From f792353dcd59948aab4da10521b32adeb990487d Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sat, 24 Sep 2011 08:56:45 -0400
Subject: [PATCH] Framework for genotype unit test

---
 .../sting/utils/variantcontext/Genotype.java  |  3 +-
 .../variantcontext/GenotypeUnitTest.java      | 84 +++++++++++++++++++
 2 files changed, 86 insertions(+), 1 deletion(-)
 create mode 100644 public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
index fd8c70abe..7ab3f81f0 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -268,7 +268,8 @@ public class Genotype {
      * @param <V> the value type
      * @return a sting, enclosed in {}, with comma seperated key value pairs in order of the keys
      */
-    public static <T extends Comparable<T>, V> String sortedString(Map<T, V> c) {
+    private static <T extends Comparable<T>, V> String sortedString(Map<T, V> c) {
+        // NOTE -- THIS IS COPIED FROM GATK UTILS TO ALLOW US TO KEEP A SEPARATION BETWEEN THE GATK AND VCF CODECS
         List<T> t = new ArrayList<T>(c.keySet());
         Collections.sort(t);
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java
new file mode 100644
index 000000000..c4f1efd04
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java
@@ -0,0 +1,84 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+// our package
+package org.broadinstitute.sting.utils.variantcontext;
+
+
+// the imports for unit testing.
+
+
+import org.broadinstitute.sting.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+import java.util.List;
+
+
+public class GenotypeUnitTest extends BaseTest {
+    Allele A, Aref, T;
+
+    @BeforeSuite
+    public void before() {
+        A = Allele.create("A");
+        Aref = Allele.create("A", true);
+        T = Allele.create("T");
+    }
+
+//    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased) {
+//    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean isPhased, double[] log10Likelihoods) {
+//    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, double[] log10Likelihoods)
+//    public Genotype(String sampleName, List<Allele> alleles, double negLog10PError)
+//    public Genotype(String sampleName, List<Allele> alleles)
+//    public List<Allele> getAlleles()
+//    public List<Allele> getAlleles(Allele allele)
+//    public Allele getAllele(int i)
+//    public boolean isPhased()
+//    public int getPloidy()
+//    public Type getType()
+//    public boolean isHom()
+//    public boolean isHomRef()
+//    public boolean isHomVar()
+//    public boolean isHet()
+//    public boolean isNoCall()
+//    public boolean isCalled()
+//    public boolean isAvailable()
+//    public boolean hasLikelihoods()
+//    public GenotypeLikelihoods getLikelihoods()
+//    public boolean sameGenotype(Genotype other)
+//    public boolean sameGenotype(Genotype other, boolean ignorePhase)
+//    public String getSampleName()
+//    public boolean hasNegLog10PError()
+//    public double getNegLog10PError()
+//    public double getPhredScaledQual()
+//    public boolean hasAttribute(String key)
+//    public Object getAttribute(String key)
+//    public Object getAttribute(String key, Object defaultValue)
+//    public String getAttributeAsString(String key, String defaultValue)
+//    public int getAttributeAsInt(String key, int defaultValue)
+//    public double getAttributeAsDouble(String key, double  defaultValue)
+//    public boolean getAttributeAsBoolean(String key, boolean  defaultValue)
+}