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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/bbcountunique.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 August 1, 2016
7
8 Description: Generates a kmer uniqueness histogram, binned by file position.
9 There are 3 columns for single reads, 6 columns for paired:
10 count number of reads or pairs processed
11 r1_first percent unique 1st kmer of read 1
12 r1_rand percent unique random kmer of read 1
13 r2_first percent unique 1st kmer of read 2
14 r2_rand percent unique random kmer of read 2
15 pair percent unique concatenated kmer from read 1 and 2
16
17 Please read bbmap/docs/guides/CalcUniquenessGuide.txt for more information.
18
19 Usage: bbcountunique.sh in=<input> out=<output>
20
21 Input parameters:
22 in2=null Second input file for paired reads
23 interleaved=auto Set true/false to override autodetection of the input file as paired interleaved.
24 samplerate=1 Set to below 1 to sample a fraction of input reads.
25 reads=-1 Only process this number of reads, then quit (-1 means all)
26
27 Output parameters:
28 out=<file> File for output stats
29
30 Processing parameters:
31 k=25 Kmer length (range 1-31).
32 interval=25000 Print one line to the histogram per this many reads.
33 cumulative=f Show cumulative numbers rather than per-interval numbers.
34 percent=t Show percentages of unique reads.
35 count=f Show raw counts of unique reads.
36 printlastbin=f (plb) Print a line for the final undersized bin.
37 minprob=0 Ignore kmers with a probability of correctness below this (based on q-scores).
38
39 Java Parameters:
40 -Xmx This will set Java's memory usage, overriding autodetection.
41 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
42 The max is typically 85% of physical memory.
43 -eoom This flag will cause the process to exit if an
44 out-of-memory exception occurs. Requires Java 8u92+.
45 -da Disable assertions.
46
47 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
48 "
49 }
50
51 #This block allows symlinked shellscripts to correctly set classpath.
52 pushd . > /dev/null
53 DIR="${BASH_SOURCE[0]}"
54 while [ -h "$DIR" ]; do
55 cd "$(dirname "$DIR")"
56 DIR="$(readlink "$(basename "$DIR")")"
57 done
58 cd "$(dirname "$DIR")"
59 DIR="$(pwd)/"
60 popd > /dev/null
61
62 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
63 CP="$DIR""current/"
64
65 z="-Xmx1g"
66 z2="-Xms1g"
67 set=0
68
69 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
70 usage
71 exit
72 fi
73
74 calcXmx () {
75 source "$DIR""/calcmem.sh"
76 setEnvironment
77 parseXmx "$@"
78 if [[ $set == 1 ]]; then
79 return
80 fi
81 freeRam 3200m 84
82 z="-Xmx${RAM}m"
83 z2="-Xms${RAM}m"
84 }
85 calcXmx "$@"
86
87 bbcountunique() {
88 local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.CalcUniqueness $@"
89 echo $CMD >&2
90 eval $CMD
91 }
92
93 bbcountunique "$@"