#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified December 10, 2019

Description:  Generates the consensus sequence of a reference
using aligned sequences.  This can be used for polishing assemblies,
making representative ribosomal sub units, correcting PacBio reads, etc.

Usage:  consensus.sh in=mapped.sam ref=ref.fa out=consensus.fa

Recommended settings for assembly polishing via Illumina reads:  mafsub=0.5


Standard parameters:
in=<file>       Reads mapped to the reference; should be sam or bam.
ref=<file>      Reference; may be fasta or fastq.
out=<file>      Modified reference; may be fasta or fastq.
overwrite=f     (ow) Set to false to force the program to abort rather than
                overwrite an existing file.

Processing parameters:
mindepth=2      Do not change to alleles present at depth below this.
mafsub=0.25     Do not incorporate substitutions below this allele fraction.
mafdel=0.50     Do not incorporate deletions below this allele fraction.
mafins=0.50     Do not incorporate insertions below this allele fraction.
mafn=0.40       Do not change Ns (noref) to calls below this allele fraction.
usemapq=f       Include mapq as a positive factor in edge weight.
nonly=f         Only change Ns to different bases.
noindels=f      Don't allow indels.
ceiling=        If set, alignments will be weighted by their inverse identity.
                For example, at ceiling=105, a read with 96% identity will get
                bonus weight of 105-96=9 while a read with 70% identity will
                get 105-70=35.  This favors low-identity reads.
name=           Set the output sequence name (for a single output sequence).

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="-Xmx4g"
z2="-Xms4g"
set=0

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

calcXmx () {
	source "$DIR""/calcmem.sh"
	setEnvironment
	parseXmx "$@"
	if [[ $set == 1 ]]; then
		return
	fi
	freeRam 4000m 84
	z="-Xmx${RAM}m"
	z2="-Xms${RAM}m"
}
calcXmx "$@"

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

consensus "$@"
