Mercurial > repos > timpalpant > java_genomics_toolkit
comparison src/edu/unc/genomics/ngs/IntervalLengthDistribution.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.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 } |