks=t       Smooth the kmer histogram for peak-calling, but does not affect the output histogram.
+smoothradius=1      Initial radius of progressive smoothing function.
+maxradius=10        Maximum radius of progressive smoothing function.
+progressivemult=2   Increment radius each time depth increases by this factor.
+logscale=t          Transform to log-scale prior to peak-calling.
+logwidth=0.1        The larger the number, the smoother.
+
+Peak calling parameters:
+peaks=<file>        Write the peaks to this file.  Default is stdout. 
+                    Also contains the genome size estimate in bp.
+minHeight=2         (h) Ignore peaks shorter than this.
+minVolume=5         (v) Ignore peaks with less area than this.
+minWidth=3          (w) Ignore peaks narrower than this.
+minPeak=2           (minp) Ignore peaks with an X-value below this.
+maxPeak=BIG         (maxp) Ignore peaks with an X-value above this.
+maxPeakCount=12     (maxpc) Print up to this many peaks (prioritizing height).
+ploidy=-1           Specify ploidy; otherwise it will be autodetected.
+
+Sketch parameters (for making a MinHashSketch):
+sketch=<file>       Write a minhash sketch to this file.
+sketchlen=10000     Output the top 10000 kmers.  Only kmers with at least mincount are included.
+sketchname=         Name of output sketch.
+sketchid=           taxID of output sketch.
+
+Quality parameters:
+qtrim=f             Trim read ends to remove bases with quality below minq.
+                    Values: t (trim both ends), f (neither end), r (right end only), l (left end only).
+trimq=4             Trim quality threshold.
+minavgquality=0     (maq) Reads with average quality (before trimming) below this will be discarded.
+
+Overlap parameters (for overlapping paired-end reads only):
+merge=f             Attempt to merge reads before counting kmers.
+ecco=f              Error correct via overlap, but do not merge reads.   
+
+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="-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${RAM}m"
+}
+calcXmx "$@"
+
+kmercountexact() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.KmerCountExact $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+kmercountexact "$@"