From cfa86d52c2c9800967a1616c72251493e2966886 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 19 Oct 2009 18:21:00 +0000
Subject: [PATCH] ensure that in the indel case we don't allow identification
 as both an insertion and deletion at the same location in the VCF ROD

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1875 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/RodVCF.java             |  9 +++++++--
 .../sting/gatk/refdata/RodVCFTest.java         | 18 ++++++++++++++++--
 .../utils/genotype/vcf/VCFReaderTest.java      |  2 +-
 3 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
index 46322d3e0..172e30c52 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
@@ -77,6 +77,10 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return vcf;
     }
 
+    public void assertBiAllelic() {
+        if (!this.isBiallelic()) throw new StingException("We're not bi-allelic.");
+    }
+
     /**
      * get the frequency of this variant
      *
@@ -116,8 +120,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public boolean isSNP() {
         this.assertNotNull();
-        if (!mCurrentRecord.hasAlternateAllele())
-            return false;
+        assertBiAllelic();
         for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
             if (alt.getType() != VCFGenotypeEncoding.TYPE.SINGLE_BASE)
                 return false;
@@ -133,6 +136,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public boolean isInsertion() {
         this.assertNotNull();
+        assertBiAllelic();
         if (!mCurrentRecord.hasAlternateAllele())
             return false;
         for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
@@ -150,6 +154,7 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
     @Override
     public boolean isDeletion() {
         this.assertNotNull();
+        assertBiAllelic();
         if (!mCurrentRecord.hasAlternateAllele())
             return false;
         for (VCFGenotypeEncoding alt : this.mCurrentRecord.getAlternateAlleles()) {
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java
index 0c77a5aea..aa3083ee2 100755
--- a/java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java
@@ -113,7 +113,7 @@ public class RodVCFTest extends BaseTest {
     }
 
     @Test
-    public void testType() {
+    public void testInsertion() {
         RodVCF vcf = getVCFObject();
         Iterator<RodVCF> iter = vcf.createIterator("VCF", vcfFile);
         RodVCF rec = iter.next();
@@ -123,10 +123,24 @@ public class RodVCFTest extends BaseTest {
         rec = iter.next();
         rec = iter.next();
         Assert.assertTrue(rec.isIndel());
-        Assert.assertTrue(rec.isInsertion());
         Assert.assertTrue(rec.isDeletion());
     }
 
+    @Test
+    public void testDeletion() {
+        RodVCF vcf = getVCFObject();
+        Iterator<RodVCF> iter = vcf.createIterator("VCF", vcfFile);
+        RodVCF rec = iter.next();
+        Assert.assertTrue(rec.isSNP());
+        rec = iter.next();
+        rec = iter.next();
+        rec = iter.next();
+        rec = iter.next();
+        rec = iter.next();
+                
+        Assert.assertTrue(rec.isIndel());
+        Assert.assertTrue(rec.isInsertion());
+    }
     @Test
     public void testGetGenotypes() {        
         RodVCF vcf = getVCFObject();
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java
index 1e8e810e6..ba004237e 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java
@@ -22,7 +22,7 @@ public class VCFReaderTest extends BaseTest {
             counter++;
             reader.next();
         }
-        Assert.assertEquals(5, counter);
+        Assert.assertEquals(6, counter);
     }
 
     @Test