rod for binary GELI files (still needs to be tested)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1198 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/rodGELI.java

@@ -0,0 +1,81 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import java.util.Iterator;
+import java.io.IOException;
+import java.io.File;
+
+import edu.mit.broad.picard.genotype.geli.GeliFileReader;
+import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+
+import net.sf.samtools.util.CloseableIterator;
+
+
+/**
+ *  This class wraps Picard Geli CHiP data and presents it as a ROD.
+ */
+
+public class rodGELI extends BasicReferenceOrderedDatum {
+	// ----------------------------------------------------------------------
+	//
+	// Constructors
+	//
+	// ----------------------------------------------------------------------
+
+	private GenotypeLikelihoods gh = null;
+
+	public rodGELI(final String name, GenotypeLikelihoods gh) {
+		super(name);
+        this.gh = gh;
+	}
+
+	@Override
+	public GenomeLoc getLocation() {
+		return GenomeLocParser.createGenomeLoc(gh.getSequenceIndex(), gh.getPosition());
+	}
+
+	/** Required by ReferenceOrderedDatum interface. This implementation provides its own iterator,
+	 * so this method does nothing at all (always returns false).
+	 *
+	 */
+	@Override
+	public boolean parseLine(Object header, String[] parts) throws IOException {
+		return false;
+	}
+
+	@Override
+	public String toString() {
+        return gh.toString();
+	}
+
+	private static class rodGELIIterator implements Iterator<rodGELI> {
+
+		private String rodName = null;
+		private GeliFileReader parser = null;
+        private CloseableIterator<GenotypeLikelihoods> iterator = null;
+
+		rodGELIIterator(String name, File f) {
+            rodName = name;
+			parser = new GeliFileReader(f);
+			iterator = parser.iterator();
+		}
+
+		public boolean hasNext() {
+			return iterator.hasNext();
+		}
+
+		public rodGELI next() {
+            return new rodGELI(rodName, iterator.next());
+		}
+
+		public void remove() {
+			throw new UnsupportedOperationException("'remove' operation is not supported for GELIs");
+		}
+
+	}
+
+	public static Iterator<rodGELI> createIterator(String name, File file) {
+		return new rodGELI.rodGELIIterator(name,file);
+	}
+}