--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/edu/unc/genomics/wigmath/LogTransform.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,55 @@
+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 LogTransform extends WigMathTool {
+
+	private static final Logger log = Logger.getLogger(LogTransform.class);
+
+	@Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
+	public WigFile inputFile;
+	@Parameter(names = {"-b", "--base"}, description = "Logarithm base (default = 2)")
+	public double base = 2;
+	
+	private double baseChange;
+
+	@Override
+	public void setup() {
+		baseChange = Math.log(base);
+		inputs.add(inputFile);
+	}
+	
+	@Override
+	public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
+		log.debug("Computing difference for chunk "+chr+":"+start+"-"+stop);
+		
+		Iterator<WigItem> data = inputFile.query(chr, start, stop);
+		float[] result = WigFile.flattenData(data, start, stop);
+		
+		for (int i = 0; i < result.length; i++) {
+			result[i] = (float) (Math.log(result[i]) / baseChange);
+		}
+		
+		return result;
+	}
+	
+	
+	/**
+	 * @param args
+	 * @throws WigFileException 
+	 * @throws IOException 
+	 */
+	public static void main(String[] args) throws IOException, WigFileException {
+		new LogTransform().instanceMain(args);
+	}
+
+}