--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/kmercoverage.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,102 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified May 23, 2014
+
+*** DEPRECATED: This should still work but is no longer maintained. ***
+
+Description:  Annotates reads with their kmer depth.
+
+Usage:        kmercoverage in=<input> out=<read output> hist=<histogram output>
+
+Input parameters:
+in2=null            Second input file for paired reads
+extra=null          Additional files to use for input (generating hash table) but not for output
+fastareadlen=2^31   Break up FASTA reads longer than this.  Can be useful when processing scaffolded genomes
+tablereads=-1       Use at most this many reads when building the hashtable (-1 means all)
+kmersample=1        Process every nth kmer, and skip the rest
+readsample=1        Process every nth read, and skip the rest
+
+Output parameters:
+hist=null           Specify a file to output the depth histogram
+histlen=10000       Max depth displayed on histogram
+reads=-1            Only process this number of reads, then quit (-1 means all)
+sampleoutput=t      Use sampling on output as well as input (not used if sample rates are 1)
+printcoverage=f     Only print coverage information instead of reads
+useheader=f         Append coverage info to the read's header
+minmedian=0         Don't output reads with median coverage below this
+minaverage=0        Don't output reads with average coverage below this
+zerobin=f           Set to true if you want kmers with a count of 0 to go in the 0 bin instead of the 1 bin in histograms.
+                    Default is false, to prevent confusion about how there can be 0-count kmers.
+                    The reason is that based on the 'minq' and 'minprob' settings, some kmers may be excluded from the bloom filter.
+
+Hashing parameters:
+k=31                Kmer length (values under 32 are most efficient, but arbitrarily high values are supported)
+cbits=8             Bits per cell in bloom filter; must be 2, 4, 8, 16, or 32.  Maximum kmer depth recorded is 2^cbits.
+                    Large values decrease accuracy for a fixed amount of memory.
+hashes=4            Number of times a kmer is hashed.  Higher is slower.
+                    Higher is MORE accurate if there is enough memory, and LESS accurate if there is not enough memory.
+prefilter=f         True is slower, but generally more accurate; filters out low-depth kmers from the main hashtable.
+prehashes=2         Number of hashes for prefilter.
+passes=1            More passes can sometimes increase accuracy by iteratively removing low-depth kmers
+minq=7              Ignore kmers containing bases with quality below this
+minprob=0.5         Ignore kmers with overall probability of correctness below this
+threads=X           Spawn exactly X hashing threads (default is number of logical processors).  Total active threads may exceed X by up to 4.
+
+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${RAM}m"
+}
+calcXmx "$@"
+
+kmercoverage() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.KmerCoverage prefilter=true bits=16 interleaved=false $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+kmercoverage "$@"