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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/countbarcodes.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 October 16, 2015
7
8 Description: Counts the number of reads with each barcode.
9
10 Usage: countbarcodes.sh in=<file> counts=<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 Input parameters:
16 in=<file> Input reads, whose names end in a colon then barcode.
17 counts=<file> Output of counts.
18 interleaved=auto (int) If true, forces fastq input to be paired and interleaved.
19 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
20 unpigz=t Use pigz to decompress.
21 expected= Comma-delimited list of expected bar codes.
22 valid= Comma-delimited list of valid bar codes.
23 countundefined=t Count barcodes that contain non-ACGT symbols.
24 printheader=t Print a header.
25 maxrows=-1 Optionally limit the number of rows printed.
26
27 Output parameters:
28 out=<file> Write bar codes and counts here. 'out=stdout' will pipe to standard out.
29
30 Java Parameters:
31 -Xmx This will set Java's memory usage, overriding autodetection.
32 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
33 The max is typically 85% of physical memory.
34 -eoom This flag will cause the process to exit if an
35 out-of-memory exception occurs. Requires Java 8u92+.
36 -da Disable assertions.
37
38 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
39 "
40 }
41
42 #This block allows symlinked shellscripts to correctly set classpath.
43 pushd . > /dev/null
44 DIR="${BASH_SOURCE[0]}"
45 while [ -h "$DIR" ]; do
46 cd "$(dirname "$DIR")"
47 DIR="$(readlink "$(basename "$DIR")")"
48 done
49 cd "$(dirname "$DIR")"
50 DIR="$(pwd)/"
51 popd > /dev/null
52
53 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
54 CP="$DIR""current/"
55
56 z="-Xmx200m"
57 set=0
58
59 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
60 usage
61 exit
62 fi
63
64 calcXmx () {
65 source "$DIR""/calcmem.sh"
66 setEnvironment
67 parseXmx "$@"
68 }
69 calcXmx "$@"
70
71 countbarcodes() {
72 local CMD="java $EA $EOOM $z -cp $CP jgi.CountBarcodes $@"
73 echo $CMD >&2
74 eval $CMD
75 }
76
77 countbarcodes "$@"