jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified April 5, 2020
jpayne@69: 
jpayne@69: Description:  Summarizes coverage information from basecov files
jpayne@69:               created by pileup.sh.  They should be named like
jpayne@69:               'sample1_basecov.txt' but other naming styles are fine too.
jpayne@69: 
jpayne@69: Usage:        summarizecoverage.sh *basecov.txt out=<output file>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>           'in=' is not necessary.  Any filename used as a
jpayne@69:                     parameter will be assumed to be an input basecov file.
jpayne@69: out=<file>          Write the summary here.  Default is stdout.
jpayne@69: reflen=-1           If positive, use this as the total reference length.
jpayne@69:                     Otherwise, assume basecov files report every ref base.
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="-Xmx200m"
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: summarize() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP covid.SummarizeCoverage $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: summarize "$@"