--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/edu/unc/genomics/wigmath/Subtract.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,61 @@
+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 Subtract extends WigMathTool {
+
+	private static final Logger log = Logger.getLogger(Subtract.class);
+
+	@Parameter(names = {"-m", "--minuend"}, description = "Minuend (top - file 1)", required = true)
+	public WigFile minuendFile;
+	@Parameter(names = {"-s", "--subtrahend"}, description = "Subtrahend (bottom - file 2)", required = true)
+	public WigFile subtrahendFile;
+
+	@Override
+	public void setup() {
+		log.debug("Initializing input files");
+		inputs.add(minuendFile);
+		inputs.add(subtrahendFile);
+		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> minuendData = minuendFile.query(chr, start, stop);
+		Iterator<WigItem> subtrahendData = subtrahendFile.query(chr, start, stop);
+		
+		float[] result = WigFile.flattenData(minuendData, start, stop);
+		while (subtrahendData.hasNext()) {
+			WigItem item = subtrahendData.next();
+			for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
+				if (i-start >= 0 && i-start < result.length) {
+					result[i-start] -= item.getWigValue();
+				}
+			}
+		}
+		
+		return result;
+	}
+	
+	
+	/**
+	 * @param args
+	 * @throws WigFileException 
+	 * @throws IOException 
+	 */
+	public static void main(String[] args) throws IOException, WigFileException {
+		new Subtract().instanceMain(args);
+	}
+
+}