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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 Subtract extends WigMathTool {
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15
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16 private static final Logger log = Logger.getLogger(Subtract.class);
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17
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18 @Parameter(names = {"-m", "--minuend"}, description = "Minuend (top - file 1)", required = true)
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19 public WigFile minuendFile;
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20 @Parameter(names = {"-s", "--subtrahend"}, description = "Subtrahend (bottom - file 2)", required = true)
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21 public WigFile subtrahendFile;
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22
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23 @Override
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24 public void setup() {
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25 log.debug("Initializing input files");
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26 inputs.add(minuendFile);
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27 inputs.add(subtrahendFile);
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28 log.debug("Initialized " + inputs.size() + " input files");
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29 }
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30
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31 @Override
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32 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
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33 log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop);
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34
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35 Iterator<WigItem> minuendData = minuendFile.query(chr, start, stop);
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36 Iterator<WigItem> subtrahendData = subtrahendFile.query(chr, start, stop);
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37
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38 float[] result = WigFile.flattenData(minuendData, start, stop);
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39 while (subtrahendData.hasNext()) {
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40 WigItem item = subtrahendData.next();
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41 for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
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42 if (i-start >= 0 && i-start < result.length) {
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43 result[i-start] -= item.getWigValue();
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44 }
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45 }
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46 }
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47
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48 return result;
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49 }
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50
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51
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52 /**
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53 * @param args
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54 * @throws WigFileException
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55 * @throws IOException
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56 */
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57 public static void main(String[] args) throws IOException, WigFileException {
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58 new Subtract().instanceMain(args);
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59 }
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60
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61 }
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