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