--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/edu/unc/genomics/visualization/StripMatrix.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,56 @@
+package edu.unc.genomics.visualization;
+
+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 org.apache.log4j.Logger;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.CommandLineTool;
+import edu.unc.genomics.ReadablePathValidator;
+
+public class StripMatrix extends CommandLineTool {
+	
+	private static final Logger log = Logger.getLogger(StripMatrix.class);
+
+	@Parameter(names = {"-i", "--input"}, description = "Input file (matrix2png format)", required = true, validateWith = ReadablePathValidator.class)
+	public Path inputFile;
+	@Parameter(names = {"-o", "--output"}, description = "Output file (tabular)", required = true)
+	public Path outputFile;
+		
+	public void run() throws IOException {		
+		try (BufferedReader reader = Files.newBufferedReader(inputFile, Charset.defaultCharset())) {
+			try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
+				String line = reader.readLine();
+				// Always copy the first (header) line
+				writer.write(line);
+				writer.newLine();
+				while ((line = reader.readLine()) != null) {
+					String[] row = line.split("\t");
+					for (int i = 1; i < row.length; i++) {
+						String cell = row[i];
+						if (cell.equalsIgnoreCase("-")) {
+							writer.write("NaN");
+						} else {
+							writer.write(cell);
+						}
+						
+						if (i > 1) {
+							writer.write("\t");
+						}
+					}
+					writer.newLine();
+				}
+			}
+		}
+	}
+	
+	public static void main(String[] args) {
+		new StripMatrix().instanceMain(args);
+	}
+}
\ No newline at end of file