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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.CommandLineToolException;
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12 import edu.unc.genomics.io.WigFile;
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13 import edu.unc.genomics.io.WigFileException;
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14
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15 public class ZScore extends WigMathTool {
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16
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17 private static final Logger log = Logger.getLogger(ZScore.class);
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18
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19 @Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
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20 public WigFile inputFile;
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21
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22 double mean;
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23 double stdev;
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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 mean = inputFile.mean();
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30 stdev = inputFile.stdev();
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31 if(stdev == 0) {
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32 log.error("Cannot Z-score a file with stdev = 0!");
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33 throw new CommandLineToolException("Cannot Z-score a file with stdev = 0!");
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34 }
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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("Computing difference for chunk "+chr+":"+start+"-"+stop);
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40 Iterator<WigItem> data = inputFile.query(chr, start, stop);
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41 float[] result = WigFile.flattenData(data, start, stop);
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42
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43 for (int i = 0; i < result.length; i++) {
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44 result[i] = (float)((result[i] - mean) / stdev);
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45 }
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46
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47 return result;
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48 }
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49
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50
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51 /**
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52 * @param args
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53 * @throws WigFileException
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54 * @throws IOException
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55 */
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56 public static void main(String[] args) throws IOException, WigFileException {
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57 new ZScore().instanceMain(args);
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58 }
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59
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60 }
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