Mercurial > repos > timpalpant > java_genomics_toolkit
comparison src/edu/unc/genomics/wigmath/Subtract.java @ 2:e16016635b2a
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author | timpalpant |
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date | Mon, 13 Feb 2012 22:12:06 -0500 |
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1:a54db233ee3d | 2:e16016635b2a |
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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 } |