From 4554ca1b28693bdec52e67eb88f6b501a8a1147e Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 6 Oct 2009 19:09:27 +0000
Subject: [PATCH] more cleanup, depecaited the old genotype, corrected
 SNPCallsFromGenotypes' imports and two other classes that depend on it.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1771 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java  | 2 +-
 .../org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java | 3 ++-
 .../sting/gatk/refdata/SNPCallFromGenotypes.java              | 2 ++
 .../org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java   | 4 ++--
 4 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java b/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
index 416f85e7e..41aa1e0b9 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.List;
@@ -12,6 +11,7 @@ import java.util.List;
  * Time: 11:02:03 AM
  * To change this template use File | Settings | File Templates.
  */
+@Deprecated
 public interface Genotype extends Comparable<ReferenceOrderedDatum> {
     // ----------------------------------------------------------------------
     //
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
index 2e4c5023b..9c90693bc 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
@@ -1,8 +1,9 @@
 package org.broadinstitute.sting.gatk.refdata;
 
+import org.broadinstitute.sting.utils.genotype.Genotype;
+
 import java.util.ArrayList;
 import java.util.List;
-
 /**
  * loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom
  * chr1:1104840 A N 0.000000 -85.341265 -85.341265 0.000000 0.000000 324.000000 162 0 0
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SNPCallFromGenotypes.java b/java/src/org/broadinstitute/sting/gatk/refdata/SNPCallFromGenotypes.java
index 1ef7fcde4..9b5ab6985 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SNPCallFromGenotypes.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SNPCallFromGenotypes.java
@@ -2,6 +2,8 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.genotype.Variation;
 
+import org.broadinstitute.sting.utils.genotype.Genotype;
+
 import java.util.List;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
index 39abea5bc..dc192fb80 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-
+import org.broadinstitute.sting.utils.GenomeLocParser; 
+import org.broadinstitute.sting.utils.genotype.Genotype;
 import java.util.Arrays;
 import java.util.List;