change genomics db test to have its own expected result file until GD…

…B and CombinedGVCFs behavior around doubled spanning deletions can be synchronized

src/test/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImportIntegrationTest.java

@@ -52,6 +52,7 @@ public final class GenomicsDBImportIntegrationTest extends CommandLineProgramTes
     private static final String NA_12878_PHASED = largeFileTestDir + "NA12878.phasedData.Chr20.vcf"; //NOTE: this is not phased according to the vcf spec but it reflects phasing currently produced by haplotype caller
     private static final String MULTIPLOID_DATA_HG37 = largeFileTestDir + "gvcfs/HapMap5plex.ploidy10.b37.g.vcf";
     private static final String NA12878_HG37 = toolsTestDir + "haplotypecaller/expected.testGVCFMode.gatk4.g.vcf";
+    private static final String MULTIPLOID_EXPECTED_RESULT = toolsTestDir + "GenomicsDBImport/expected.testGenomicsDBImportWithNonDiploidData.vcf";
     private static final String ARTIFICIAL_PHASED = getTestDataDir() + "/ArtificalPhasedData.1.g.vcf";
     private static final String HG_00268_WITH_SPACES = largeFileTestDir + "gvcfs/HG00268.spaceInSampleName.g.vcf";
     private static final List<String> LOCAL_GVCFS = Arrays.asList(HG_00096, HG_00268, NA_19625);
@@ -174,7 +175,11 @@ public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithMultipleNonAdjac
 
     @Test
     public void testGenomicsDBImportFileInputsAgainstCombineGVCFWithNonDiploidData() throws IOException {
-        testGenomicsDBAgainstCombineGVCFs(Arrays.asList(NA12878_HG37, MULTIPLOID_DATA_HG37), INTERVAL_NONDIPLOID, b37_reference_20_21, new String[0]);
+        testGenomicsDBImporterWithGenotypes(Arrays.asList(NA12878_HG37, MULTIPLOID_DATA_HG37), INTERVAL_NONDIPLOID,
+                MULTIPLOID_EXPECTED_RESULT, b37_reference_20_21,
+                true,
+                false,
+                false);
     }
 
     @Test