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1 package edu.unc.genomics;
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2
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3 import java.io.IOException;
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4
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5 import com.beust.jcommander.JCommander;
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6 import com.beust.jcommander.ParameterException;
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7
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8 /**
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9 * A command-line script
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10 * @author timpalpant
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11 *
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12 */
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13 public abstract class CommandLineTool {
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14
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15 /**
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16 * JCommander command-line argument parser
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17 */
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18 private final JCommander jc = new JCommander(this);
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19
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20 public CommandLineTool() {
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21 // Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
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22 jc.addConverterFactory(new PathFactory());
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23 jc.addConverterFactory(new AssemblyFactory());
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24 jc.addConverterFactory(new IntervalFileFactory());
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25 jc.addConverterFactory(new WigFileFactory());
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26
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27 // Set the program name to be the class name
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28 jc.setProgramName(this.getClass().getSimpleName());
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29 }
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30
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31 /**
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32 * The default bite-size to use for applications that process files in chunks
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33 */
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34 public static final int DEFAULT_CHUNK_SIZE = 500_000;
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35
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36 /**
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37 * Do the main computation of this tool
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38 * @throws IOException
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39 */
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40 public abstract void run() throws IOException;
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41
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42 /**
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43 * Parse command-line arguments and run the tool
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44 * Exit on parameter exceptions
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45 * @param args
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46 */
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47 public void instanceMain(String[] args) throws CommandLineToolException {
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48 try {
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49 toolRunnerMain(args);
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50 } catch (ParameterException e) {
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51 System.err.println(e.getMessage());
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52 jc.usage();
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53 System.exit(-1);
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54 }
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55 }
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56
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57 /**
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58 * Parse command-line arguments and run the tool
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59 * @param args
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60 * @throws ParameterException if there are invalid/missing parameters
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61 * @throws CommandLineToolException if an exception occurs while running the tool
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62 */
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63 public void toolRunnerMain(String[] args) throws ParameterException, CommandLineToolException {
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64 jc.parse(args);
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65
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66 try {
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67 run();
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68 } catch (IOException e) {
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69 e.printStackTrace();
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70 throw new CommandLineToolException("IO error while running tool");
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71 }
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72 }
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73 }
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