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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 fake read pairs from ends of contigs or single reads.
9
10 Usage: bbfakereads.sh in=<file> out=<outfile> out2=<outfile2>
11
12 Out2 is optional; if there is only one output file, it will be written interleaved.
13
14 Standard parameters:
15 ow=f (overwrite) Overwrites files that already exist.
16 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
17 fastawrap=100 Length of lines in fasta output.
18 tuc=f (touppercase) Change lowercase letters in reads to uppercase.
19 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
20 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
21 qfin=<.qual file> Read qualities from this qual file, for the reads coming from 'in=<fasta file>'
22 qfout=<.qual file> Write qualities from this qual file, for the reads going to 'out=<fasta file>'
23 qfout2=<.qual file> Write qualities from this qual file, for the reads coming from 'out2=<fasta file>'
24 verifyinterleaved=f (vint) When true, checks a file to see if the names look paired. Prints an error message if not.
25 tossbrokenreads=f (tbr) Discard reads that have different numbers of bases and qualities. By default this will be detected and cause a crash.
26
27 Faking parameters:
28 length=250 Generate reads of this length.
29 minlength=1 Don't generate reads shorter than this.
30 overlap=0 If you set overlap, then reads will by variable length, overlapping by 'overlap' in the middle.
31 identifier=null (id) Output read names are prefixed with this.
32 addspace=t Set to false to omit the space before /1 and /2 of paired reads.
33
34 Java Parameters:
35 -Xmx This will set Java's memory usage, overriding autodetection.
36 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
37 The max is typically 85% of physical memory.
38 -eoom This flag will cause the process to exit if an
39 out-of-memory exception occurs. Requires Java 8u92+.
40 -da Disable assertions.
41
42 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
43 "
44 }
45
46 #This block allows symlinked shellscripts to correctly set classpath.
47 pushd . > /dev/null
48 DIR="${BASH_SOURCE[0]}"
49 while [ -h "$DIR" ]; do
50 cd "$(dirname "$DIR")"
51 DIR="$(readlink "$(basename "$DIR")")"
52 done
53 cd "$(dirname "$DIR")"
54 DIR="$(pwd)/"
55 popd > /dev/null
56
57 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
58 CP="$DIR""current/"
59
60 z="-Xmx600m"
61 set=0
62
63 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
64 usage
65 exit
66 fi
67
68
69 calcXmx () {
70 source "$DIR""/calcmem.sh"
71 setEnvironment
72 parseXmx "$@"
73 }
74 calcXmx "$@"
75
76 function fakereads() {
77 local CMD="java $EA $EOOM $z -cp $CP jgi.FakeReads $@"
78 echo $CMD >&2
79 eval $CMD
80 }
81
82 fakereads "$@"