--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/tetramerfreq.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,79 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Shijie Yao 
+Last modified May 31, 2018
+
+Description: DNA Tetramer analysis.
+DNA tetramers are counted for each sub-sequence of window size in the sequence.  
+The window slides along the sequence by the step length.
+Sub-sequence shorter than the window size is ignored. Tetramers containing N are ignored. 
+
+Usage: TetramerFreq.sh in=<input file> out=<output file> step=500 window=2000
+
+Input may be fasta or fastq, compressed or uncompressed.
+
+Standard parameters:
+in=<file>       DNA sequence input file 
+out=<file>      Output file name
+step/s=INT      Step size (default 500) 
+window/w=INT    Window size (default 2kb); <=0 turns windowing off (e.g. short reads)
+short=T/F       Print lines for sequences shorter than window (default F)
+k=INT           Kmer length (default 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="-Xmx4g"
+z2="-Xms4g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 4000m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+tetramerfreq () {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.TetramerFrequencies $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+tetramerfreq "$@"