From 5a6468c11ea1f3e72e4079f2073d66c0bff00e99 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 19 Oct 2011 11:52:05 -0400
Subject: [PATCH] Allowing ./X genotypes and adding a unit test to ensure that
 this case is covered from now on (especially given that we may want to revert
 in the future).  Reverting this change is really easy and entails
 uncommenting a few lines of code.  But for now, despite Mark's objections,
 this case is allowed in the VCF spec and we are wrong not to allow it.

---
 .../sting/utils/variantcontext/Genotype.java    | 10 ++++++----
 .../variantcontext/VariantContextUnitTest.java  | 17 +++++++++++++++++
 2 files changed, 23 insertions(+), 4 deletions(-)

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 7ab3f81f0..5639ef30e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -197,14 +197,16 @@ public class Genotype {
         if ( alleles == null ) return;
         if ( alleles.size() == 0) throw new IllegalArgumentException("BUG: alleles cannot be of size 0");
 
-        int nNoCalls = 0;
+        // int nNoCalls = 0;
         for ( Allele allele : alleles ) {
             if ( allele == null )
                 throw new IllegalArgumentException("BUG: allele cannot be null in Genotype");
-            nNoCalls += allele.isNoCall() ? 1 : 0;
+            // nNoCalls += allele.isNoCall() ? 1 : 0;
         }
-        if ( nNoCalls > 0 && nNoCalls != alleles.size() )
-            throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
+
+        // Technically, the spec does allow for the below case so this is not an illegal state
+        //if ( nNoCalls > 0 && nNoCalls != alleles.size() )
+        //    throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
     }
 
     public String getGenotypeString() {
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 9026f09d6..a5060e54e 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
@@ -252,6 +252,23 @@ public class VariantContextUnitTest extends BaseTest {
         Assert.assertEquals(vc.getSampleNames().size(), 0);
     }
 
+    @Test
+    public void testCreatingPartiallyCalledGenotype() {
+        List<Allele> alleles = Arrays.asList(Aref, C);
+        Genotype g = new Genotype("foo", Arrays.asList(C, Allele.NO_CALL), 10);
+        VariantContext vc = new VariantContext("test", snpLoc, snpLocStart, snpLocStop, alleles, Arrays.asList(g));
+
+        Assert.assertTrue(vc.isSNP());
+        Assert.assertEquals(vc.getNAlleles(), 2);
+        Assert.assertTrue(vc.hasGenotypes());
+        Assert.assertFalse(vc.isMonomorphic());
+        Assert.assertTrue(vc.isPolymorphic());
+        Assert.assertEquals(vc.getGenotype("foo"), g);
+        Assert.assertEquals(vc.getChromosomeCount(), 2); // we know that there are 2 chromosomes, even though one isn't called
+        Assert.assertEquals(vc.getChromosomeCount(Aref), 0);
+        Assert.assertEquals(vc.getChromosomeCount(C), 1);
+    }
+
     @Test (expectedExceptions = IllegalArgumentException.class)
     public void testBadConstructorArgs1() {
         new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref));