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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified April 5, 2020
Description: Summarizes coverage information from basecov files
created by pileup.sh. They should be named like
'sample1_basecov.txt' but other naming styles are fine too.
Usage: summarizecoverage.sh *basecov.txt out=<output file>
Parameters:
in=<file> 'in=' is not necessary. Any filename used as a
parameter will be assumed to be an input basecov file.
out=<file> Write the summary here. Default is stdout.
reflen=-1 If positive, use this as the total reference length.
Otherwise, assume basecov files report every ref base.
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/"
z="-Xmx200m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
summarize() {
local CMD="java $EA $EOOM $z -cp $CP covid.SummarizeCoverage $@"
# echo $CMD >&2
eval $CMD
}
summarize "$@"
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