--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/ngs/IntervalStats.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,102 @@
+package edu.unc.genomics.ngs;
+
+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.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.math.stat.descriptive.SummaryStatistics;
+import org.apache.log4j.Logger;
+import org.broad.igv.bbfile.WigItem;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.CommandLineTool;
+import edu.unc.genomics.Interval;
+import edu.unc.genomics.io.IntervalFile;
+import edu.unc.genomics.io.WigFile;
+import edu.unc.genomics.io.WigFileException;
+
+public class IntervalStats extends CommandLineTool {
+
+	private static final Logger log = Logger.getLogger(IntervalStats.class);
+
+	@Parameter(description = "Input files", required = true)
+	public List<String> inputFiles = new ArrayList<String>();
+	@Parameter(names = {"-l", "--loci"}, description = "Loci file (Bed)", required = true)
+	public IntervalFile<? extends Interval> lociFile;
+	@Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
+	public Path outputFile;
+	
+	private List<WigFile> wigs = new ArrayList<>();
+	
+	@Override
+	public void run() throws IOException {		
+		log.debug("Initializing input Wig file(s)");
+		for (String inputFile : inputFiles) {
+			try {
+				WigFile wig = WigFile.autodetect(Paths.get(inputFile));
+				wigs.add(wig);
+			} catch (WigFileException e) {
+				log.error("Error initializing Wig input file: " + inputFile);
+				e.printStackTrace();
+				throw new RuntimeException("Error initializing Wig input file: " + inputFile);
+			}
+		}
+		
+		log.debug("Initializing output file");
+		int count = 0, skipped = 0;
+		try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
+			writer.write("#Chr\tStart\tStop\tID\tValue\tStrand");
+			for (String inputFile : inputFiles) {
+				Path p = Paths.get(inputFile);
+				writer.write("\t" + p.getFileName().toString());
+			}
+			writer.newLine();
+			
+			log.debug("Iterating over all intervals and computing statistics");
+			SummaryStatistics stats = new SummaryStatistics();
+			for (Interval interval : lociFile) {
+				List<Double> means = new ArrayList<>(wigs.size());
+				for (WigFile wig : wigs) {
+					stats.clear();
+					try {
+						Iterator<WigItem> result = wig.query(interval);
+						while(result.hasNext()) {
+							WigItem item = result.next();
+							for (int i = item.getStartBase(); i <= item.getEndBase(); i++) {
+								stats.addValue(item.getWigValue());
+							}
+						}
+						means.add(stats.getMean());
+					} catch (WigFileException e) {
+						means.add(Double.NaN);
+						skipped++;
+					}
+				}
+				
+				writer.write(interval.toBed() + "\t" + StringUtils.join(means, "\t"));
+				writer.newLine();
+				count++;
+			}
+		}
+		
+		lociFile.close();
+		for (WigFile wig : wigs) {
+			wig.close();
+		}
+		log.info(count + " intervals processed");
+		log.info(skipped + " interval skipped");
+	}
+	
+	public static void main(String[] args) {
+		new IntervalStats().instanceMain(args);
+	}
+
+}