--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/representative.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,100 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified September 4, 2019
+
+Description:  Makes a representative set of taxa from all-to-all identity
+comparison.  Input should be in 3+ column TSV format (first 3 are required):
+(query, ref, ANI, qsize, rsize, qbases, rbases)
+...as produced by CompareSketch with format=3 and usetaxidname.
+Additional columns are allowed and will be ignored.
+
+Usage:  representative.sh in=<input file> out=<output file>
+
+Parameters:
+overwrite=f     (ow) Set to false to force the program to abort rather than
+                overwrite an existing file.
+threshold=0     Ignore edges under threshold value.  This also affects the
+                choice of centroids; a high threshold gives more weight to 
+                higher-value edges.
+minratio=0      Ignores edges with a ratio below this value.
+invertratio=f   Invert the ratio when greater than 1.
+printheader=t   Print a header line in the output.
+printsize=t     Print the size of retained nodes.
+printclusters=t Print the nodes subsumed by each retained node.
+minsize=0       Ignore nodes under this size (in unique kmers).
+maxsize=0       If positive, ignore nodes over this size (unique kmers).
+minbases=0      Ignore nodes under this size (in total bases).
+maxbases=0      If positive, ignore nodes over this size (total bases).
+
+Taxonomy parameters:
+level=          Taxonomic level, such as phylum.  Filtering will operate on
+                sequences within the same taxonomic level as specified ids.
+                If not set, only matches to a node or its descendants will 
+                be considered.
+ids=            Comma-delimited list of NCBI numeric IDs.  Can also be a
+                file with one taxID per line.
+names=          Alternately, a list of names (such as 'Homo sapiens').
+                Note that spaces need special handling.
+include=f       'f' will discard filtered sequences, 't' will keep them.
+tree=<file>     Specify a TaxTree file like tree.taxtree.gz.  
+                On Genepool, use 'auto'.
+
+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 around 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${RAM}m"
+}
+calcXmx "$@"
+
+a_sample_mt() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.RepresentativeSet $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+a_sample_mt "$@"