Restore gnarly tests (#8893)

* Update no-calls in Gnarly haploid test
* Put back turned off tests

src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java

@@ -53,7 +53,7 @@ public void assertThatExpectedOutputUpdateToggleIsDisabled() {
     @DataProvider(name="VCFdata")
     public Object[][] getVCFdata() {
         return new Object[][]{
-               /*
+
                 //chrX haploid sample plus diploid sample -- expected results validated with vcf-validator (samtools?)
                 {new File[]{getTestFile("NA12891.chrX.haploid.rb.g.vcf"), getTestFile("NA12892.chrX.diploid.rb.g.vcf")},
                         getTestFile("haploidPlusDiploid.expected.vcf"), null, Arrays.asList(new SimpleInterval("chrX", 1000000, 5000000)), Arrays.asList("--merge-input-intervals", "--only-output-calls-starting-in-intervals"), b38_reference_20_21},
@@ -64,7 +64,7 @@ public Object[][] getVCFdata() {
                 //6 ALT alleles -- yes PLs
                 {new File[]{getTestFile("sample6.vcf"), getTestFile("sample7.vcf"), getTestFile("sample8.vcf")},
                         getTestFile("lotsOfAltsYesPLs.vcf"), null, Arrays.asList(new SimpleInterval("chr20", 257008, 257008)), Arrays.asList("--merge-input-intervals", "--only-output-calls-starting-in-intervals"), b38_reference_20_21},
-        */
+
         // Simple Test, spanning deletions; standard calling confidence
                 //No variants outside requested intervals; no SNPs with QUAL < 60, no INDELs with QUAL < 69?; has star alleles after deletion at chr20:263497; has AC, AF, AN, DP, ExcessHet, FS, MQ, (MQRankSum), (ReadPosRankSum), SOR, QD; has called genotypes
                 {new File[]{getTestFile("sample1.vcf"), getTestFile("sample2.vcf"), getTestFile("sample3.vcf"), getTestFile("sample4.vcf"), getTestFile("sample5.vcf")},