diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java index b9cc98baf41..b3942729084 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyperIntegrationTest.java +++ b/src/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