More bug fixes on the way to passing all tests

public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeCollection.java

@@ -219,12 +219,9 @@ public class GenotypeCollection implements List<Genotype> {
     public Genotype get(final String sampleName) {
         buildCache();
         Integer offset = sampleNameToOffset.get(sampleName);
-        if ( offset == null )
+        return offset == null ? null : genotypes.get(offset);
-            throw new IllegalArgumentException("Sample " + sampleName + " not found in this GenotypeCollection");
-        return genotypes.get(offset);
     }
 
-
     @Override
     public int indexOf(final Object o) {
         return genotypes.indexOf(o);

public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/MergeMNPsIntegrationTest.java

@@ -1,51 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.phasing;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.testng.annotations.Test;
-
-import java.util.Arrays;
-
-public class MergeMNPsIntegrationTest extends WalkerTest {
-
-    public static String baseTestString(String reference, String VCF, int maxDistMNP) {
-        return "-T MergeMNPs" +
-                " -R " + reference +
-                " --variant:vcf " + validationDataLocation + VCF +
-                " --maxGenomicDistanceForMNP " + maxDistMNP +
-                " -o %s" +
-                " -NO_HEADER";
-    }
-
-
-    @Test
-    public void test1() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 1)
-                        + " -L chr20:556259-756570",
-                1,
-                Arrays.asList("7f11f7f75d1526077f0173c7ed1fc6c4"));
-        executeTest("Merge MNP sites within genomic distance of 1 [TEST ONE]", spec);
-    }
-
-    @Test
-    public void test2() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 10)
-                        + " -L chr20:556259-756570",
-                1,
-                Arrays.asList("53dd312468296826bdd3c22387390c88"));
-        executeTest("Merge MNP sites within genomic distance of 10 [TEST TWO]", spec);
-    }
-
-    @Test
-    public void test3() {
-        WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString(hg18Reference, "merging_test_chr20_556259_756570.vcf", 100)
-                        + " -L chr20:556259-756570",
-                1,
-                Arrays.asList("e26f92d2fb9f4eaeac7f9d8ee27410ee"));
-        executeTest("Merge MNP sites within genomic distance of 100 [TEST THREE]", spec);
-    }
-
-
-}