--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/visualization/IntervalAverager.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,118 @@
+package edu.unc.genomics.visualization;
+
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.commons.lang3.ArrayUtils;
+import org.apache.log4j.Logger;
+import org.broad.igv.bbfile.WigItem;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.BedEntry;
+import edu.unc.genomics.CommandLineTool;
+import edu.unc.genomics.ReadablePathValidator;
+import edu.unc.genomics.io.BedFile;
+import edu.unc.genomics.io.WigFile;
+import edu.unc.genomics.io.WigFileException;
+
+public class IntervalAverager extends CommandLineTool {
+	
+	private static final Logger log = Logger.getLogger(IntervalAverager.class);
+	
+	@Parameter(names = {"-i", "--input"}, description = "Input file (Wig)", required = true)
+	public WigFile inputFile;
+	@Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true, validateWith = ReadablePathValidator.class)
+	public Path lociFile;
+	@Parameter(names = {"-o", "--output"}, description = "Output file (matrix2png format)", required = true)
+	public Path outputFile;
+	
+	private List<BedEntry> loci;
+	
+	@Override
+	public void run() throws IOException {		
+		log.debug("Loading alignment intervals");
+		try (BedFile bed = new BedFile(lociFile)) {
+			loci = bed.loadAll();
+		}
+		
+		// Compute the matrix dimensions
+		int leftMax = Integer.MIN_VALUE;
+		int rightMax = Integer.MIN_VALUE;
+		for (BedEntry entry : loci) {
+			int left = Math.abs(entry.getValue().intValue()-entry.getStart());
+			int right = Math.abs(entry.getValue().intValue()-entry.getStop());
+			if (left > leftMax) {
+				leftMax = left;
+			}
+			if (right > rightMax) {
+				rightMax = right;
+			}
+		}
+		
+		int m = loci.size();
+		int n = leftMax + rightMax + 1;
+		int alignmentPoint = leftMax;
+		log.info("Intervals aligned into: " + m+"x"+n + " matrix");
+		log.info("Alignment point: " + alignmentPoint);
+				
+		float[] sum = new float[n];
+		int[] counts = new int[n];
+		int count = 0, skipped = 0;	
+		log.debug("Iterating over all intervals");
+		for (BedEntry entry : loci) {
+			Iterator<WigItem> result = null;
+			try {
+				result = inputFile.query(entry);
+			} catch (WigFileException e) {
+				skipped++;
+				continue;
+			}
+			
+			float[] data = WigFile.flattenData(result, entry.getStart(), entry.getStop());
+			// Reverse if on the Crick strand
+			if (entry.isCrick()) {
+				ArrayUtils.reverse(data);
+			}
+			
+			// Locus alignment point (entry value) should be positioned over the global alignment point
+			int n1 = alignmentPoint - Math.abs(entry.getValue().intValue()-entry.getStart());
+			int n2 = alignmentPoint + Math.abs(entry.getValue().intValue()-entry.getStop());
+			for (int bp = n1; bp <= n2; bp++) {
+				sum[bp] += data[bp-n1];
+				counts[bp]++;
+			}
+		}
+		
+		inputFile.close();
+		log.info(count + " intervals processed");
+		log.info(skipped + " intervals skipped");
+		
+		log.debug("Computing average");
+		float[] avg = new float[n];
+		for (int i = 0; i < n; i++) {
+			if (counts[i] == 0) {
+				avg[i] = Float.NaN;
+			} else {
+				avg[i] = sum[i] / counts[i];
+			}
+		}
+		
+		log.debug("Writing average to output");
+		try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
+			for (int i = 0; i < n; i++) {
+				writer.write(i-alignmentPoint + "\t" + avg[i]);
+				writer.newLine();				
+			}
+		}
+	}
+	
+	public static void main(String[] args) {
+		new IntervalAverager().instanceMain(args);
+	}
+}
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