--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/edu/unc/genomics/converters/RomanNumeralize.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,61 @@
+package edu.unc.genomics.converters;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.CommandLineTool;
+import edu.unc.genomics.ReadablePathValidator;
+import edu.unc.utils.RomanNumeral;
+
+public class RomanNumeralize extends CommandLineTool {
+
+	private static final Logger log = Logger.getLogger(RomanNumeralize.class);
+
+	@Parameter(names = {"-i", "--input"}, description = "Input file", required = true, validateWith = ReadablePathValidator.class)
+	public Path inputFile;
+	@Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
+	public Path outputFile;
+	
+	/**
+	 * Pattern for finding "chr12" tokens (will find "chr1" through "chr99")
+	 */
+	Pattern p = Pattern.compile("/chr[\\d]{1,2}/i");
+	
+	@Override
+	public void run() throws IOException {
+		try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset());
+				 BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
+			log.debug("Copying input to output and replacing with Roman Numerals");
+			String line;
+			while ((line = reader.readLine()) != null) {
+				Matcher m = p.matcher(line);
+				StringBuffer converted = new StringBuffer(line.length());
+				while (m.find()) {
+					String chrNum = line.substring(m.start()+3, m.end());
+					int arabic = Integer.parseInt(chrNum);
+					String roman = RomanNumeral.int2roman(arabic);
+					m.appendReplacement(converted, "chr"+roman);
+				}
+				m.appendTail(converted);
+				
+				writer.write(converted.toString());
+				writer.newLine();
+			}
+		}
+	}
+	
+	public static void main(String[] args) {
+		new RomanNumeralize().instanceMain(args);
+	}
+
+}