--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/mergesketch.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,99 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified December 19, 2019
+
+Description:  Merges multiple sketches into a single sketch.
+
+Please read bbmap/docs/guides/BBSketchGuide.txt for more information.
+
+Usage:           mergesketch.sh in=a.sketch,b.sketch out=c.sketch
+With wildcards:  mergesketch.sh *.sketch out=c.sketch
+
+Standard parameters:
+in=<file>       Input sketches or fasta files; may be a comma-delimited
+                list.  in= is optional so wildcards may be used.
+out=<file>      Output sketch.
+amino=f         Use amino acid mode.
+
+Sketch-making parameters:
+mode=single     Possible modes, for fasta input:
+                   single: Generate one sketch per file.
+                   sequence: Generate one sketch per sequence.
+autosize=t      Produce an output sketch of whatever size the union 
+                happens to be.
+size=           Restrict output sketch to this upper bound of size.
+k=32,24         Kmer length, 1-32.
+keyfraction=0.2 Only consider this upper fraction of keyspace.
+minkeycount=1   Ignore kmers that occur fewer times than this.  Values
+                over 1 can be used with raw reads to avoid error kmers.
+depth=f         Retain kmer counts if available.
+
+Metadata parameters: (if blank the values of the first sketch will be used)
+taxid=-1        Set the NCBI taxid.
+imgid=-1        Set the IMG id.
+spid=-1         Set the JGI sequencing project id.
+name=           Set the name (taxname).
+name0=          Set name0 (normally the first sequence header).
+fname=          Set fname (normally the file name).
+meta_=          Set an arbitrary metadata field.
+                For example, meta_Month=March.
+
+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.
+
+For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
+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 [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 3200m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+sendsketch() {
+	local CMD="java $EA $EOOM $z -cp $CP sketch.MergeSketch $@"
+#	echo $CMD >&2
+	eval $CMD
+}
+
+sendsketch "$@"