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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 Divide extends WigMathTool {
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15
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16 private static final Logger log = Logger.getLogger(Divide.class);
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17
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18 @Parameter(names = {"-n", "--numerator"}, description = "Dividend / Numerator (file 1)", required = true)
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19 public WigFile dividendFile;
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20 @Parameter(names = {"-d", "--denominator"}, description = "Divisor / Denominator (file 2)", required = true)
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21 public WigFile divisorFile;
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22
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23 @Override
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24 public void setup() {
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25 inputs.add(dividendFile);
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26 inputs.add(divisorFile);
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27 log.debug("Initialized " + inputs.size() + " input files");
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28 }
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29
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30 @Override
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31 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
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32 log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop);
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33
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34 Iterator<WigItem> dividendData = dividendFile.query(chr, start, stop);
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35 Iterator<WigItem> divisorData = divisorFile.query(chr, start, stop);
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36
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37 float[] result = WigFile.flattenData(dividendData, start, stop);
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38 while (divisorData.hasNext()) {
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39 WigItem item = divisorData.next();
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40 for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
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41 if (i-start >= 0 && i-start < result.length) {
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42 if (item.getWigValue() != 0) {
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43 result[i-start] /= item.getWigValue();
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44 } else {
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45 result[i-start] = Float.NaN;
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46 }
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47 }
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48 }
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49 }
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50
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51 return result;
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52 }
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53
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54
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55 /**
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56 * @param args
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57 * @throws WigFileException
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58 * @throws IOException
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59 */
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60 public static void main(String[] args) throws IOException, WigFileException {
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61 new Divide().instanceMain(args);
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62 }
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63
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64 }
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