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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/repair.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 November 9, 2016
7
8 Description: Re-pairs reads that became disordered or had some mates eliminated.
9 Please read bbmap/docs/guides/RepairGuide.txt for more information.
10
11 Usage: repair.sh in=<input file> out=<pair output> outs=<singleton output>
12
13 Input may be fasta, fastq, or sam, compressed or uncompressed.
14
15 Parameters:
16 in=<file> The 'in=' flag is needed if the input file is not the first
17 parameter. 'in=stdin' will pipe from standard in.
18 in2=<file> Use this if 2nd read of pairs are in a different file.
19 out=<file> The 'out=' flag is needed if the output file is not the second
20 parameter. 'out=stdout' will pipe to standard out.
21 out2=<file> Use this to write 2nd read of pairs to a different file.
22 outs=<file> (outsingle) Write singleton reads here.
23 overwrite=t (ow) Set to false to force the program to abort rather than
24 overwrite an existing file.
25 showspeed=t (ss) Set to 'f' to suppress display of processing speed.
26 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
27 level; lower compression is faster.
28 fint=f (fixinterleaving) Fixes corrupted interleaved files using read
29 names. Only use on files with broken interleaving - correctly
30 interleaved files from which some reads were removed.
31 repair=t (rp) Fixes arbitrarily corrupted paired reads by using read
32 names. Uses much more memory than 'fint' mode.
33 ain=f (allowidenticalnames) When detecting pair names, allows
34 identical names, instead of requiring /1 and /2 or 1: and 2:
35
36 Java Parameters:
37 -Xmx This will set Java's memory usage, overriding autodetection.
38 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
39 specify 200 megs. The max is typically 85% of physical memory.
40 -eoom This flag will cause the process to exit if an out-of-memory
41 exception occurs. Requires Java 8u92+.
42 -da Disable assertions.
43
44 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
45 "
46 }
47
48 #This block allows symlinked shellscripts to correctly set classpath.
49 pushd . > /dev/null
50 DIR="${BASH_SOURCE[0]}"
51 while [ -h "$DIR" ]; do
52 cd "$(dirname "$DIR")"
53 DIR="$(readlink "$(basename "$DIR")")"
54 done
55 cd "$(dirname "$DIR")"
56 DIR="$(pwd)/"
57 popd > /dev/null
58
59 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
60 CP="$DIR""current/"
61
62 z="-Xmx4g"
63 z2="-Xms4g"
64 set=0
65
66 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
67 usage
68 exit
69 fi
70
71 calcXmx () {
72 source "$DIR""/calcmem.sh"
73 setEnvironment
74 parseXmx "$@"
75 if [[ $set == 1 ]]; then
76 return
77 fi
78 freeRam 4000m 84
79 z="-Xmx${RAM}m"
80 z2="-Xms${RAM}m"
81 }
82 calcXmx "$@"
83
84 repair() {
85 local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles rp $@"
86 echo $CMD >&2
87 eval $CMD
88 }
89
90 repair "$@"