#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified July 6, 2015

Description:  Filters lines by exact match or substring.

Usage:  filterlines.sh in=<file> out=<file> names=<file> include=<t/f>

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).
substring=f     Allow one name to be a substring of the other, rather than a full match.
                   f:    No substring matching.
                   t:    Bidirectional substring matching.
                   line: Allow input lines to be substrings of names in list.
                   name: Allow names in list to be substrings of input lines.
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).
names=          A list of strings or files, comma-delimited.  Files must have one name per line.

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.

To read from stdin, set 'in=stdin'.  The format should be specified with an extension, like 'in=stdin.fq.gz'
To write to stdout, set 'out=stdout'.  The format should be specified with an extension, like 'out=stdout.fasta'

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 filterlines() {
	local CMD="java $EA $EOOM $z -cp $CP driver.FilterLines $@"
	echo $CMD >&2
	eval $CMD
}

filterlines "$@"
