Mercurial > repos > timpalpant > java_genomics_toolkit

comparison src/edu/unc/genomics/wigmath/Subtract.java @ 2:e16016635b2a

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author timpalpant
date Mon, 13 Feb 2012 22:12:06 -0500
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1:a54db233ee3d 2:e16016635b2a
1 package edu.unc.genomics.wigmath;
2
3 import java.io.IOException;
4 import java.util.Iterator;
5
6 import org.apache.log4j.Logger;
7 import org.broad.igv.bbfile.WigItem;
8
9 import com.beust.jcommander.Parameter;
10
11 import edu.unc.genomics.io.WigFile;
12 import edu.unc.genomics.io.WigFileException;
13
14 public class Subtract extends WigMathTool {
15
16 private static final Logger log = Logger.getLogger(Subtract.class);
17
18 @Parameter(names = {"-m", "--minuend"}, description = "Minuend (top - file 1)", required = true)
19 public WigFile minuendFile;
20 @Parameter(names = {"-s", "--subtrahend"}, description = "Subtrahend (bottom - file 2)", required = true)
21 public WigFile subtrahendFile;
22
23 @Override
24 public void setup() {
25 log.debug("Initializing input files");
26 inputs.add(minuendFile);
27 inputs.add(subtrahendFile);
28 log.debug("Initialized " + inputs.size() + " input files");
29 }
30
31 @Override
32 public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
33 log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop);
34
35 Iterator<WigItem> minuendData = minuendFile.query(chr, start, stop);
36 Iterator<WigItem> subtrahendData = subtrahendFile.query(chr, start, stop);
37
38 float[] result = WigFile.flattenData(minuendData, start, stop);
39 while (subtrahendData.hasNext()) {
40 WigItem item = subtrahendData.next();
41 for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
42 if (i-start >= 0 && i-start < result.length) {
43 result[i-start] -= item.getWigValue();
44 }
45 }
46 }
47
48 return result;
49 }
50
51
52 /**
53 * @param args
54 * @throws WigFileException
55 * @throws IOException
56 */
57 public static void main(String[] args) throws IOException, WigFileException {
58 new Subtract().instanceMain(args);
59 }
60
61 }