1#!/usr/local/bin/bash 2 3usage(){ 4echo " 5Written by Brian Bushnell 6Last modified April 5, 2020 7 8Description: Summarizes coverage information from basecov files 9 created by pileup.sh. They should be named like 10 'sample1_basecov.txt' but other naming styles are fine too. 11 12Usage: summarizecoverage.sh *basecov.txt out=<output file> 13 14Parameters: 15in=<file> 'in=' is not necessary. Any filename used as a 16 parameter will be assumed to be an input basecov file. 17out=<file> Write the summary here. Default is stdout. 18reflen=-1 If positive, use this as the total reference length. 19 Otherwise, assume basecov files report every ref base. 20 21Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. 22" 23} 24 25#This block allows symlinked shellscripts to correctly set classpath. 26pushd . > /dev/null 27DIR="${BASH_SOURCE[0]}" 28while [ -h "$DIR" ]; do 29 cd "$(dirname "$DIR")" 30 DIR="$(readlink "$(basename "$DIR")")" 31done 32cd "$(dirname "$DIR")" 33DIR="$(pwd)/" 34popd > /dev/null 35 36#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" 37CP="$DIR""current/" 38 39z="-Xmx200m" 40set=0 41 42if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then 43 usage 44 exit 45fi 46 47calcXmx () { 48 source "$DIR""/calcmem.sh" 49 setEnvironment 50 parseXmx "$@" 51} 52calcXmx "$@" 53 54summarize() { 55 local CMD="java $EA $EOOM $z -cp $CP covid.SummarizeCoverage $@" 56# echo $CMD >&2 57 eval $CMD 58} 59 60summarize "$@" 61