1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
|
#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified October 22, 2015
Description: Generates synthetic reads following an MDA-amplified single cell's coverage distribution.
Usage: synthmda.sh in=<reference> out=<reads out file>
Input may be fasta or fastq, compressed or uncompressed.
Parameters:
reads=12000000 Generate this many reads.
paired=t Generate paired reads.
length=150 Reads should be this long.
minlen=4000 Min length of MDA contig.
maxlen=150000 Max length of MDA contig.
cycles=9 Number of MDA cycles; higher is more spiky.
initialratio=1.3 Fraction of genome initially replicated;
lower is more spiky.
ratio=1.7 Fraction of genome replicated per cycle.
refout=null Write MDA'd genome to this file.
perfect=0 This fraction of reads will be error-free.
amp=200 'amp' flag sent to RandomReads (higher is more spiky).
build=7 Index MDA'd genome in this location.
prefix=null Generated reads will start with this prefix.
overwrite=t (ow) Set to false to force the program to abort rather
than overwrite an existing file.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an
out-of-memory exception occurs. Requires Java 8u92+.
-da Disable assertions.
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="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 80
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
synthmda() {
local CMD="java $EA $EOOM $z -cp $CP jgi.SynthMDA $@"
echo $CMD >&2
eval $CMD
}
synthmda "$@"
|
