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
|
#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified October 25, 2016
Description: Generates the conservative consensus of multiple
error-correction tools. Corrections will be accepted only
if all tools agree. This tool is designed for substitutions only,
not indel corrections.
Usage: consect.sh in=<file,file,file,...> out=<file>
Standard parameters:
in= A comma-delimited list of files; minimum of 3.
All files must have reads in the same order.
The first file must contain the uncorrected reads.
All additional files must contain corrected reads.
out=<file> Output of consensus reads.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
Processing parameters:
None yet!
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="-Xmx2g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
consect() {
local CMD="java $EA $EOOM $z -cp $CP jgi.Consect $@"
echo $CMD >&2
eval $CMD
}
consect "$@"
|
