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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/callpeaks.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 December 19, 2018
7
8 Description: Calls peaks from a 2-column (x, y) tab-delimited histogram.
9
10 Usage: callpeaks.sh in=<histogram file> out=<output file>
11
12 Peak-calling parameters:
13 in=<file> 'in=stdin.fq' will pipe from standard in.
14 out=<file> Write the peaks to this file. Default is stdout.
15 minHeight=2 (h) Ignore peaks shorter than this.
16 minVolume=5 (v) Ignore peaks with less area than this.
17 minWidth=3 (w) Ignore peaks narrower than this.
18 minPeak=2 (minp) Ignore peaks with an X-value below this.
19 Useful when low-count kmers are filtered).
20 maxPeak=BIG (maxp) Ignore peaks with an X-value above this.
21 maxPeakCount=10 (maxpc) Print up to this many peaks (prioritizing height).
22 countColumn=1 (col) For multi-column input, this column, zero-based,
23 contains the counts.
24 ploidy=-1 Specify ploidy; otherwise it will be autodetected.
25 logscale=f Transform to log-scale prior to peak-calling. Useful
26 for kmer-frequency histograms.
27
28 Smoothing parameters:
29 smoothradius=0 Integer radius of triangle filter. Set above zero to
30 smooth data prior to peak-calling. Higher values are
31 smoother.
32 smoothprogressive=f Set to true to widen the filter as the x-coordinate
33 increases. Useful for kmer-frequency histograms.
34 maxradius=10 Maximum radius of progressive smoothing function.
35 progressivemult=2 Increment radius each time depth increases by this factor.
36
37 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
38 "
39 }
40
41 #This block allows symlinked shellscripts to correctly set classpath.
42 pushd . > /dev/null
43 DIR="${BASH_SOURCE[0]}"
44 while [ -h "$DIR" ]; do
45 cd "$(dirname "$DIR")"
46 DIR="$(readlink "$(basename "$DIR")")"
47 done
48 cd "$(dirname "$DIR")"
49 DIR="$(pwd)/"
50 popd > /dev/null
51
52 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
53 CP="$DIR""current/"
54
55 z="-Xmx200m"
56 set=0
57
58 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
59 usage
60 exit
61 fi
62
63 calcXmx () {
64 source "$DIR""/calcmem.sh"
65 setEnvironment
66 parseXmx "$@"
67 }
68 calcXmx "$@"
69
70 stats() {
71 local CMD="java $EA $EOOM -Xmx120m -cp $CP jgi.CallPeaks $@"
72 # echo $CMD >&2
73 eval $CMD
74 }
75
76 stats "$@"