diff --git a/.gitignore b/.gitignore
index 694f85de06..f10fff99c0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,5 @@
 htsjdk.iws
 .command_tmp
-.DS_Store
 atlassian-ide-plugin.xml
 /htsjdk.version.properties
 /test-output/
diff --git a/src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java b/src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java
index bcccbeab4e..d4e288f978 100644
--- a/src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java
+++ b/src/main/java/htsjdk/variant/variantcontext/VariantContextComparator.java
@@ -83,20 +83,11 @@ public int compare(final VariantContext firstVariantContext, final VariantContex
 		// Will throw NullPointerException -- happily -- if either of the chromosomes/contigs aren't
 		// present. This error checking should already have been done in the constructor but it's left
 		// in as defence anyway.
-		int contigCompare = this.contigIndexLookup.get(firstVariantContext.getContig()).compareTo(this.contigIndexLookup.get(secondVariantContext.getContig()));
-		contigCompare = contigCompare == 0 ? firstVariantContext.getStart() - secondVariantContext.getStart() : contigCompare;
-		if (contigCompare == 0) {
-			// Compare variants that have the same genomic span (chr:start-end) lexicographically by all alleles (ref and alts).
-			for (int i = 0; i < firstVariantContext.getAlleles().size(); i++) {
-				// If all previous alleles are identical and the first variant has additional alleles, make the first variant greater.
-				if (i >= secondVariantContext.getAlleles().size()) { return 1; }
-				contigCompare = firstVariantContext.getAlleles().get(i).compareTo(secondVariantContext.getAlleles().get(i));
-				if (contigCompare != 0) return contigCompare;
-			}
-		}
-		// If all previous alleles are identical and the second variant has additional alleles, make the second variant greater.
-		if (firstVariantContext.getAlleles().size() < secondVariantContext.getAlleles().size()) { return -1; }
-		return contigCompare;
+		final int contigCompare =
+				this.contigIndexLookup.get(firstVariantContext.getContig()) - this.contigIndexLookup.get(secondVariantContext.getContig());
+		return contigCompare != 0
+				? contigCompare
+				: firstVariantContext.getStart() - secondVariantContext.getStart();
 	}
 
 	/**
diff --git a/src/test/java/htsjdk/variant/variantcontext/VariantContextComparatorUnitTest.java b/src/test/java/htsjdk/variant/variantcontext/VariantContextComparatorUnitTest.java
deleted file mode 100644
index 578f673ae4..0000000000
--- a/src/test/java/htsjdk/variant/variantcontext/VariantContextComparatorUnitTest.java
+++ /dev/null
@@ -1,75 +0,0 @@
-package htsjdk.variant.variantcontext;
-
-import htsjdk.HtsjdkTest;
-import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
-import org.testng.annotations.Test;
-
-import java.util.Arrays;
-import java.util.Collections;
-
-/**
- * Unit tests for VariantContextComparator.
- */
-public class VariantContextComparatorUnitTest extends HtsjdkTest {
-    private Allele refA, altG, altT;
-
-    @BeforeSuite
-    public void before() {
-        refA = Allele.create("A", true);
-        altG = Allele.create("G", false);
-        altT = Allele.create("T", false);
-    }
-
-    @Test
-    public void testVariantContextsWithSameSiteSortLexicographicallyByAlleleIdentical() {
-        final String contig = "chr1";
-        final VariantContextComparator comparator = new VariantContextComparator(Collections.singletonList(contig));
-        final VariantContextBuilder builder = new VariantContextBuilder("test", contig, 1, 1, Collections.emptyList());
-
-        final VariantContext variant1 = builder.alleles(Arrays.asList(refA, altG)).make();
-        final VariantContext variant2 = builder.alleles(Arrays.asList(refA, altG)).make();
-
-        final int compare = comparator.compare(variant1, variant2);
-        Assert.assertEquals(compare, 0); // TODO: What other criteria might we sort by to break this tie?
-    }
-
-    @Test
-    public void testVariantContextsWithSameSiteSortLexicographicallyByAllele() {
-        final String contig = "chr1";
-        final VariantContextComparator comparator = new VariantContextComparator(Collections.singletonList(contig));
-        final VariantContextBuilder builder = new VariantContextBuilder("test", contig, 1, 1, Collections.emptyList());
-
-        final VariantContext variant1 = builder.alleles(Arrays.asList(refA, altG)).make();
-        final VariantContext variant2 = builder.alleles(Arrays.asList(refA, altT)).make();
-
-        final int compare = comparator.compare(variant1, variant2);
-        Assert.assertEquals(compare, -1);
-    }
-
-    @Test
-    public void testVariantContextsWithSameSiteSortLexicographicallyByAlleleThenExtraAllelesForFirstVariant() {
-        final String contig = "chr1";
-        final VariantContextComparator comparator = new VariantContextComparator(Collections.singletonList(contig));
-        final VariantContextBuilder builder = new VariantContextBuilder("test", contig, 1, 1, Collections.emptyList());
-
-        final VariantContext variant1 = builder.alleles(Arrays.asList(refA, altG, altT)).make();
-        final VariantContext variant2 = builder.alleles(Arrays.asList(refA, altG)).make();
-
-        final int compare = comparator.compare(variant1, variant2);
-        Assert.assertEquals(compare, 1);
-    }
-
-    @Test
-    public void testVariantContextsWithSameSiteSortLexicographicallyByAlleleThenExtraAllelesForSecondVariant() {
-        final String contig = "chr1";
-        final VariantContextComparator comparator = new VariantContextComparator(Collections.singletonList(contig));
-        final VariantContextBuilder builder = new VariantContextBuilder("test", contig, 1, 1, Collections.emptyList());
-
-        final VariantContext variant1 = builder.alleles(Arrays.asList(refA, altG)).make();
-        final VariantContext variant2 = builder.alleles(Arrays.asList(refA, altG, altT)).make();
-
-        final int compare = comparator.compare(variant1, variant2);
-        Assert.assertEquals(compare, -1);
-    }
-}