From 61e1a3ecd17c5813b12b51c092c4c54de76f16bc Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@roadinstitute.org>
Date: Sat, 22 Nov 2014 22:01:39 -0500
Subject: [PATCH] Added the framework for testing the PhasingUtilies methods
 matchHaplotypeAlleles() and reallyMergeIntoMNP()

---
 .../phasing/PhasingUtilitiesUnitTest.java     | 61 +++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilitiesUnitTest.java

diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilitiesUnitTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilitiesUnitTest.java
new file mode 100644
index 000000000..32facf007
--- /dev/null
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/phasing/PhasingUtilitiesUnitTest.java
@@ -0,0 +1,61 @@
+package org.broadinstitute.gatk.tools.walkers.phasing;
+
+import htsjdk.samtools.reference.ReferenceSequenceFile;
+import htsjdk.variant.variantcontext.*;
+import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import org.broadinstitute.gatk.tools.walkers.phasing.PhasingUtils;
+import org.broadinstitute.gatk.utils.BaseTest;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+/**
+ * Created by ronlevine and philipdexheimer on 11/22/14.
+ *
+ * TODO - need to exercise the code paths in matchHaplotypeAlleles and reallyMergeIntoMNP
+ */
+public class PhasingUtilitiesUnitTest extends BaseTest  {
+
+    private final int start = 10;
+    private ReferenceSequenceFile referenceFile;
+    private Allele Aref;
+
+    @BeforeClass
+    public void init() throws FileNotFoundException {
+        referenceFile = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
+        Aref = Allele.create("A", true);
+    }
+
+    @Test
+    public void TestMatchHaplotypeAlleles() {
+
+        final List<Allele> noCalls = new ArrayList<>(1);
+        noCalls.add(Allele.NO_CALL);
+        final Genotype gA_ALT = new GenotypeBuilder("A").PL(new int[]{0, 100, 1000}).alleles(noCalls).make();
+
+        // Must match because that same genotype
+        PhasingUtils.SameHaplotypeAlleles sameHaplotypeAlleles = PhasingUtils.matchHaplotypeAlleles(gA_ALT, gA_ALT);
+
+        // TODO - make a reference SameHaplotypeAlleles to test against
+        Assert.assertEquals(sameHaplotypeAlleles, sameHaplotypeAlleles);
+    }
+
+    @Test
+    public void TestReallyMergeIntoMNP() {
+
+        final VariantContext VCbase = new VariantContextBuilder("test", "20", start, start, Arrays.asList(Aref)).make();
+
+        // Merging the same variant context
+        VariantContext variantContext = PhasingUtils.reallyMergeIntoMNP(VCbase, VCbase, referenceFile);
+
+        // TODO - make a reference VariantContext to test against
+        Assert.assertEquals(variantContext, variantContext);
+    }
+}