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
|
#!/bin/bash
usage(){
echo "
Written by Brian Bushnell.
Last modified March 5, 2018
Description: Removes reads with barcodes containing non-ACGT bases.
Read headers must be in standard Illumina format.
Usage: removebadbarcodes.sh in=<file> out=<file>
Parameters:
in=<file> Input reads; required parameter.
out=<file> Destination for good reads; optional.
ziplevel=2 (zl) Compression level for gzip output.
pigz=f Spawn a pigz (parallel gzip) process for faster
compression than Java. Requires pigz to be installed.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx800m will specify 800 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/"
JNI="-Djava.library.path=""$DIR""jni/"
JNI=""
z="-Xmx200m"
z2="-Xms200m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
removebadbarcodes() {
local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.RemoveBadBarcodes $@"
echo $CMD >&2
eval $CMD
}
removebadbarcodes "$@"
|
