--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/java-genomics-toolkit/src/edu/unc/genomics/ngs/BaseAlignCounts.java	Mon Feb 13 21:55:55 2012 -0500
@@ -0,0 +1,94 @@
+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.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.CommandLineTool;
+import edu.unc.genomics.Interval;
+import edu.unc.genomics.io.IntervalFile;
+
+public class BaseAlignCounts extends CommandLineTool {
+	
+	private static final Logger log = Logger.getLogger(BaseAlignCounts.class);
+		
+	@Parameter(names = {"-i", "--input"}, description = "Input file (reads)", required = true)
+	public IntervalFile<? extends Interval> intervalFile;
+	@Parameter(names = {"-a", "--assembly"}, description = "Genome assembly", required = true)
+	public Assembly assembly;
+	@Parameter(names = {"-x", "--extend"}, description = "Extend reads from 5' end (default = read length)")
+	public Integer extend;
+	@Parameter(names = {"-o", "--output"}, description = "Output file (Wig)", required = true)
+	public Path outputFile;
+	
+	@Override
+	public void run() throws IOException {
+		log.debug("Initializing output file");
+		int mapped = 0;
+		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];
+					
+					Iterator<? extends Interval> it = intervalFile.query(chr, start, stop);
+					while (it.hasNext()) {
+						Interval entry = it.next();
+						int entryStop = entry.getStop();
+						if (extend != null) {
+							if (entry.isWatson()) {
+								entryStop = entry.getStart() + extend;
+							} else {
+								entryStop = entry.getStart() - extend;
+							}
+						}
+						
+						for (int i = entry.getStart(); i <= entryStop; i++) {
+							count[i-start]++;
+						}
+						mapped++;
+					}
+					
+					// Write the count at each base pair to the output file
+					for (int i = 0; i < count.length; i++) {
+						writer.write(count[i]);
+						writer.newLine();
+					}
+					
+					// Process the next chunk
+					start = stop + 1;
+				}
+			}
+		}
+		
+		log.info("Mapped "+mapped+" reads");
+	}
+	
+	public static void main(String[] args) {
+		new BaseAlignCounts().instanceMain(args);
+	}
+}
\ No newline at end of file