countsharedlines.sh

#!/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.
For documentation and the latest version, visit: https://bbmap.org
"
}

if [ -z "$1" ] || [ "$1" = "-h" ] || [ "$1" = "--help" ]; then
	usage
	exit
fi

resolveSymlinks(){
	SCRIPT="$(cd "$(dirname "$0")" && pwd)/$(basename "$0")"
	while [ -h "$SCRIPT" ]; do
		DIR="$(dirname "$SCRIPT")"
		SCRIPT="$(readlink "$SCRIPT")"
		[ "${SCRIPT#/}" = "$SCRIPT" ] && SCRIPT="$DIR/$SCRIPT"
	done
	DIR="$(cd "$(dirname "$SCRIPT")" && pwd)"
	if [ -f "$DIR/bbtools.jar" ]; then
		CP="$DIR/bbtools.jar"
	else
		CP="$DIR/current/"
	fi
}

setEnv(){
	. "$DIR/javasetup.sh"
	. "$DIR/memdetect.sh"

	parseJavaArgs "--xmx=800m" "--xms=800m" "--percent=84" "--mode=auto" "$@"
	setEnvironment
}

launch() {
	CMD="java $EA $EOOM $SIMD $XMX $XMS -cp $CP driver.CountSharedLines $@"
	echo "$CMD" >&2
	eval $CMD
}

resolveSymlinks
setEnv "$@"
launch "$@"