--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/analyzesketchresults.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified December 19, 2019
+
+Description:  Analyzes sketch results from query, ref, ani format.
+
+Usage:  analyzesketchresults.sh in=<file> out=<outfile>
+
+
+Parameters and their defaults:
+
+in=<file>           Required input file of Sketch results in 3column format.
+in2=<file>          Optional second input file of Sketch results in amino mode.
+out=stdout.txt      Output file for summary of per-tax-level averages.
+outaccuracy=<file>  Output file for accuracy results; requires query taxIDs and printcal.
+outmap=<file>       Output file for ANI vs AAI.  Requires in2.
+bbsketch            Parse BBSketch output format (default).
+mash                Parse Mash output format.  Files should be named like this:
+                    tid_511145_Escherichia_coli_str._K-12_substr._MG1655.fa.gz
+blast               Parse Blast output format (TODO).
+
+ow=f                (overwrite) Overwrites files that already exist.
+app=f               (append) Append to files that already exist.
+
+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="-Xmx300m"
+z="-Xms300m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+function analyzesketchresults() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP sketch.AnalyzeSketchResults $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+analyzesketchresults "$@"