--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/wigmath/Add.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,76 @@
+package edu.unc.genomics.wigmath;
+
+import java.io.IOException;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.broad.igv.bbfile.WigItem;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.CommandLineToolException;
+import edu.unc.genomics.io.WigFile;
+import edu.unc.genomics.io.WigFileException;
+
+public class Add extends WigMathTool {
+
+	private static final Logger log = Logger.getLogger(Add.class);
+
+	@Parameter(description = "Input files", required = true)
+	public List<String> inputFiles = new ArrayList<String>();
+
+	@Override
+	public void setup() {
+		if (inputFiles.size() < 2) {
+			throw new CommandLineToolException("No reason to add < 2 files.");
+		}
+		
+		log.debug("Initializing input files");
+		for (String inputFile : inputFiles) {
+			try {
+				addInputFile(WigFile.autodetect(Paths.get(inputFile)));
+			} catch (IOException | WigFileException e) {
+				log.error("Error initializing input Wig file: " + inputFile);
+				e.printStackTrace();
+				throw new CommandLineToolException(e.getMessage());
+			}
+		}
+		log.debug("Initialized " + inputs.size() + " input files");
+	}
+	
+	@Override
+	public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
+		log.debug("Computing sum for chunk "+chr+":"+start+"-"+stop);
+		
+		int length = stop - start + 1;
+		float[] sum = new float[length];
+		
+		for (WigFile wig : inputs) {
+			Iterator<WigItem> data = wig.query(chr, start, stop);
+			while (data.hasNext()) {
+				WigItem item = data.next();
+				for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
+					if (i-start >= 0 && i-start < sum.length) {
+						sum[i-start] += item.getWigValue();
+					}
+				}
+			}
+		}
+		
+		return sum;
+	}
+	
+	
+	/**
+	 * @param args
+	 * @throws WigFileException 
+	 * @throws IOException 
+	 */
+	public static void main(String[] args) throws IOException, WigFileException {
+		new Add().instanceMain(args);
+	}
+
+}