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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.nio.file.Paths;
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5 import java.util.ArrayList;
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6 import java.util.Iterator;
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7 import java.util.List;
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8
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9 import org.apache.log4j.Logger;
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10 import org.broad.igv.bbfile.WigItem;
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11
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12 import com.beust.jcommander.Parameter;
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13
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14 import edu.unc.genomics.CommandLineToolException;
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15 import edu.unc.genomics.io.WigFile;
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16 import edu.unc.genomics.io.WigFileException;
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17
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18 public class Average extends WigMathTool {
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19
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20 private static final Logger log = Logger.getLogger(Average.class);
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21
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22 @Parameter(description = "Input files", required = true)
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23 public List<String> inputFiles = new ArrayList<String>();
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24
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25 int numFiles;
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26
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27 @Override
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28 public void setup() {
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29 if (inputFiles.size() < 2) {
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30 throw new CommandLineToolException("No reason to add < 2 files.");
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31 }
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32
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33 log.debug("Initializing input files");
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34 for (String inputFile : inputFiles) {
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35 try {
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36 addInputFile(WigFile.autodetect(Paths.get(inputFile)));
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37 } catch (IOException | WigFileException e) {
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38 log.error("Error initializing input Wig file: " + inputFile);
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39 e.printStackTrace();
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40 throw new CommandLineToolException(e.getMessage());
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41 }
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42 }
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43 log.debug("Initialized " + inputs.size() + " input files");
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44
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45 numFiles = inputs.size();
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46 }
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47
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48 @Override
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49 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
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50 log.debug("Computing average for chunk "+chr+":"+start+"-"+stop);
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51
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52 int length = stop - start + 1;
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53 float[] avg = new float[length];
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54
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55 for (WigFile wig : inputs) {
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56 Iterator<WigItem> data = wig.query(chr, start, stop);
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57 while (data.hasNext()) {
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58 WigItem item = data.next();
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59 for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
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60 if (i-start >= 0 && i-start < avg.length) {
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61 avg[i-start] += item.getWigValue();
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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
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67 for (int i = 0; i < avg.length; i++) {
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68 avg[i] = avg[i] / numFiles;
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69 }
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70
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71 return avg;
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72 }
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73
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74
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75 /**
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76 * @param args
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77 * @throws WigFileException
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78 * @throws IOException
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79 */
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80 public static void main(String[] args) throws IOException, WigFileException {
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81 new Average().instanceMain(args);
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82 }
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83
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84 }
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