#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified May 4, 2025

Description:  Bins contigs using coverage and kmer frequencies.
If reads or covstats are provided, coverage will be calculated from those;
otherwise, it will be parsed from contig headers.  Coverage can be parsed
from Spades or Tadpole contig headers; alternatively, renamebymapping.sh
can be used to annotate the headers with coverage from multiple sam files.
Any number of sam files may be used (from different samples of the same
environment, usually).  The more sam files, the more accurate.  Ideally,
sam files will be generated from paired reads like this:
bbmap.sh ref=contigs.fa in=reads.fq ambig=random mateqtag minid=0.9 maxindel=10 out=mapped.sam
For PacBio-only metagenomes, it is best to generate synthetic paired 
reads from the PacBio CCS reads and align them:
randomreadsmg.sh in=ccs.fa out=synth.fq depth=10 variance=0 paired length=250 avginsert=600 

Usage:  
quickbin.sh in=contigs.fa out=bins *.sam covout=cov.txt
or
quickbin.sh in=contigs.fa out=bins cov=cov.txt
or
quickbin.sh contigs.fa out=bins *.sam

File parameters:
in=<file>       Assembly input.  A file named *.fa does not need 'in='.
reads=<file>    Read input (sam or bam).  Multiple sam files may be used,
                comma-delimited, or as plain arguments without 'reads='.
                Multiple files will be assumed to be independent samples.
covout=<file>   Coverage file summarizing sam files; allows rerunning
                QuickBin much faster.
cov=<file>      Cov file generated by QuickBin via 'covout'; can be used
                instead of sam/bam.  Files named cov*.txt do not need 'cov='
out=<pattern>   Output pattern.  If this contains a % symbol, like bin%.fa,
                one file will be created per bin.  If not, all contigs will
                be written to the same file, with the name modified to
                indicate their bin number.  A term without a '.' symbol
                like 'out=output' will be considered a directory.
chaff           Enable to write small clusters to a shared file.

Size parameters:
mincluster=50k  (mcs) Minimum output cluster size in base pairs; smaller 
                clusters will share a residual file if chaff=t.
mincontig=100   Don't load contigs smaller than this; reduces memory usage.
minseed=3000    Minimum contig length to create a new cluster; reducing this
                can increase speed dramatically for large metagenomes,
                increase sensitivity for small contigs, and slightly increase
                contamination.  In particular, large metagenomes with only 
                1 sample will run slowly if this is below 2000; with 
                at least 3 samples the speed should not be affected much.
minresidue=200  Discard unclustered contigs shorter than this; reduces memory.
dumpsequence    (TODO) Discard sequence to reduce memory usage.
dumpheaders     (TODO) Discard headers to reduce memory usage.
minpentamersize=2k  Increase this to reduce memory usage.

Stringency parameters:
normal          Default stringency is 'normal'.  All settings, in order of
                increasing sensitivity, are:  xstrict, ustrict, vstrict,
                strict, normal, loose, vloose, uloose, xloose.  'normal'
                aims at under 1% contamination; 'uloose' is more comparable
                in stringency to other binners.  To set a stringency just add
                that flag (without an = sign).  Acceptable shorthand is
                xs, us, vs, s, n, l, vl, ul, xl.

Quantization parameters:
gcwidth=0.02    Width of GC matrix gridlines.  Smaller is faster.
depthwidth=0.5  Width of depth matrix gridlines.  Smaller is faster.  This
                is on a log2 scale so 0.5 would mean 2 gridlines per power
                of 2 depth - lines at 0.707, 1, 1.414, 2, 2.818, 4, etc.
Note: Halving either quantization parameter can roughly double speed,
but may decrease recovery of shorter contigs.

Neural network parameters:
net=auto        Specify a neural network file to use; default is 
                bbmap/resources/quickbin1D_all.bbnet
cutoff=0.52     Neural network output threshold; higher increases specificity,
                lower increases sensitivity.  This is a soft cutoff that
                moderates other stringency settings, so increasing it would
                make 'strict' mode stricter.

Edge-processing parameters:
e1=0                  Edge-first clustering passes; may increase speed
                      at the cost of purity.
e2=4                  Later edge-based clustering passes.
edgeStringency1=0.25  Stringency for edge-first clustering; 
                      lower is more stringent.
edgeStringency2=1.1    Stringency for later edge-based clustering.
maxEdges=3            Follow up to this many edges per contig.
minEdgeWeight=2       Ignore edges made from fewer read pairs.
minEdgeRatio=0.4      Ignore edges under this fraction of max edge weight.
goodEdgeMult=1.4      Merge stringency multiplier for contigs joined by
                      an edge; lower is more stringent.
minmapq=20            When loading sam files, do not make edges from reads
                      with map lower than this.  Setting it to 0 will allow
                      ambigiously-mapped reads and may improve completeness.
                      Reads below minmapq are still used for depth.
minid=0.96            When loading sam files, ignore reads aligned with
                      identity below this, both for edges and coverage.

Other parameters:
sketchoutput=f        Use SendSketch to identify taxonomy of output clusters.
validate=f            If contig headers have a term such as 'tid_1234', this
                      will be parsed and used to evaluate correctness.
printcc=f             Print completeness/contam after each step.
callssu=f             Call 16S and 18S genes; do not merge clusters with
                      incompatible SSU sequence.
minssuid=0.98         SSUs with identity below this are incompatible.
aligner=quantum       Options include ssa2, glocal, drifting, banded, crosscut.

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/"

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

calcXmx () {
    # Source the new scripts
    source "$DIR""/memdetect.sh"
    source "$DIR""/javasetup.sh"
    
    # Parse Java arguments with tool-specific defaults
    # Use auto mode with 84% of available RAM, minimum 4000MB
    parseJavaArgs "--mem=4000m" "--percent=84" "--mode=auto" "$@"
    
    # Set environment paths
    setEnvironment
    
    # Set the Java memory parameters
    z="-Xmx${RAM}m"
    z2="-Xms${RAM}m"
}
calcXmx "$@"

quickbin() {
	local CMD="java $EA $EOOM $SIMD $XMX $XMS -cp $CP bin.QuickBin $@"
	echo $CMD >&2
	eval $CMD
}

quickbin "$@"
