--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/edu/unc/genomics/CommandLineTool.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,73 @@
+package edu.unc.genomics;
+
+import java.io.IOException;
+
+import com.beust.jcommander.JCommander;
+import com.beust.jcommander.ParameterException;
+
+/**
+ * A command-line script
+ * @author timpalpant
+ *
+ */
+public abstract class CommandLineTool {
+	
+	/**
+	 * JCommander command-line argument parser
+	 */
+	private final JCommander jc = new JCommander(this);
+	
+	public CommandLineTool() {
+		// Add factories for parsing Paths, Assemblies, IntervalFiles, and WigFiles
+		jc.addConverterFactory(new PathFactory());
+		jc.addConverterFactory(new AssemblyFactory());
+		jc.addConverterFactory(new IntervalFileFactory());
+		jc.addConverterFactory(new WigFileFactory());
+		
+		// Set the program name to be the class name
+		jc.setProgramName(this.getClass().getSimpleName());
+	}
+	
+	/**
+	 * The default bite-size to use for applications that process files in chunks
+	 */
+	public static final int DEFAULT_CHUNK_SIZE = 500_000;
+	
+	/**
+	 * Do the main computation of this tool
+	 * @throws IOException
+	 */
+	public abstract void run() throws IOException;
+	
+	/**
+	 * Parse command-line arguments and run the tool
+	 * Exit on parameter exceptions
+	 * @param args
+	 */
+	public void instanceMain(String[] args) throws CommandLineToolException {
+		try {
+			toolRunnerMain(args);
+		} catch (ParameterException e) {
+			System.err.println(e.getMessage());
+			jc.usage();
+			System.exit(-1);
+		}
+	}
+	
+	/**
+	 * Parse command-line arguments and run the tool
+	 * @param args
+	 * @throws ParameterException if there are invalid/missing parameters
+	 * @throws CommandLineToolException if an exception occurs while running the tool
+	 */
+	public void toolRunnerMain(String[] args) throws ParameterException, CommandLineToolException {
+		jc.parse(args);
+		
+		try {
+			run();
+		} catch (IOException e) {
+			e.printStackTrace();
+			throw new CommandLineToolException("IO error while running tool");
+		}
+	}
+}