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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/crosscontaminate.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 February 17, 2015
7
8 Description: Generates synthetic cross-contaminated files from clean files.
9 Intended for use with synthetic reads generated by SynthMDA or RandomReads.
10
11 Usage: crosscontaminate.sh in=<file,file,...> out=<file,file,...>
12
13 Input parameters:
14 in=<file,file,...> Clean input reads.
15 innamefile=<file> A file containing the names of input files,
16 one name per line.
17 interleaved=auto (int) t/f overrides interleaved autodetection.
18 qin=auto Input quality offset: 33 (Sanger), 64, or auto.
19 reads=-1 If positive, quit after processing X reads or pairs.
20
21 Processing Parameters:
22 minsinks=1 Min contamination destinations from one source.
23 maxsinks=8 Max contamination destinations from one source.
24 minprob=0.000005 Min allowed contamination rate (geometric distribution).
25 maxprob=0.025 Max allowed contamination rate.
26
27 Output parameters:
28 out=<file,file,...> Contaminated output reads.
29 outnamefile=<file> A file containing the names of output files,
30 one name per line.
31 overwrite=t (ow) Grant permission to overwrite files.
32 #showspeed=t (ss) 'f' suppresses display of processing speed.
33 ziplevel=2 (zl) Compression level; 1 (min) through 9 (max).
34 threads=auto (t) Set number of threads to use; default is number of
35 logical processors.
36 qout=auto Output quality offset: 33 (Sanger), 64, or auto.
37 shuffle=f Shuffle contents of output files.
38 shufflethreads=3 Use this many threads for shuffling (uses more memory).
39
40 Java Parameters:
41 -Xmx This will set Java's memory usage, overriding autodetection.
42 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
43 The max is typically 85% of physical memory.
44 -eoom This flag will cause the process to exit if an
45 out-of-memory exception occurs. Requires Java 8u92+.
46 -da Disable assertions.
47
48 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
49 "
50 }
51
52 #This block allows symlinked shellscripts to correctly set classpath.
53 pushd . > /dev/null
54 DIR="${BASH_SOURCE[0]}"
55 while [ -h "$DIR" ]; do
56 cd "$(dirname "$DIR")"
57 DIR="$(readlink "$(basename "$DIR")")"
58 done
59 cd "$(dirname "$DIR")"
60 DIR="$(pwd)/"
61 popd > /dev/null
62
63 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
64 CP="$DIR""current/"
65
66 z="-Xmx4g"
67 z2="-Xms4g"
68 set=0
69
70 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
71 usage
72 exit
73 fi
74
75 calcXmx () {
76 source "$DIR""/calcmem.sh"
77 setEnvironment
78 parseXmx "$@"
79 if [[ $set == 1 ]]; then
80 return
81 fi
82 freeRam 4000m 42
83 z="-Xmx${RAM}m"
84 }
85 calcXmx "$@"
86
87 crosscontaminate() {
88 local CMD="java $EA $EOOM $z -cp $CP jgi.CrossContaminate $@"
89 echo $CMD >&2
90 eval $CMD
91 }
92
93 crosscontaminate "$@"