fix fix test

broadinstitute · Aug 19, 2024 · cec1af1 · cec1af1
1 parent 62e36c5
commit cec1af1
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/...test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java b/...test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java
@@ -57,14 +57,14 @@ public Object[][] getVCFdata() {
 
                 //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", "--" + StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME, IntervalFilteringVcfWriter.Mode.STARTS_IN), b38_reference_20_21},
+                        getTestFile("haploidPlusDiploid.expected.vcf"), null, Arrays.asList(new SimpleInterval("chrX", 1000000, 5000000)), Arrays.asList("--merge-input-intervals", "--" + StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME, IntervalFilteringVcfWriter.Mode.STARTS_IN.toString()), b38_reference_20_21},
 
                 //8 ALT alleles -- no PLs
                 {new File[]{getTestFile("sample6.vcf"), getTestFile("sample7.vcf"), getTestFile("sample8.vcf"), getTestFile("sample9.vcf")},
-                        getTestFile("lotsOfAltsNoPLs.vcf"), null, Arrays.asList(new SimpleInterval("chr20", 257008, 257008)), Arrays.asList("--merge-input-intervals", "--" + StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME, IntervalFilteringVcfWriter.Mode.STARTS_IN), b38_reference_20_21},
+                        getTestFile("lotsOfAltsNoPLs.vcf"), null, Arrays.asList(new SimpleInterval("chr20", 257008, 257008)), Arrays.asList("--merge-input-intervals", "--" + StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME, IntervalFilteringVcfWriter.Mode.STARTS_IN.toString()), b38_reference_20_21},
                 //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","--" + StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME, IntervalFilteringVcfWriter.Mode.STARTS_IN), b38_reference_20_21},
+                        getTestFile("lotsOfAltsYesPLs.vcf"), null, Arrays.asList(new SimpleInterval("chr20", 257008, 257008)), Arrays.asList("--merge-input-intervals","--" + StandardArgumentDefinitions.VARIANT_OUTPUT_INTERVAL_FILTERING_MODE_LONG_NAME, IntervalFilteringVcfWriter.Mode.STARTS_IN.toString()), 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