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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/splitnextera.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 March 6, 2015
7
8 Description: Splits Nextera LMP libraries into subsets based on linker orientation:
9 LMP, fragment, unknown, and singleton.
10 Please read bbmap/docs/guides/SplitNexteraGuide.txt for more information.
11
12 Usage: splitnextera.sh in=<file> out=<file> outf=<file> outu=<file> outs=<file>
13
14 For pairs in two files, use in1, in2, out1, out2, etc.
15
16 *** Note ***
17 For maximal speed, before running splitnextera, the linkers can be replaced with a constant first.
18
19 In other words, you can either do this (which is slightly faster):
20 bbduk.sh in=reads.fq out=replaced.fq ktmask=J k=19 hdist=1 mink=11 hdist2=0 literal=CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG
21 splitnextera.sh in=replaced.fq out=longmate.fq outf=frag.fq outu=unknown.fq outs=singleton.fq
22
23 Or this:
24 splitnextera.sh in=reads.fq out=longmate.fq outf=frag.fq outu=unknown.fq outs=singleton.fq mask=t
25
26
27 I/O parameters:
28 in=<file> Input reads. Set to 'stdin.fq' to read from stdin.
29 out=<file> Output for pairs with LMP orientation.
30 outf=<file> Output for pairs with fragment orientation.
31 outu=<file> Pairs with unknown orientation.
32 outs=<file> Singleton output.
33 ow=f (overwrite) Overwrites files that already exist.
34 app=f (append) Append to files that already exist.
35 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
36 int=f (interleaved) Determines whether INPUT file is considered interleaved.
37 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
38 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
39
40 Processing Parameters:
41 mask=f Set to true if you did not already convert junctions to some symbol, and it will be done automatically.
42 junction=J Look for this symbol to designate the junction bases.
43 innerlmp=f Generate long mate pairs from the inner pair also, when the junction is found in both reads.
44 rename=t Rename read 2 of output when using single-ended input.
45 minlength=40 (ml) Do not output reads shorter than this.
46 merge=f Attempt to merge overlapping reads before looking for junctions.
47 testmerge=0.0 If nonzero, only merge reads if at least the fraction of input reads are mergable.
48
49 Sampling parameters:
50
51 reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
52 samplerate=1 Randomly output only this fraction of reads; 1 means sampling is disabled.
53 sampleseed=-1 Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
54
55 Java Parameters:
56 -Xmx This will set Java's memory usage, overriding autodetection.
57 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
58 The max is typically 85% of physical memory.
59 -eoom This flag will cause the process to exit if an out-of-memory
60 exception occurs. Requires Java 8u92+.
61 -da Disable assertions.
62
63 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
64 "
65 }
66
67 #This block allows symlinked shellscripts to correctly set classpath.
68 pushd . > /dev/null
69 DIR="${BASH_SOURCE[0]}"
70 while [ -h "$DIR" ]; do
71 cd "$(dirname "$DIR")"
72 DIR="$(readlink "$(basename "$DIR")")"
73 done
74 cd "$(dirname "$DIR")"
75 DIR="$(pwd)/"
76 popd > /dev/null
77
78 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
79 CP="$DIR""current/"
80
81 z="-Xmx200m"
82 set=0
83
84 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
85 usage
86 exit
87 fi
88
89 calcXmx () {
90 source "$DIR""/calcmem.sh"
91 setEnvironment
92 parseXmx "$@"
93 }
94 calcXmx "$@"
95
96 function splitnextera() {
97 local CMD="java $EA $EOOM $z -cp $CP jgi.SplitNexteraLMP $@"
98 echo $CMD >&2
99 eval $CMD
100 }
101
102 splitnextera "$@"