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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/kmerlimit.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 July 31, 2018
7
8 Description: Stops producing reads when the unique kmer limit is reached.
9 This is approximate. If the input has been Clumpified, the order should be
10 randomized first with shuffle2.sh or sortbyname.sh with the flowcell flag.
11
12 Differences between versions:
13 kmerlimit.sh uses 1 pass and outputs all reads until a limit is hit,
14 meaning the input reads should be in random order with respect to sequence.
15 kmerlimit2.sh uses 2 passes and randomly subsamples from the file, so
16 it works with reads in any order.
17
18 Usage: kmerlimit.sh in=<input file> out=<output file> limit=<number>
19
20 Standard parameters:
21 in=<file> Primary input, or read 1 input.
22 in2=<file> Read 2 input if reads are in two files.
23 out=<file> Primary output, or read 1 output.
24 out2=<file> Read 2 output if reads are in two files.
25 overwrite=t (ow) Set to false to force the program to abort rather than
26 overwrite an existing file.
27 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
28 level; lower compression is faster.
29
30 Processing parameters:
31 k=31 Kmer length, 1-32.
32 limit= The number of unique kmers to produce.
33 mincount=1 Ignore kmers seen fewer than this many times.
34 minqual=0 Ignore bases with quality below this.
35 minprob=0.2 Ignore kmers with correctness probability below this.
36
37 Java Parameters:
38 -Xmx This will set Java's memory usage, overriding autodetection.
39 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
40 specify 200 megs. The max is typically 85% of physical memory.
41 -eoom This flag will cause the process to exit if an out-of-memory
42 exception occurs. Requires Java 8u92+.
43 -da Disable assertions.
44
45 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
46 "
47 }
48
49 #This block allows symlinked shellscripts to correctly set classpath.
50 pushd . > /dev/null
51 DIR="${BASH_SOURCE[0]}"
52 while [ -h "$DIR" ]; do
53 cd "$(dirname "$DIR")"
54 DIR="$(readlink "$(basename "$DIR")")"
55 done
56 cd "$(dirname "$DIR")"
57 DIR="$(pwd)/"
58 popd > /dev/null
59
60 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
61 CP="$DIR""current/"
62
63 z="-Xmx1000m"
64 z2="-Xms1000m"
65 set=0
66
67 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
68 usage
69 exit
70 fi
71
72 calcXmx () {
73 source "$DIR""/calcmem.sh"
74 setEnvironment
75 parseXmx "$@"
76 }
77 calcXmx "$@"
78
79 kmerlimit() {
80 local CMD="java $EA $EOOM $z -cp $CP sketch.KmerLimit $@"
81 echo $CMD >&2
82 eval $CMD
83 }
84
85 kmerlimit "$@"