1#!/usr/local/bin/bash
2
3usage(){
4echo "
5Written by Brian Bushnell
6Last modified October 17, 2016
7
8Description:  Summarizes the output of multiple Quast reports for
9making box plots.
10
11Usage:  summarizequast.sh */quast/report.tsv
12
13Parameters:
14out=stdout      Destination for summary.
15required=       A required substring in assembly names for filtering.
16normalize=t     Normalize each metric to the average per report.
17box=t           Print only 5 points per metric for box plots.
18
19Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
20"
21}
22
23#This block allows symlinked shellscripts to correctly set classpath.
24pushd . > /dev/null
25DIR="${BASH_SOURCE[0]}"
26while [ -h "$DIR" ]; do
27  cd "$(dirname "$DIR")"
28  DIR="$(readlink "$(basename "$DIR")")"
29done
30cd "$(dirname "$DIR")"
31DIR="$(pwd)/"
32popd > /dev/null
33
34#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
35CP="$DIR""current/"
36
37z="-Xmx400m"
38set=0
39
40if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
41	usage
42	exit
43fi
44
45calcXmx () {
46	source "$DIR""/calcmem.sh"
47	setEnvironment
48	parseXmx "$@"
49}
50calcXmx "$@"
51
52summarizequast() {
53	local CMD="java $EA $EOOM $z -cp $CP driver.SummarizeQuast $@"
54#	echo $CMD >&2
55	eval $CMD
56}
57
58summarizequast "$@"
59