From a88708ebfa4435aa1778426969fb490f63e38308 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 15 Jan 2011 22:42:42 +0000
Subject: [PATCH] Moving GLF code to archive

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5006 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../java/src/org/broadinstitute/sting}/glf/GLFReader.java       | 1 +
 .../src/org/broadinstitute/sting}/glf/GLFReaderUnitTest.java    | 0
 .../java/src/org/broadinstitute/sting}/glf/GLFRecord.java       | 1 +
 .../src/org/broadinstitute/sting}/glf/GLFRecordUnitTest.java    | 0
 .../java/src/org/broadinstitute/sting}/glf/GLFSingleCall.java   | 1 +
 .../org/broadinstitute/sting}/glf/GLFVariableLengthCall.java    | 1 +
 .../java/src/org/broadinstitute/sting}/glf/GLFWriter.java       | 1 +
 .../src/org/broadinstitute/sting}/glf/GLFWriterUnitTest.java    | 0
 .../java/src/org/broadinstitute/sting/glf}/IndelLikelihood.java | 1 +
 .../src/org/broadinstitute/sting/glf}/LikelihoodObject.java     | 2 ++
 .../org/broadinstitute/sting/glf}/LikelihoodObjectUnitTest.java | 0
 11 files changed, 8 insertions(+)
 rename {java/src/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting}/glf/GLFReader.java (99%)
 rename {java/test/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting}/glf/GLFReaderUnitTest.java (100%)
 rename {java/src/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting}/glf/GLFRecord.java (99%)
 rename {java/test/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting}/glf/GLFRecordUnitTest.java (100%)
 rename {java/src/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting}/glf/GLFSingleCall.java (99%)
 rename {java/src/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting}/glf/GLFVariableLengthCall.java (99%)
 rename {java/src/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting}/glf/GLFWriter.java (99%)
 rename {java/test/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting}/glf/GLFWriterUnitTest.java (100%)
 rename {java/src/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting/glf}/IndelLikelihood.java (98%)
 rename {java/src/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting/glf}/LikelihoodObject.java (99%)
 rename {java/test/org/broadinstitute/sting/utils/genotype => archive/java/src/org/broadinstitute/sting/glf}/LikelihoodObjectUnitTest.java (100%)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java b/archive/java/src/org/broadinstitute/sting/glf/GLFReader.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java
rename to archive/java/src/org/broadinstitute/sting/glf/GLFReader.java
index 86c53fe99..4032faca0 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java
+++ b/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
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFReaderUnitTest.java b/archive/java/src/org/broadinstitute/sting/glf/GLFReaderUnitTest.java
similarity index 100%
rename from java/test/org/broadinstitute/sting/utils/genotype/glf/GLFReaderUnitTest.java
rename to archive/java/src/org/broadinstitute/sting/glf/GLFReaderUnitTest.java
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java b/archive/java/src/org/broadinstitute/sting/glf/GLFRecord.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
rename to archive/java/src/org/broadinstitute/sting/glf/GLFRecord.java
index 242d3a092..77fbbfa09 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
+++ b/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;
 
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFRecordUnitTest.java b/archive/java/src/org/broadinstitute/sting/glf/GLFRecordUnitTest.java
similarity index 100%
rename from java/test/org/broadinstitute/sting/utils/genotype/glf/GLFRecordUnitTest.java
rename to archive/java/src/org/broadinstitute/sting/glf/GLFRecordUnitTest.java
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFSingleCall.java b/archive/java/src/org/broadinstitute/sting/glf/GLFSingleCall.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/genotype/glf/GLFSingleCall.java
rename to archive/java/src/org/broadinstitute/sting/glf/GLFSingleCall.java
index 2f52fc193..6bdd9ffc7 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFSingleCall.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFVariableLengthCall.java b/archive/java/src/org/broadinstitute/sting/glf/GLFVariableLengthCall.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/genotype/glf/GLFVariableLengthCall.java
rename to archive/java/src/org/broadinstitute/sting/glf/GLFVariableLengthCall.java
index d670ff4d0..2f28d5fe5 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFVariableLengthCall.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java b/archive/java/src/org/broadinstitute/sting/glf/GLFWriter.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
rename to archive/java/src/org/broadinstitute/sting/glf/GLFWriter.java
index c998b5221..48569db9a 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
+++ b/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;
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java b/archive/java/src/org/broadinstitute/sting/glf/GLFWriterUnitTest.java
similarity index 100%
rename from java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java
rename to archive/java/src/org/broadinstitute/sting/glf/GLFWriterUnitTest.java
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/IndelLikelihood.java b/archive/java/src/org/broadinstitute/sting/glf/IndelLikelihood.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/utils/genotype/IndelLikelihood.java
rename to archive/java/src/org/broadinstitute/sting/glf/IndelLikelihood.java
index 1800f023c..ae969c254 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/IndelLikelihood.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java b/archive/java/src/org/broadinstitute/sting/glf/LikelihoodObject.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
rename to archive/java/src/org/broadinstitute/sting/glf/LikelihoodObject.java
index f68523479..7227278e5 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
+++ b/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 {
 
 
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/LikelihoodObjectUnitTest.java b/archive/java/src/org/broadinstitute/sting/glf/LikelihoodObjectUnitTest.java
similarity index 100%
rename from java/test/org/broadinstitute/sting/utils/genotype/LikelihoodObjectUnitTest.java
rename to archive/java/src/org/broadinstitute/sting/glf/LikelihoodObjectUnitTest.java