#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified July 31, 2018

Description:  Subsamples reads to reach a target unique kmer limit.

Differences between versions:
kmerlimit.sh uses 1 pass and outputs all reads until a limit is hit,
meaning the input reads should be in random order with respect to sequence.
kmerlimit2.sh uses 2 passes and randomly subsamples from the file, so
it works with reads in any order.

Usage:  kmerlimit2.sh in=<input file> out=<output file> limit=<number>

Standard parameters:
in=<file>       Primary input, or read 1 input.
in2=<file>      Read 2 input if reads are in two files.
out=<file>      Primary output, or read 1 output.
out2=<file>     Read 2 output if reads are in two files.
overwrite=t     (ow) Set to false to force the program to abort rather than
                overwrite an existing file.
ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression
                level; lower compression is faster.

Processing parameters:
k=31            Kmer length, 1-32.
limit=          The number of unique kmers to produce.
mincount=1      Ignore kmers seen fewer than this many times.
minqual=0       Ignore bases with quality below this.
minprob=0.2     Ignore kmers with correctness probability below this.
trials=25       Simulation trials.
seed=-1         Set to a positive number for deterministic output.
maxlen=50m      Max length of a temp array used in simulation.

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="-Xmx1000m"
z2="-Xms1000m"
set=0

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

calcXmx () {
	source "$DIR""/calcmem.sh"
	setEnvironment
	parseXmx "$@"
}
calcXmx "$@"

kmerlimit2() {
	local CMD="java $EA $EOOM $z -cp $CP sketch.KmerLimit2 $@"
	echo $CMD >&2
	eval $CMD
}

kmerlimit2 "$@"