--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/comparevcf.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,86 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified April 30, 2019
+
+Description:  Performs set operations on VCF files:
+Union, intersection, and subtraction.
+
+Usage:  comparevcf.sh in=<file,file,...> out=<file>
+
+I/O parameters:
+in=<file>       Input; must be at least 2 files.
+out=<file>      Output file.
+ref=<file>      Reference file; optional.  Usually not needed.
+shist=<file>    (scorehist) Output for variant score histogram.
+overwrite=f     (ow) Set to false to force the program to abort rather than
+bgzip=f         Use bgzip for gzip compression.
+
+Processing Mode (choose one only):
+subtract=t      Subtract all other files from the first file.
+union=f         Make a union of all files.
+intersection=f  Make an intersection of all files.
+
+Processing Parameters:
+addsamples=t    Include all samples in the output lines. (TODO)
+splitalleles=f  Split multi-allelic lines into multiple lines.
+splitsubs=f     Split multi-base substitutions into SNPs.
+canonize=t      Trim variations down to a canonical representation.
+
+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${RAM}m"
+}
+calcXmx "$@"
+
+comparevcf() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP var2.CompareVCF $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+comparevcf "$@"