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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified October 17, 2016
Description: Summarizes the output of multiple Quast reports for
making box plots.
Usage: summarizequast.sh */quast/report.tsv
Parameters:
out=stdout Destination for summary.
required= A required substring in assembly names for filtering.
normalize=t Normalize each metric to the average per report.
box=t Print only 5 points per metric for box plots.
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="-Xmx400m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
summarizequast() {
local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeQuast $@"
# echo $CMD >&2
eval $CMD
}
summarizequast "$@"
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