Moving GLF code to archive

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5006 348d0f76-0448-11de-a6fe-93d51630548a

archive/java/src/org/broadinstitute/sting/glf/GLFReader.java

@@ -38,6 +38,7 @@ import java.util.Iterator;
  */
 
 /** an object for reading in GLF files */
+// TODO -- DELETE ME GLF
 public class GLFReader implements Iterator<GLFRecord> {
 
     // our next record

archive/java/src/org/broadinstitute/sting/glf/GLFRecord.java

@@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
  *         which represents the accepted FASTA nucleotide symbols and their assocated GLF
  *         field values.
  */
+// TODO -- DELETE ME GLF
 public abstract class GLFRecord {
     public final static double LIKELIHOOD_SCALE_FACTOR = 10;
 

archive/java/src/org/broadinstitute/sting/glf/GLFSingleCall.java

@@ -36,6 +36,7 @@ import org.broadinstitute.sting.utils.Utils;
  *         <p/>
  *         This class represents a single point geneotype call in GLF vernacular
  */
+// TODO -- DELETE ME GLF
 public class GLFSingleCall extends GLFRecord {
 
     // our likelihoods array

archive/java/src/org/broadinstitute/sting/glf/GLFVariableLengthCall.java

@@ -36,6 +36,7 @@ import net.sf.samtools.util.BinaryCodec;
  *         Currently a lot of parameters need to be provided, but we may be able to thin
  *         those down as we understand what we have to specify and what we can infer.
  */
+// TODO -- DELETE ME GLF
 public class GLFVariableLengthCall extends GLFRecord {
     // our fields, corresponding to the glf spec
     private short lkHom1 = 0;

archive/java/src/org/broadinstitute/sting/glf/GLFWriter.java

@@ -43,6 +43,7 @@ import java.io.OutputStream;
  *          single and variable length genotype calls using the provided functions.  When you've finished
  *          generating GLF records, make sure you close the file.
  */
+// TODO -- DELETE ME GLF
 public class GLFWriter {
     // our output codec
     private final BinaryCodec outputBinaryCodec;

archive/java/src/org/broadinstitute/sting/glf/IndelLikelihood.java

@@ -33,6 +33,7 @@ package org.broadinstitute.sting.utils.genotype;
  *         <p/>
  *         The representation of an indel allele.
  */
+// TODO -- DELETE ME GLF
 public class IndelLikelihood {
 
     protected double loglikelihood;

archive/java/src/org/broadinstitute/sting/glf/LikelihoodObject.java

@@ -43,6 +43,8 @@ import java.util.HashMap;
  *         This allows the consumer to make an empty LikelihoodObject, and just set
  *         those values which have associated likelihood values.
  */
+
+// TODO -- DELETE ME GLF
 public class LikelihoodObject {