jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified December 19, 2019
jpayne@69: 
jpayne@69: Description:  Analyzes sketch results from query, ref, ani format.
jpayne@69: 
jpayne@69: Usage:  analyzesketchresults.sh in=<file> out=<outfile>
jpayne@69: 
jpayne@69: 
jpayne@69: Parameters and their defaults:
jpayne@69: 
jpayne@69: in=<file>           Required input file of Sketch results in 3column format.
jpayne@69: in2=<file>          Optional second input file of Sketch results in amino mode.
jpayne@69: out=stdout.txt      Output file for summary of per-tax-level averages.
jpayne@69: outaccuracy=<file>  Output file for accuracy results; requires query taxIDs and printcal.
jpayne@69: outmap=<file>       Output file for ANI vs AAI.  Requires in2.
jpayne@69: bbsketch            Parse BBSketch output format (default).
jpayne@69: mash                Parse Mash output format.  Files should be named like this:
jpayne@69:                     tid_511145_Escherichia_coli_str._K-12_substr._MG1655.fa.gz
jpayne@69: blast               Parse Blast output format (TODO).
jpayne@69: 
jpayne@69: ow=f                (overwrite) Overwrites files that already exist.
jpayne@69: app=f               (append) Append to files that already exist.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx                This will set Java's memory usage, overriding autodetection.
jpayne@69:                     -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
jpayne@69:                     The max is typically 85% of physical memory.
jpayne@69: -eoom               This flag will cause the process to exit if an out-of-memory exception occurs.  Requires Java 8u92+.
jpayne@69: -da                 Disable assertions.
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: 
jpayne@69: z="-Xmx300m"
jpayne@69: z="-Xms300m"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: function analyzesketchresults() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 -cp $CP sketch.AnalyzeSketchResults $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: analyzesketchresults "$@"