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
|
#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified September 6, 2023
Description: Splits a sequence file evenly into multiple files.
Usage: partition.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> ways=<number>
in2 and out2 are for paired reads and are optional.
If input is paired and out2 is not specified, data will be written interleaved.
Output filenames MUST contain a '%' symbol. This will be replaced by a number.
Parameters and their defaults:
in=<file> Input file.
out=<file> Output file pattern (containing a % symbol, like 'part%.fa').
ways=-1 The number of output files to create; must be positive.
pacbio=f Set to true to keep PacBio subreads together.
bp=f Optimize for an even split by base pairs instead of sequences.
Not compatible with PacBio mode.
ow=f (overwrite) Overwrites files that already exist.
app=f (append) Append to files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
int=f (interleaved) Determines whether INPUT file is considered interleaved.
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="-Xmx1g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
function partition() {
local CMD="java $EA $EOOM $z -cp $CP jgi.PartitionReads $@"
echo $CMD >&2
eval $CMD
}
partition "$@"
|
