--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/countsharedlines.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,76 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified September 15, 2015
+
+Description:  Counts the number of lines shared between sets of files.
+One output file will be printed for each input file.  For example,
+an output file for a file in the 'in1' set will contain one line per
+file in the 'in2' set, indicating how many lines are shared.
+
+Usage:  countsharedlines.sh in1=<file,file...> in2=<file,file...>
+
+Parameters:
+include=f       Set to 'true' to include the filtered names rather than excluding them.
+prefix=f        Allow matching of only the line's prefix (all characters up to first whitespace).
+case=t          (casesensitive) Match case also.
+ow=t            (overwrite) Overwrites files that already exist.
+app=f           (append) Append to files that already exist.
+zl=4            (ziplevel) Set compression level, 1 (low) to 9 (max).
+
+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="-Xmx800m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+		return
+	fi
+	freeRam 800m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+function countsharedlines() {
+	local CMD="java $EA $EOOM $z -cp $CP driver.CountSharedLines $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+countsharedlines "$@"