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comparison java-genomics-toolkit/src/edu/unc/genomics/wigmath/GaussianSmooth.java @ 0:1daf3026d231

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Upload alpha version
author timpalpant
date Mon, 13 Feb 2012 21:55:55 -0500
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1 package edu.unc.genomics.wigmath;
2
3 import java.io.IOException;
4 import java.util.Iterator;
5
6 import org.apache.log4j.Logger;
7 import org.broad.igv.bbfile.WigItem;
8
9 import com.beust.jcommander.Parameter;
10
11 import edu.unc.genomics.io.WigFile;
12 import edu.unc.genomics.io.WigFileException;
13
14 public class GaussianSmooth extends WigMathTool {
15
16 private static final Logger log = Logger.getLogger(GaussianSmooth.class);
17
18 @Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
19 public WigFile inputFile;
20 @Parameter(names = {"-s", "--stdev"}, description = "Standard deviation of Gaussian (bp)")
21 public int stdev = 20;
22
23 float[] filter;
24
25 @Override
26 public void setup() {
27 inputs.add(inputFile);
28
29 // Use a window size equal to +/- 3 SD's
30 filter = new float[6*stdev+1];
31 float sum = 0;
32 for (int i = 0; i < filter.length; i++) {
33 float x = i - 3*stdev;
34 float value = (float) Math.exp(-(x*x) / (2*stdev*stdev));
35 filter[i] = value;
36 sum += value;
37 }
38 for (int i = 0; i < filter.length; i++) {
39 filter[i] /= sum;
40 }
41 }
42
43 @Override
44 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
45 log.debug("Smoothing chunk "+chr+":"+start+"-"+stop);
46
47 // Pad the query for smoothing
48 int paddedStart = Math.max(start-3*stdev, inputFile.getChrStart(chr));
49 int paddedStop = Math.min(stop+3*stdev, inputFile.getChrStop(chr));
50 Iterator<WigItem> result = inputFile.query(chr, paddedStart, paddedStop);
51 float[] data = WigFile.flattenData(result, start-3*stdev, stop+3*stdev);
52
53 // Convolve the data with the filter
54 float[] smoothed = new float[stop-start+1];
55 for (int i = 0; i < smoothed.length; i++) {
56 for (int j = 0; j < filter.length; j++) {
57 smoothed[i] += data[i+j] * filter[j];
58 }
59 }
60
61 return smoothed;
62 }
63
64
65 /**
66 * @param args
67 * @throws WigFileException
68 * @throws IOException
69 */
70 public static void main(String[] args) throws IOException, WigFileException {
71 new GaussianSmooth().instanceMain(args);
72 }
73
74 }