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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/mergebarcodes.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 February 17, 2015
7
8 Description: Concatenates barcodes and quality onto read names.
9
10 Usage: mergebarcodes.sh in=<file> out=<file> barcode=<file>
11
12 Input may be stdin or a fasta or fastq file, raw or gzipped.
13 If you pipe via stdin/stdout, please include the file type; e.g. for gzipped fasta input, set in=stdin.fa.gz
14
15 Optional parameters (and their defaults)
16
17 Input parameters:
18 in=<file> Input reads. 'in=stdin.fq' will pipe from standard in.
19 bar=<file> File containing barcodes.
20 int=auto (interleaved) If true, forces fastq input to be paired and interleaved.
21 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
22
23 Output parameters:
24 out=<file> Write muxed sequences here. 'out=stdout.fa' will pipe to standard out.
25 overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.
26 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
27 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
28
29 Other parameters:
30 pigz=t Use pigz to compress. If argument is a number, that will set the number of pigz threads.
31 unpigz=t Use pigz to decompress.
32
33 Java Parameters:
34 -Xmx This will set Java's memory usage, overriding autodetection.
35 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
36 The max is typically 85% of physical memory.
37 -eoom This flag will cause the process to exit if an out-of-memory
38 exception occurs. Requires Java 8u92+.
39 -da Disable assertions.
40
41 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
42 "
43 }
44
45 #This block allows symlinked shellscripts to correctly set classpath.
46 pushd . > /dev/null
47 DIR="${BASH_SOURCE[0]}"
48 while [ -h "$DIR" ]; do
49 cd "$(dirname "$DIR")"
50 DIR="$(readlink "$(basename "$DIR")")"
51 done
52 cd "$(dirname "$DIR")"
53 DIR="$(pwd)/"
54 popd > /dev/null
55
56 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
57 CP="$DIR""current/"
58
59 z="-Xmx1g"
60 z2="-Xms1g"
61 set=0
62
63 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
64 usage
65 exit
66 fi
67
68 calcXmx () {
69 source "$DIR""/calcmem.sh"
70 setEnvironment
71 parseXmx "$@"
72 if [[ $set == 1 ]]; then
73 return
74 fi
75 freeRam 3200m 84
76 z="-Xmx${RAM}m"
77 z2="-Xms${RAM}m"
78 }
79 calcXmx "$@"
80
81 mergebarcodes() {
82 local CMD="java $EA $EOOM $z -cp $CP jgi.MergeBarcodes $@"
83 echo $CMD >&2
84 eval $CMD
85 }
86
87 mergebarcodes "$@"