copyfile.sh

#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified October 9, 2023

Description:  Copies a file.
The main purpose is to recompress it.

Usage:  copyfile.sh in=<file> out=<file>

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=120m" "--xms=120m" "$@"
	setEnvironment
}

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

resolveSymlinks
setEnv "$@"
launch "$@"