Mercurial > repos > timpalpant > java_genomics_toolkit

comparison java-genomics-toolkit/src/edu/unc/genomics/ngs/IntervalLengthDistribution.java @ 0:1daf3026d231

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Upload alpha version
author timpalpant
date Mon, 13 Feb 2012 21:55:55 -0500
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1 package edu.unc.genomics.ngs;
2
3 import java.io.BufferedWriter;
4 import java.io.IOException;
5 import java.nio.charset.Charset;
6 import java.nio.file.Files;
7 import java.nio.file.Path;
8
9 import org.apache.commons.math.stat.Frequency;
10 import org.apache.log4j.Logger;
11
12 import com.beust.jcommander.Parameter;
13
14 import edu.unc.genomics.CommandLineTool;
15 import edu.unc.genomics.Interval;
16 import edu.unc.genomics.io.IntervalFile;
17
18 public class IntervalLengthDistribution extends CommandLineTool {
19
20 private static final Logger log = Logger.getLogger(IntervalLengthDistribution.class);
21
22 @Parameter(names = {"-i", "--input"}, description = "Interval file", required = true)
23 public IntervalFile<? extends Interval> inputFile;
24 @Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
25 public Path outputFile;
26
27
28 @Override
29 public void run() throws IOException {
30 log.debug("Generating histogram of interval lengths");
31 Frequency freq = new Frequency();
32 int min = Integer.MAX_VALUE;
33 int max = -1;
34 for (Interval i : inputFile) {
35 int L = i.length();
36 freq.addValue(L);
37
38 if (L < min) {
39 min = L;
40 }
41 if (L > max) {
42 max = L;
43 }
44 }
45
46 log.debug("Writing histogram output");
47 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
48 for (int i = min; i <= max; i++) {
49 writer.write(i+"\t"+freq.getCount(i));
50 writer.newLine();
51 }
52 }
53 }
54
55 public static void main(String[] args) {
56 new IntervalLengthDistribution().instanceMain(args);
57 }
58
59 }