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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/kmerlimit2.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: Subsamples reads to reach a target unique kmer limit.
9
10 Differences between versions:
11 kmerlimit.sh uses 1 pass and outputs all reads until a limit is hit,
12 meaning the input reads should be in random order with respect to sequence.
13 kmerlimit2.sh uses 2 passes and randomly subsamples from the file, so
14 it works with reads in any order.
15
16 Usage: kmerlimit2.sh in=<input file> out=<output file> limit=<number>
17
18 Standard parameters:
19 in=<file> Primary input, or read 1 input.
20 in2=<file> Read 2 input if reads are in two files.
21 out=<file> Primary output, or read 1 output.
22 out2=<file> Read 2 output if reads are in two files.
23 overwrite=t (ow) Set to false to force the program to abort rather than
24 overwrite an existing file.
25 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
26 level; lower compression is faster.
27
28 Processing parameters:
29 k=31 Kmer length, 1-32.
30 limit= The number of unique kmers to produce.
31 mincount=1 Ignore kmers seen fewer than this many times.
32 minqual=0 Ignore bases with quality below this.
33 minprob=0.2 Ignore kmers with correctness probability below this.
34 trials=25 Simulation trials.
35 seed=-1 Set to a positive number for deterministic output.
36 maxlen=50m Max length of a temp array used in simulation.
37
38 Java Parameters:
39 -Xmx This will set Java's memory usage, overriding autodetection.
40 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
41 specify 200 megs. The max is typically 85% of physical memory.
42 -eoom This flag will cause the process to exit if an out-of-memory
43 exception occurs. Requires Java 8u92+.
44 -da Disable assertions.
45
46 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
47 "
48 }
49
50 #This block allows symlinked shellscripts to correctly set classpath.
51 pushd . > /dev/null
52 DIR="${BASH_SOURCE[0]}"
53 while [ -h "$DIR" ]; do
54 cd "$(dirname "$DIR")"
55 DIR="$(readlink "$(basename "$DIR")")"
56 done
57 cd "$(dirname "$DIR")"
58 DIR="$(pwd)/"
59 popd > /dev/null
60
61 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
62 CP="$DIR""current/"
63
64 z="-Xmx1000m"
65 z2="-Xms1000m"
66 set=0
67
68 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
69 usage
70 exit
71 fi
72
73 calcXmx () {
74 source "$DIR""/calcmem.sh"
75 setEnvironment
76 parseXmx "$@"
77 }
78 calcXmx "$@"
79
80 kmerlimit2() {
81 local CMD="java $EA $EOOM $z -cp $CP sketch.KmerLimit2 $@"
82 echo $CMD >&2
83 eval $CMD
84 }
85
86 kmerlimit2 "$@"