Mercurial > repos > timpalpant > java_genomics_toolkit

comparison src/edu/unc/genomics/wigmath/LogTransform.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 LogTransform extends WigMathTool {
15
16 private static final Logger log = Logger.getLogger(LogTransform.class);
17
18 @Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
19 public WigFile inputFile;
20 @Parameter(names = {"-b", "--base"}, description = "Logarithm base (default = 2)")
21 public double base = 2;
22
23 private double baseChange;
24
25 @Override
26 public void setup() {
27 baseChange = Math.log(base);
28 inputs.add(inputFile);
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> data = inputFile.query(chr, start, stop);
36 float[] result = WigFile.flattenData(data, start, stop);
37
38 for (int i = 0; i < result.length; i++) {
39 result[i] = (float) (Math.log(result[i]) / baseChange);
40 }
41
42 return result;
43 }
44
45
46 /**
47 * @param args
48 * @throws WigFileException
49 * @throws IOException
50 */
51 public static void main(String[] args) throws IOException, WigFileException {
52 new LogTransform().instanceMain(args);
53 }
54
55 }