jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified January 25, 2018
jpayne@69: 
jpayne@69: Description:  Summarizes the output of BBSketch. 
jpayne@69: 
jpayne@69: Usage:  summarizesketch.sh in=<file,file...> out=<file>
jpayne@69: 
jpayne@69: You can alternately run 'summarizesketch.sh *.txt out=out.txt'
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>       A list of stats files, or a text file containing one stats file name per line.
jpayne@69: out=<file>      Destination for summary.
jpayne@69: tree=           A TaxTree file.
jpayne@69: level=genus     Ignore contaminants with the same taxonomy as the primary hit at this level.
jpayne@69: unique=f        Use the contaminant with the most unique hits rather than highest score.
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="-Xmx2g"
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: summarizesketch() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP sketch.SummarizeSketchStats $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: summarizesketch "$@"