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
87
88
89
90
91
|
#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified January 26, 2021
Description: Mutates a reference by applying a set of variants.
When 2 variants overlap, the one with the higher allele count is used.
Usage: applyvariants.sh in=<input file> vcf=<vcf file> out=<output file>
Standard parameters:
in=<file> Reference fasta.
vcf=<file> Variants.
basecov=<file> Optional per-base coverage from BBMap or Pileup.
out=<file> Output fasta.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
level; lower compression is faster.
Processing parameters:
mincov=0 If positive and depth is below this, change ref to N.
Requires a coverage file.
maxindel=-1 If positive, ignore indels longer than this.
noframeshifts=f Ignore indels that are not a multiple of 3 in length.
Renaming:
name= Optionally rename sequences to this.
addnumbers=f Add _1 and so forth to ensure sequence names are unique.
prefix=t Use the name as a prefix to the old name, instead of replacing
the old name.
delimiter=_ Symbol to place between parts of the new name.
For space or tab, use the literal word.
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 [[ $set == 1 ]]; then
return
fi
freeRam 4000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
applyvariants() {
local CMD="java $EA $EOOM $z -cp $CP var2.ApplyVariants $@"
echo $CMD >&2
eval $CMD
}
applyvariants "$@"
|
