--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/AssemblyConverter.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,43 @@
+package edu.unc.genomics;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.zip.DataFormatException;
+
+import com.beust.jcommander.IStringConverter;
+import com.beust.jcommander.ParameterException;
+
+/**
+ * @author timpalpant
+ *
+ */
+public class AssemblyConverter implements IStringConverter<Assembly> {
+	
+	public static final Path ASSEMBLIES_DIR = Paths.get("resources", "assemblies");
+
+	@Override
+	public Assembly convert(String value) throws ParameterException {
+		// Look for the assembly in the resources/assemblies directory
+		Path p = ASSEMBLIES_DIR.resolve(value+".len");
+		
+		// If it does not exist in the assemblies directory, check if it is a path to a file
+		if (!Files.isReadable(p)) {
+			PathConverter converter = new PathConverter();
+			p = converter.convert(value);
+			// If it does not exist, then throw an exception that the assembly cannot be found
+			if (!Files.isReadable(p)) {
+				throw new ParameterException("Cannot find Assembly file: " + value);
+			}
+		}
+		
+		// Attempt to load the assembly from file
+		try {
+			return new Assembly(p);
+		} catch (IOException | DataFormatException e) {
+			throw new ParameterException("Error loading Assembly from file: " + p);
+		}
+	}
+	
+}