--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/edu/unc/genomics/wigmath/MovingAverageSmooth.java	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,67 @@
+package edu.unc.genomics.wigmath;
+
+import java.io.IOException;
+import java.util.Iterator;
+
+import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
+import org.apache.log4j.Logger;
+import org.broad.igv.bbfile.WigItem;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.PositiveIntegerValidator;
+import edu.unc.genomics.io.WigFile;
+import edu.unc.genomics.io.WigFileException;
+
+public class MovingAverageSmooth extends WigMathTool {
+
+	private static final Logger log = Logger.getLogger(MovingAverageSmooth.class);
+
+	@Parameter(names = {"-i", "--input"}, description = "Input file", required = true)
+	public WigFile inputFile;
+	@Parameter(names = {"-w", "--width"}, description = "Width of kernel (bp)")
+	public int width = 10;
+	
+	WigFile input;
+	DescriptiveStatistics stats;
+
+	@Override
+	public void setup() {
+		inputs.add(inputFile);
+		
+		log.debug("Initializing statistics");
+		stats = new DescriptiveStatistics();
+		stats.setWindowSize(width);
+	}
+	
+	@Override
+	public float[] compute(String chr, int start, int stop) throws IOException, WigFileException {
+		log.debug("Smoothing chunk "+chr+":"+start+"-"+stop);
+		// Pad the query so that we can provide values for the ends
+		int queryStart = Math.max(start-width/2, input.getChrStart(chr));
+		int queryStop = Math.min(stop+width/2, input.getChrStop(chr));
+		Iterator<WigItem> result = input.query(chr, queryStart, queryStop);
+		float[] data = WigFile.flattenData(result, queryStart, queryStop);
+		
+		float[] smoothed = new float[stop-start+1];
+		for (int bp = start; bp <= stop; bp++) {
+			stats.addValue(data[bp-queryStart]);
+			if (bp-start-width/2 >= 0) {
+				smoothed[bp-start-width/2] = (float) stats.getMean();
+			}
+		}
+		
+		return smoothed;
+	}
+	
+	
+	/**
+	 * @param args
+	 * @throws WigFileException 
+	 * @throws IOException 
+	 */
+	public static void main(String[] args) throws IOException, WigFileException {
+		new MovingAverageSmooth().instanceMain(args);
+	}
+
+}