1#!/usr/local/bin/bash
2
3usage(){
4echo "
5Written by Brian Bushnell
6Last modified February 17, 2015
7
8Description:  Generates synthetic cross-contaminated files from clean files.
9Intended for use with synthetic reads generated by SynthMDA or RandomReads.
10
11Usage:        crosscontaminate.sh in=<file,file,...> out=<file,file,...>
12
13Input parameters:
14in=<file,file,...>  Clean input reads.
15innamefile=<file>   A file containing the names of input files,
16                    one name per line.
17interleaved=auto    (int) t/f overrides interleaved autodetection.
18qin=auto            Input quality offset: 33 (Sanger), 64, or auto.
19reads=-1            If positive, quit after processing X reads or pairs.
20
21Processing Parameters:
22minsinks=1          Min contamination destinations from one source.
23maxsinks=8          Max contamination destinations from one source.
24minprob=0.000005    Min allowed contamination rate (geometric distribution).
25maxprob=0.025       Max allowed contamination rate.
26
27Output parameters:
28out=<file,file,...> Contaminated output reads.
29outnamefile=<file>  A file containing the names of output files,
30                    one name per line.
31overwrite=t         (ow) Grant permission to overwrite files.
32#showspeed=t        (ss) 'f' suppresses display of processing speed.
33ziplevel=2          (zl) Compression level; 1 (min) through 9 (max).
34threads=auto        (t) Set number of threads to use; default is number of
35                    logical processors.
36qout=auto           Output quality offset: 33 (Sanger), 64, or auto.
37shuffle=f           Shuffle contents of output files.
38shufflethreads=3    Use this many threads for shuffling (uses more memory).
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 [[ $set == 1 ]]; then
80	return
81	fi
82	freeRam 4000m 42
83	z="-Xmx${RAM}m"
84}
85calcXmx "$@"
86
87crosscontaminate() {
88	local CMD="java $EA $EOOM $z -cp $CP jgi.CrossContaminate $@"
89	echo $CMD >&2
90	eval $CMD
91}
92
93crosscontaminate "$@"
94