From 6e1a86bc3eb2a6031a0c40d83a9979c2f9fde97b Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Tue, 15 Nov 2011 09:21:30 -0500
Subject: [PATCH] Bug fixes to VariantContext and GenotypeCollection

---
 .../sting/utils/variantcontext/GenotypeCollection.java     | 4 ++--
 .../sting/utils/variantcontext/VariantContext.java         | 7 +++++--
 .../utils/variantcontext/VariantContextUtilsUnitTest.java  | 6 ++----
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java
index f12a8e531..260543031 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java
@@ -74,7 +74,7 @@ public class GenotypeCollection implements List<Genotype> {
     // todo -- create constructor (Genotype ... genotypes)
 
     public static final GenotypeCollection create(final ArrayList<Genotype> genotypes) {
-        return new GenotypeCollection(genotypes, false);
+        return genotypes == null ? NO_GENOTYPES : new GenotypeCollection(genotypes, false);
     }
 
     public static final GenotypeCollection create(final Genotype... genotypes) {
@@ -86,7 +86,7 @@ public class GenotypeCollection implements List<Genotype> {
     }
 
     public static final GenotypeCollection copy(final Collection<Genotype> toCopy) {
-        return create(new ArrayList<Genotype>(toCopy));
+        return toCopy == null ? NO_GENOTYPES : create(new ArrayList<Genotype>(toCopy));
     }
 
 //    public static final GenotypeMap create(final Collection<Genotype> genotypes) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index b394517bf..06efd22d3 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -360,8 +360,11 @@ public class VariantContext implements Feature { // to enable tribble intergrati
         // we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles
         this.alleles = makeAlleles(alleles);
 
-        if ( genotypes == null ) { genotypes = NO_GENOTYPES; }
-        this.genotypes = genotypes;
+        if ( genotypes == null ) {
+            genotypes = NO_GENOTYPES;
+        } else {
+            this.genotypes = genotypes.immutable();
+        }
 
         // cache the REF and ALT alleles
         int nAlleles = alleles.size();
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
index b21a32174..8aded831a 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
@@ -249,16 +249,14 @@ public class VariantContextUtilsUnitTest extends BaseTest {
         final List<VariantContext> inputs = new ArrayList<VariantContext>();
 
         for ( final String id : cfg.inputs ) {
-            if ( id.equals(".") )
-                snpVC1 = VariantContext.modifyID(snpVC1, id);
-            inputs.add(snpVC1);
+            inputs.add(VariantContext.modifyID(snpVC1, id));
         }
 
         final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
                 inputs, null,
                 VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                 VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false);
-        Assert.assertEquals(merged.getID(), cfg.expected.equals(".") ? null : cfg.expected);
+        Assert.assertEquals(merged.getID(), cfg.expected);
     }
 
     // --------------------------------------------------------------------------------