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1 package edu.unc.genomics.wigmath;
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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.log4j.Logger;
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10
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11 import com.beust.jcommander.Parameter;
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12
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13 import edu.unc.genomics.CommandLineTool;
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14 import edu.unc.genomics.io.WigFile;
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15 import edu.unc.genomics.io.WigFileException;
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16 import edu.unc.genomics.ngs.Autocorrelation;
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17
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18 public class WigSummary extends CommandLineTool {
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19
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20 private static final Logger log = Logger.getLogger(Autocorrelation.class);
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21
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22 @Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
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23 public WigFile inputFile;
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24 @Parameter(names = {"-o", "--output"}, description = "Output file")
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25 public Path outputFile;
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26
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27 public void run() throws IOException {
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28 String summary = inputFile.toString();
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29
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30 if (outputFile != null) {
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31 log.debug("Writing to output file");
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32 try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
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33 writer.write(summary);
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34 }
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35 } else {
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36 System.out.println(summary);
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37 }
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38 }
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39
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40 public static void main(String[] args) throws IOException, WigFileException {
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41 new WigSummary().instanceMain(args);
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42 }
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43
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44 }
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