Kt varient context change

src/main/java/htsjdk/variant/variantcontext/VariantContext.java

@@ -37,18 +37,7 @@
 import htsjdk.variant.vcf.VCFHeaderLineType;
 
 import java.io.Serializable;
-import java.util.AbstractMap;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.EnumSet;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.util.*;
 import java.util.stream.Collectors;
 
 /**
@@ -1699,10 +1688,8 @@ public Allele getAltAlleleWithHighestAlleleCount() {
             return getAlternateAllele(0);
 
         return getAlternateAlleles().stream()
-                .map(allele -> new Tuple<>(allele, getCalledChrCount(allele)))
-                .max((alleleAndCount1, alleleAndCount2) -> Integer.compare(alleleAndCount1.b, alleleAndCount2.b))
-                .get()
-                .a;
+                .max(Comparator.comparing(this::getCalledChrCount))
+                .orElse(null);
     }
 
     /**

src/test/java/htsjdk/variant/variantcontext/VariantContextUnitTest.java

@@ -464,6 +464,8 @@ public void testAccessingCompleteGenotypes() {
         Assert.assertEquals(4, vc.getCalledChrCount(T));
         Assert.assertEquals(3, vc.getCalledChrCount(ATC));
         Assert.assertEquals(2, vc.getCalledChrCount(Allele.NO_CALL));
+
+        Assert.assertEquals(T, vc.getAltAlleleWithHighestAlleleCount());
     }
 
     @Test
@@ -487,6 +489,16 @@ public void testAccessingRefGenotypes() {
             Assert.assertEquals(4, vc.getCalledChrCount(Aref));
             Assert.assertEquals(0, vc.getCalledChrCount(T));
             Assert.assertEquals(2, vc.getCalledChrCount(Allele.NO_CALL));
+
+            //bi allelic, only one alt allele
+            Allele expected;
+            if (alleles.size()>1) {
+                expected = alleles.get(1);
+            } else {
+                expected = null;
+            }
+
+            Assert.assertEquals( vc.getAltAlleleWithHighestAlleleCount(), expected);
         }
     }
 
@@ -600,6 +612,21 @@ public void testVCFfromGenotypes() {
         Assert.assertEquals(4, vc125.getCalledChrCount(Aref));
     }
 
+    @Test
+    public void testMonomorphicVariant() {
+        Genotype g1 = GenotypeBuilder.create("AA", Arrays.asList(Aref, Aref));
+        Genotype g2 = GenotypeBuilder.create("BB", Arrays.asList(Aref, Allele.NO_CALL));
+        Genotype g3 = GenotypeBuilder.create("CC", Arrays.asList(Allele.NO_CALL,Allele.NO_CALL));
+        GenotypesContext gc = GenotypesContext.create(g1, g2, g3);
+        VariantContext vc = new VariantContextBuilder("genotypes", snpLoc, snpLocStart, snpLocStop, Collections.singletonList(Aref)).genotypes(gc).make();
+
+        Assert.assertEquals(vc.getType(), VariantContext.Type.NO_VARIATION);
+        Assert.assertNull(vc.getAltAlleleWithHighestAlleleCount());
+        Assert.assertEquals(vc.getCalledChrCount(Aref), 3);
+
+    }
+
+
     public void testGetGenotypeMethods() {
         Genotype g1 = GenotypeBuilder.create("AA", Arrays.asList(Aref, Aref));
         Genotype g2 = GenotypeBuilder.create("AT", Arrays.asList(Aref, T));