--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/ngs/IntervalLengthDistribution.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,59 @@
+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 org.apache.commons.math.stat.Frequency;
+import org.apache.log4j.Logger;
+
+import com.beust.jcommander.Parameter;
+
+import edu.unc.genomics.CommandLineTool;
+import edu.unc.genomics.Interval;
+import edu.unc.genomics.io.IntervalFile;
+
+public class IntervalLengthDistribution extends CommandLineTool {
+
+	private static final Logger log = Logger.getLogger(IntervalLengthDistribution.class);
+
+	@Parameter(names = {"-i", "--input"}, description = "Interval file", required = true)
+	public IntervalFile<? extends Interval> inputFile;
+	@Parameter(names = {"-o", "--output"}, description = "Output file", required = true)
+	public Path outputFile;
+	
+	
+	@Override
+	public void run() throws IOException {
+		log.debug("Generating histogram of interval lengths");
+		Frequency freq = new Frequency();
+		int min = Integer.MAX_VALUE;
+		int max = -1;
+		for (Interval i : inputFile) {
+			int L = i.length();
+			freq.addValue(L);
+			
+			if (L < min) {
+				min = L;
+			}
+			if (L > max) {
+				max = L;
+			}
+		}
+		
+		log.debug("Writing histogram output");
+		try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
+			for (int i = min; i <= max; i++) {
+				writer.write(i+"\t"+freq.getCount(i));
+				writer.newLine();
+			}
+		}
+	}
+	
+	public static void main(String[] args) {
+		new IntervalLengthDistribution().instanceMain(args);
+	}
+
+}