1#!/usr/local/bin/bash
2
3usage(){
4echo "
5Written by Brian Bushnell
6Last modified April 24, 2019
7
8Description:  Reformats a fungal assembly for release.
9Also creates contig and agp files.
10
11Usage:  fungalrelease.sh in=<input file> out=<output file>
12
13I/O parameters:
14in=<file>           Input scaffolds.
15out=<file>          Output scaffolds.
16outc=<file>         Output contigs.
17qfin=<file>         Optional quality scores input.
18qfout=<file>        Optional quality scores output.
19qfoutc=<file>       Optional contig quality scores output.
20agp=<file>          Output AGP file.
21legend=<file>       Output name legend file.
22overwrite=f         (ow) Set to false to force the program to abort rather than
23                    overwrite an existing file.
24
25Processing parameters:
26fastawrap=60        Wrap length for fasta lines.
27tuc=t               Convert sequence to upper case.
28baniupac=t          Crash on encountering a non-ACGTN base call.
29mingap=10           Expand all gaps (Ns) to be at least this long.
30mingapin=1          Only expand gaps that are at least this long.
31sortcscaffolds=t    Sort scaffolds descending by length.
32sortcontigs=f       Sort contigs descending by length.
33renamescaffolds=t   Rename scaffolds to 'scaffold_#'.
34scafnum=1           Number of first scaffold.
35renamecontigs=f     Rename contigs to 'contig_#' instead of 'scafname_c#'.
36contignum=1         Number of first contig; only used if renamecontigs=t.
37minscaf=1           Only retain scaffolds at least this long.
38mincontig=1         Only retain contigs at least this long.
39
40Java Parameters:
41-Xmx                This will set Java's memory usage, overriding autodetection.
42                    -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
43                    The max is typically 85% of physical memory.
44-eoom               This flag will cause the process to exit if an
45                    out-of-memory exception occurs.  Requires Java 8u92+.
46-da                 Disable assertions.
47
48Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
49"
50}
51
52#This block allows symlinked shellscripts to correctly set classpath.
53pushd . > /dev/null
54DIR="${BASH_SOURCE[0]}"
55while [ -h "$DIR" ]; do
56  cd "$(dirname "$DIR")"
57  DIR="$(readlink "$(basename "$DIR")")"
58done
59cd "$(dirname "$DIR")"
60DIR="$(pwd)/"
61popd > /dev/null
62
63#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
64CP="$DIR""current/"
65
66z="-Xmx4g"
67z2="-Xms4g"
68set=0
69
70if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
71	usage
72	exit
73fi
74
75calcXmx () {
76	source "$DIR""/calcmem.sh"
77	setEnvironment
78	parseXmx "$@"
79	if [[ $set == 1 ]]; then
80		return
81	fi
82}
83calcXmx "$@"
84
85fungalrelease() {
86	local CMD="java $EOOM $EA $EOOM $z $z2 -cp $CP jgi.FungalRelease $@"
87	echo $CMD >&2
88	eval $CMD
89}
90
91fungalrelease "$@"
92