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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/replaceheaders.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 May 23, 2016
7
8 Description: Replaces read names with names from another file.
9 The other file can either be sequences or simply names, with
10 one name per line (and no > or @ symbols). If you use one name
11 per line, please give the file a .header extension.
12
13 Usage: replaceheaders.sh in=<file> hin=<headers file> out=<out file>
14
15 Parameters:
16 in= Input sequences. Use in2 for a second paired file.
17 in= Header input sequences. Use hin2 for a second paired file.
18 out= Output sequences. Use out2 for a second paired file.
19 ow=f (overwrite) Overwrites files that already exist.
20 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
21 int=f (interleaved) Determines whether INPUT file is considered interleaved.
22 fastawrap=70 Length of lines in fasta output.
23 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
24 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
25
26 Renaming modes (if not default):
27 addprefix=f Rename the read by prepending the new name to the existing name.
28
29 Sampling parameters:
30 reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
31
32 Java Parameters:
33 -Xmx This will set Java's memory usage, overriding autodetection.
34 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
35 The max is typically 85% of physical memory.
36 -eoom This flag will cause the process to exit if an
37 out-of-memory exception occurs. Requires Java 8u92+.
38 -da Disable assertions.
39
40 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
41 "
42 }
43
44 #This block allows symlinked shellscripts to correctly set classpath.
45 pushd . > /dev/null
46 DIR="${BASH_SOURCE[0]}"
47 while [ -h "$DIR" ]; do
48 cd "$(dirname "$DIR")"
49 DIR="$(readlink "$(basename "$DIR")")"
50 done
51 cd "$(dirname "$DIR")"
52 DIR="$(pwd)/"
53 popd > /dev/null
54
55 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
56 CP="$DIR""current/"
57
58 z="-Xmx1g"
59 set=0
60
61 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
62 usage
63 exit
64 fi
65
66 calcXmx () {
67 source "$DIR""/calcmem.sh"
68 setEnvironment
69 parseXmx "$@"
70 }
71 calcXmx "$@"
72
73 function reheader() {
74 local CMD="java $EA $EOOM $z -cp $CP jgi.ReplaceHeaders $@"
75 echo $CMD >&2
76 eval $CMD
77 }
78
79 reheader "$@"