--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/converters/IntervalToWig.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,91 @@
+package edu.unc.genomics.converters;
+
+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 org.apache.log4j.Logger;
+
+import com.beust.jcommander.Parameter;
+
+import edu.ucsc.genome.TrackHeader;
+import edu.unc.genomics.Assembly;
+import edu.unc.genomics.Interval;
+import edu.unc.genomics.CommandLineTool;
+import edu.unc.genomics.ValuedInterval;
+import edu.unc.genomics.io.IntervalFile;
+
+public class IntervalToWig extends CommandLineTool {
+
+	private static final Logger log = Logger.getLogger(IntervalToWig.class);
+
+	@Parameter(names = {"-i", "--input"}, description = "Input file (Bed/BedGraph)", required = true)
+	public IntervalFile<? extends Interval> intervalFile;
+	@Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true)
+	public Assembly assembly;
+	@Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true)
+	public Path outputFile;
+	
+	@Override
+	public void run() throws IOException {
+		log.info(intervalFile.count() + " entries in input");
+		
+		log.debug("Initializing output file");
+		try (BufferedWriter writer = Files.newBufferedWriter(outputFile, Charset.defaultCharset())) {
+			// Write the Wiggle track header to the output file
+			TrackHeader header = new TrackHeader("wiggle_0");
+			header.setName("Converted " + intervalFile.getPath().getFileName());
+			header.setDescription("Converted " + intervalFile.getPath().getFileName());
+			writer.write(header.toString());
+			writer.newLine();
+			
+			// Process each chromosome in the assembly
+			for (String chr : assembly) {
+				log.debug("Processing chromosome " + chr);
+				// Write the contig header to the output file
+				writer.write("fixedStep chrom="+chr+" start=1 step=1 span=1");
+				writer.newLine();
+				
+				int start = 1;
+				while (start < assembly.getChrLength(chr)) {
+					int stop = start + DEFAULT_CHUNK_SIZE - 1;
+					int length = stop - start + 1;
+					int[] count = new int[length];
+					float[] sum = new float[length];
+					
+					Iterator<? extends Interval> it = intervalFile.query(chr, start, stop);
+					while (it.hasNext()) {
+						ValuedInterval entry = (ValuedInterval) it.next();
+						if (entry.getValue() != null) {
+							for (int i = entry.getStart(); i <= entry.getStop(); i++) {
+								sum[i-start] += entry.getValue().floatValue();
+								count[i-start]++;
+							}
+						}
+					}
+					
+					// Write the average at each base pair to the output file
+					for (int i = 0; i < sum.length; i++) {
+						if (count[i] == 0) {
+							writer.write(String.valueOf(Float.NaN));
+						} else {
+							writer.write(String.valueOf(sum[i]/count[i]));
+						}
+						writer.newLine();
+					}
+					
+					// Process the next chunk
+					start = stop + 1;
+				}
+			}
+		}
+	}
+	
+	public static void main(String[] args) {
+		new IntervalToWig().instanceMain(args);
+	}
+
+}