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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/applyvariants.sh @ 69:33d812a61356

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
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67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell
6 Last modified January 26, 2021
7
8 Description: Mutates a reference by applying a set of variants.
9 When 2 variants overlap, the one with the higher allele count is used.
10
11 Usage: applyvariants.sh in=<input file> vcf=<vcf file> out=<output file>
12
13 Standard parameters:
14 in=<file> Reference fasta.
15 vcf=<file> Variants.
16 basecov=<file> Optional per-base coverage from BBMap or Pileup.
17 out=<file> Output fasta.
18 overwrite=f (ow) Set to false to force the program to abort rather than
19 overwrite an existing file.
20 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
21 level; lower compression is faster.
22
23 Processing parameters:
24 mincov=0 If positive and depth is below this, change ref to N.
25 Requires a coverage file.
26 maxindel=-1 If positive, ignore indels longer than this.
27 noframeshifts=f Ignore indels that are not a multiple of 3 in length.
28
29 Renaming:
30 name= Optionally rename sequences to this.
31 addnumbers=f Add _1 and so forth to ensure sequence names are unique.
32 prefix=t Use the name as a prefix to the old name, instead of replacing
33 the old name.
34 delimiter=_ Symbol to place between parts of the new name.
35 For space or tab, use the literal word.
36
37 Java Parameters:
38 -Xmx This will set Java's memory usage, overriding autodetection.
39 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
40 specify 200 megs. The max is typically 85% of physical memory.
41 -eoom This flag will cause the process to exit if an out-of-memory
42 exception occurs. Requires Java 8u92+.
43 -da Disable assertions.
44
45 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
46 "
47 }
48
49 #This block allows symlinked shellscripts to correctly set classpath.
50 pushd . > /dev/null
51 DIR="${BASH_SOURCE[0]}"
52 while [ -h "$DIR" ]; do
53 cd "$(dirname "$DIR")"
54 DIR="$(readlink "$(basename "$DIR")")"
55 done
56 cd "$(dirname "$DIR")"
57 DIR="$(pwd)/"
58 popd > /dev/null
59
60 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
61 CP="$DIR""current/"
62
63 z="-Xmx4g"
64 z2="-Xms4g"
65 set=0
66
67 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
68 usage
69 exit
70 fi
71
72 calcXmx () {
73 source "$DIR""/calcmem.sh"
74 setEnvironment
75 parseXmx "$@"
76 if [[ $set == 1 ]]; then
77 return
78 fi
79 freeRam 4000m 84
80 z="-Xmx${RAM}m"
81 z2="-Xms${RAM}m"
82 }
83 calcXmx "$@"
84
85 applyvariants() {
86 local CMD="java $EA $EOOM $z -cp $CP var2.ApplyVariants $@"
87 echo $CMD >&2
88 eval $CMD
89 }
90
91 applyvariants "$@"