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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.commons.math.stat.descriptive.DescriptiveStatistics;
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7 import org.apache.log4j.Logger;
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8 import org.broad.igv.bbfile.WigItem;
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9
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10 import com.beust.jcommander.Parameter;
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11
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12 import edu.unc.genomics.PositiveIntegerValidator;
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13 import edu.unc.genomics.io.WigFile;
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14 import edu.unc.genomics.io.WigFileException;
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15
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16 public class MovingAverageSmooth extends WigMathTool {
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17
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18 private static final Logger log = Logger.getLogger(MovingAverageSmooth.class);
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19
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20 @Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
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21 public WigFile inputFile;
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22 @Parameter(names = {"-w", "--width"}, description = "Width of kernel (bp)")
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23 public int width = 10;
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24
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25 WigFile input;
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26 DescriptiveStatistics stats;
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27
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28 @Override
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29 public void setup() {
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30 inputs.add(inputFile);
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31
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32 log.debug("Initializing statistics");
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33 stats = new DescriptiveStatistics();
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34 stats.setWindowSize(width);
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35 }
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36
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37 @Override
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38 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
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39 log.debug("Smoothing chunk "+chr+":"+start+"-"+stop);
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40 // Pad the query so that we can provide values for the ends
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41 int queryStart = Math.max(start-width/2, input.getChrStart(chr));
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42 int queryStop = Math.min(stop+width/2, input.getChrStop(chr));
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43 Iterator<WigItem> result = input.query(chr, queryStart, queryStop);
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44 float[] data = WigFile.flattenData(result, queryStart, queryStop);
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45
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46 float[] smoothed = new float[stop-start+1];
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47 for (int bp = start; bp <= stop; bp++) {
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48 stats.addValue(data[bp-queryStart]);
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49 if (bp-start-width/2 >= 0) {
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50 smoothed[bp-start-width/2] = (float) stats.getMean();
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51 }
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52 }
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53
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54 return smoothed;
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55 }
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56
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57
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58 /**
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59 * @param args
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60 * @throws WigFileException
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61 * @throws IOException
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62 */
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63 public static void main(String[] args) throws IOException, WigFileException {
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64 new MovingAverageSmooth().instanceMain(args);
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65 }
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66
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67 }
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