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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbsplitpairs.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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1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell
6 Last modified February 17, 2015
7
8 Description: Separates paired reads into files of 'good' pairs and 'good' singletons by removing 'bad' reads that are shorter than a min length.
9 Designed to handle situations where reads become too short to be useful after trimming. This program also optionally performs quality trimming.
10
11 Usage: bbsplitpairs.sh in=<input file> out=<pair output file> outs=<singleton output file> minlen=<minimum read length, an integer>
12
13 Input may be fasta or fastq, compressed or uncompressed.
14
15 Optional parameters (and their defaults)
16
17 in=<file> The 'in=' flag is needed if the input file is not the first 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 parameter. 'out=stdout' will pipe to standard out.
20 out2=<file> Use this to write 2nd read of pairs to a different file.
21 outsingle=<file> (outs) Write singleton reads here.
22
23 overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.
24 showspeed=t (ss) Set to 'f' to suppress display of processing speed.
25 interleaved=auto (int) If true, forces fastq input to be paired and interleaved.
26 qtrim=f Trim read ends to remove bases with quality below trimq.
27 Values: rl (trim both ends), f (neither end), r (right end only), l (left end only).
28 trimq=6 Trim quality threshold.
29 minlen=20 (ml) Reads shorter than this after trimming will be discarded.
30 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
31 fixinterleaving=f (fint) Fixes corrupted interleaved files by examining pair names. Only use on files with broken interleaving.
32 repair=f (rp) Fixes arbitrarily corrupted paired reads by examining read names. High memory.
33 ain=f (allowidenticalnames) When detecting pair names, allows identical names, instead of requiring /1 and /2 or 1: and 2:
34
35 Java Parameters:
36 -Xmx This will set Java's memory usage, overriding autodetection.
37 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
38 The max is typically 85% of physical memory.
39 -eoom This flag will cause the process to exit if an
40 out-of-memory exception occurs. Requires Java 8u92+.
41 -da Disable assertions.
42
43 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
44 "
45 }
46
47 #This block allows symlinked shellscripts to correctly set classpath.
48 pushd . > /dev/null
49 DIR="${BASH_SOURCE[0]}"
50 while [ -h "$DIR" ]; do
51 cd "$(dirname "$DIR")"
52 DIR="$(readlink "$(basename "$DIR")")"
53 done
54 cd "$(dirname "$DIR")"
55 DIR="$(pwd)/"
56 popd > /dev/null
57
58 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
59 CP="$DIR""current/"
60
61 z="-Xmx200m"
62 set=0
63
64 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
65 usage
66 exit
67 fi
68
69 calcXmx () {
70 source "$DIR""/calcmem.sh"
71 setEnvironment
72 parseXmx "$@"
73 }
74 calcXmx "$@"
75
76 splitpairs() {
77 local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles $@"
78 echo $CMD >&2
79 eval $CMD
80 }
81
82 splitpairs "$@"