From 822654b119ec6e2efefa11c82bc1a86069bac06d Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 9 Oct 2011 10:36:14 -0700
Subject: [PATCH] UnitTests for allele getting functions in VC in prep for move
 from set to list

---
 .../VariantContextUnitTest.java               | 72 ++++++++++++++++---
 1 file changed, 64 insertions(+), 8 deletions(-)

diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
index cee7a4782..39f8c0f39 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
@@ -6,10 +6,10 @@ package org.broadinstitute.sting.utils.variantcontext;
 
 
 import org.broadinstitute.sting.BaseTest;
-import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
-import org.testng.annotations.BeforeTest;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
+import org.testng.Assert;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -455,14 +455,70 @@ public class VariantContextUnitTest extends BaseTest {
         Assert.assertEquals(0, vc5.getChromosomeCount(Aref));
     }
 
+    // --------------------------------------------------------------------------------
+    //
+    // Test allele merging
+    //
+    // --------------------------------------------------------------------------------
 
-    @Test
-    public void testManipulatingAlleles() {
-        // todo -- add tests that call add/set/remove
+    private class GetAllelesTest extends TestDataProvider {
+        List<Allele> alleles;
+
+        private GetAllelesTest(String name, Allele... arg) {
+            super(GetAllelesTest.class, name);
+            this.alleles = Arrays.asList(arg);
+        }
+
+        public String toString() {
+            return String.format("%s input=%s", super.toString(), alleles);
+        }
     }
 
-    @Test
-    public void testManipulatingGenotypes() {
-        // todo -- add tests that call add/set/remove
+    @DataProvider(name = "getAlleles")
+    public Object[][] mergeAllelesData() {
+        new GetAllelesTest("A*",   Aref);
+        new GetAllelesTest("-*",   delRef);
+        new GetAllelesTest("A*/C", Aref, C);
+        new GetAllelesTest("A*/C/T", Aref, C, T);
+        new GetAllelesTest("A*/T/C", Aref, T, C);
+        new GetAllelesTest("A*/C/T/-", Aref, C, T, del);
+        new GetAllelesTest("A*/T/C/-", Aref, T, C, del);
+        new GetAllelesTest("A*/-/T/C", Aref, del, T, C);
+
+        return GetAllelesTest.getTests(GetAllelesTest.class);
+    }
+
+    @Test(dataProvider = "getAlleles")
+    public void testMergeAlleles(GetAllelesTest cfg) {
+        final List<Allele> altAlleles = cfg.alleles.subList(1, cfg.alleles.size());
+        final VariantContext vc = new VariantContext("test", snpLoc, snpLocStart, snpLocStop, cfg.alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
+
+        Assert.assertEquals(vc.getAlleles(), cfg.alleles, "VC alleles not the same as input alleles");
+        Assert.assertEquals(vc.getNAlleles(), cfg.alleles.size(), "VC getNAlleles not the same as input alleles size");
+        Assert.assertEquals(vc.getAlternateAlleles(), altAlleles, "VC alt alleles not the same as input alt alleles");
+
+
+        for ( int i = 0; i < cfg.alleles.size(); i++ ) {
+            final Allele inputAllele = cfg.alleles.get(i);
+
+            Assert.assertTrue(vc.hasAllele(inputAllele));
+            if ( inputAllele.isReference() ) {
+                final Allele nonRefVersion = Allele.create(inputAllele.getBases(), false);
+                Assert.assertTrue(vc.hasAllele(nonRefVersion, true));
+                Assert.assertFalse(vc.hasAllele(nonRefVersion, false));
+            }
+
+            Assert.assertEquals(inputAllele, vc.getAllele(inputAllele.getBaseString()));
+            Assert.assertEquals(inputAllele, vc.getAllele(inputAllele.getBases()));
+
+            if ( i > 0 ) { // it's an alt allele
+                Assert.assertEquals(inputAllele, vc.getAlternateAllele(i-1));
+            }
+        }
+
+        final Allele missingAllele = Allele.create("AACCGGTT"); // does not exist
+        Assert.assertNull(vc.getAllele(missingAllele.getBases()));
+        Assert.assertFalse(vc.hasAllele(missingAllele));
+        Assert.assertFalse(vc.hasAllele(missingAllele, true));
     }
 }