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