--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/wigmath/Divide.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,64 @@
+package edu.unc.genomics.wigmath;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.apache.log4j.Logger;
+import org.broad.igv.bbfile.WigItem;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.io.WigFile;
+import edu.unc.genomics.io.WigFileException;
+
+public class Divide extends WigMathTool {
+
+	private static final Logger log = Logger.getLogger(Divide.class);
+
+	@Parameter(names = {"-n", "--numerator"}, description = "Dividend / Numerator (file 1)", required = true)
+	public WigFile dividendFile;
+	@Parameter(names = {"-d", "--denominator"}, description = "Divisor / Denominator (file 2)", required = true)
+	public WigFile divisorFile;
+
+	@Override
+	public void setup() {		
+		inputs.add(dividendFile);
+		inputs.add(divisorFile);
+		log.debug("Initialized " + inputs.size() + " input files");
+	}
+	
+	@Override
+	public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
+		log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop);
+		
+		Iterator<WigItem> dividendData = dividendFile.query(chr, start, stop);
+		Iterator<WigItem> divisorData = divisorFile.query(chr, start, stop);
+		
+		float[] result = WigFile.flattenData(dividendData, start, stop);
+		while (divisorData.hasNext()) {
+			WigItem item = divisorData.next();
+			for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
+				if (i-start >= 0 && i-start < result.length) {
+					if (item.getWigValue() != 0) {
+						result[i-start] /= item.getWigValue();
+					} else {
+						result[i-start] = Float.NaN;
+					}
+				}
+			}
+		}
+		
+		return result;
+	}
+	
+	
+	/**
+	 * @param args
+	 * @throws WigFileException 
+	 * @throws IOException 
+	 */
+	public static void main(String[] args) throws IOException, WigFileException {
+		new Divide().instanceMain(args);
+	}
+
+}