#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified October 30, 2019

Description:  Filters reads based on positional quality over a flowcell.
Quality is estimated based on quality scores and kmer uniqueness.
All reads within a small unit of area called a micro-tile are averaged,
then the micro-tile is either retained or discarded as a unit.
Please read bbmap/docs/guides/FilterByTileGuide.txt for more information.

Usage:	filterbytile.sh in=<input> out=<output>

Input parameters:
in=<file>           Primary input file.
in2=<file>          Second input file for paired reads in two files.
indump=<file>       Specify an already-made dump file to use instead of
                    analyzing the input reads.
reads=-1            Process this number of reads, then quit (-1 means all).
interleaved=auto    Set true/false to override autodetection of the
                    input file as paired interleaved.
seed=-1             Set to a positive numver for deterministic output.

Output parameters:
out=<file>          Output file for filtered reads.
dump=<file>         Write a summary of quality information by coordinates.

Tile parameters:
xsize=500           Initial width of micro-tiles.
ysize=500           Initial height of micro-tiles.
size=               Allows setting xsize and ysize tot he same value.
target=800          Iteratively increase the size of micro-tiles until they
                    contain an average of at least this number of reads.

A micro-tile is discarded if any of 3 metrics indicate a problem.
The metrics are kmer uniqueness (u), average quality (q), and probability
of being error-free (e).  Each has 3 parameters: deviations (d),
fraction (f), and absolute (a).  After calculating the difference (delta)
between a micro-tile and average, it is discarded only if all three of these
conditions are true for at least one metric (using quality as the example):
1) delta is greater than (qd) standard deviations.
2) delta is greater than average times the fraction (qf).
3) delta is greater than the absolute value (qa).

Filtering parameters:
udeviations=1.5     (ud) Standard deviations for uniqueness discarding.
qdeviations=2       (qd) Standard deviations for quality discarding.
edeviations=2       (ed) Standard deviations for error-free probablity 
                    discarding.
ufraction=0.01      (uf) Min fraction for uniqueness discarding.
qfraction=0.01      (qf) Min fraction for quality discarding.
efraction=0.01      (ef) Min fraction for error-free probablity discarding.
uabsolute=1         (ua) Min absolute value for uniqueness discarding.
qabsolute=1         (qa) Min absolute value for quality discarding.
eabsolute=1         (ea) Min absolute value for error-free probablity discarding.

Other parameters:
lowqualityonly=t    (lqo) Only filter low quality reads within low quality 
                    micro-tiles, rather than the whole micro-tile.
trimq=-1            If set to a positive number, trim reads to that quality
                    level instead of filtering them.
qtrim=r             If trimq is positive, to quality trimming on this end
                    of the reads.  Values are r, l, and rl for right,
                    left, and both ends.

Java Parameters:
-Xmx                This will set Java's memory usage, overriding autodetection.
                    -Xmx20g will specify 20 GB of RAM; -Xmx200m will specify 
                    200 MB.  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="-Xmx8g"
z2="-Xms8g"
set=0

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

calcXmx () {
	source "$DIR""/calcmem.sh"
	setEnvironment
	parseXmx "$@"
	if [[ $set == 1 ]]; then
	return
	fi
	freeRam 3200m 84
	z="-Xmx${RAM}m"
	z2="-Xms${RAM}m"
}
calcXmx "$@"

filterbytile() {
	local CMD="java $EA $EOOM $z $z2 -cp $CP hiseq.AnalyzeFlowCell $@"
	echo $CMD >&2
	eval $CMD
}

filterbytile "$@"
