Package org.broadinstitute.hellbender.tools.walkers

Failed tests

• GenotypeGVCFsIntegrationTest. assertMatchingAnnotationsFromGenomicsDB_newMQformat[0](/home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/expected.testGVCFMode.gatk4.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.singleSample.genotyped.vcf, 20:1-11000000, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
• GenotypeGVCFsIntegrationTest. assertMatchingGenotypesFromGenomicsDB[0](src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gvcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/gvcf.basepairResolution.gatk3.7_30_ga4f720357.output.vcf, 20:1-11000000, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
• GenotypeGVCFsIntegrationTest. assertMatchingGenotypesFromGenomicsDB[2](/home/runner/work/gatk/gatk/src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.20.gatk3.7_30_ga4f720357.expected.vcf, 20:1-11000000, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
• GenotypeGVCFsIntegrationTest. assertMatchingGenotypesFromGenomicsDB[4](/home/runner/work/gatk/gatk/src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/CEUTrio.21.gatk3.7_30_ga4f720357.expected.vcf, 21:1-11000000, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
• GenotypeGVCFsIntegrationTest. testGDBMaxAltsEqualsGGVCFsMaxAlts
• GenotypeGVCFsIntegrationTest. testGDBMaxAltsLessThanGGVCFsMaxAlts
• GenotypeGVCFsIntegrationTest. testGenotypeGVCFsMultiIntervalGDBQuery[0](/home/runner/work/gatk/gatk/src/test/resources/large/gvcfs/CEUTrio.20.21.gatk3.4.g.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/NA12878.mergedIntervals.vcf, [20:10000117-10000127, 20:10000137-10000147, 20:10000157-10000167, 20:10000177-10000187, 20:10000197-10000207, 20:10000217-10000227, 20:10000237-10000247, 20:10000257-10000267, 20:10000277-10000287, 20:10000297-10000307, 20:10000317-10000327, 20:10000337-10000347, 20:10000357-10000367, 20:10000377-10000387, 20:10000397-10000407, 20:10000417-10000427, 20:10000437-10000447, 20:10000457-10000467, 20:10000477-10000487, 20:10000497-10000507, 20:10000517-10000527, 20:10000537-10000547, 20:10000557-10000567, 20:10000577-10000587, 20:10000597-10000607, 20:10000617-10000627, 20:10000637-10000647, 20:10000657-10000667, 20:10000677-10000687, 20:10000697-10000707, 20:10000717-10000727, 20:10000737-10000747, 20:10000757-10000767, 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20:10019677-10019687, 20:10019697-10019707, 20:10019717-10019727, 20:10019737-10019747, 20:10019757-10019767, 20:10019777-10019787, 20:10019797-10019807, 20:10019817-10019827, 20:10019837-10019847, 20:10019857-10019867, 20:10019877-10019887, 20:10019897-10019907, 20:10019917-10019927, 20:10019937-10019947, 20:10019957-10019967, 20:10019977-10019987, 20:10019997-10020007, 20:10020017-10020027, 20:10020037-10020047, 20:10020057-10020067, 20:10020077-10020087, 20:10020097-10020107], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
• GenotypeGVCFsIntegrationTest. testMaxAltsToCombineInGenomicsDB
• GenotypeGVCFsIntegrationTest. testMixHaploidDiploidHighAltSite
• GenotypeGVCFsIntegrationTest. testNoReadsOutputAsNoCall
• GenotypeGVCFsIntegrationTest. testNoReadsReblockedOutputAsNoCall
• GnarlyGenotyperIntegrationTest. gnarlyHomRefNullPLs
• GnarlyGenotyperIntegrationTest. testNoReadsOutputAsNoCall
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[0]([Ljava.io.File;@999e3ea, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/haploidPlusDiploid.expected.vcf, null, [chrX:1000000-5000000], [--merge-input-intervals, --variant-output-filtering, STARTS_IN], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[1]([Ljava.io.File;@760799e1, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/lotsOfAltsNoPLs.vcf, null, [chr20:257008-257008], [--merge-input-intervals, --variant-output-filtering, STARTS_IN], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[2]([Ljava.io.File;@569945cc, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/lotsOfAltsYesPLs.vcf, null, [chr20:257008-257008], [--merge-input-intervals, --variant-output-filtering, STARTS_IN], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[3]([Ljava.io.File;@10fd833b, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/fiveSampleTest.vcf, null, [chr20:251370-252000, chr20:263000-265600], [--merge-input-intervals, --variant-output-filtering, STARTS_IN], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[4]([Ljava.io.File;@6957cbef, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/fiveSampleTest.vcf, null, [chr20:251370-252000, chr20:263000-265600], [--merge-input-intervals, --variant-output-filtering, STARTS_IN, --genomicsdb-use-bcf-codec], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[5]([Ljava.io.File;@478bc828, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/fiveSampleTest.lowerCallThreshold.vcf, null, [chr20:250865-348163], [-stand-call-conf 10], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[6]([Ljava.io.File;@6967b531, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/fiveSampleTest.lowerCallThreshold.vcf, null, [chr20:250865-348163], [-stand-call-conf 10, --genomicsdb-use-bcf-codec], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[7]([Ljava.io.File;@9fe6edc, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleAS.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf, [20:1-2147483647], [], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[8]([Ljava.io.File;@66d208c5, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleAS.vcf, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/twoSampleASDB.vcf, [20:1-2147483647], [--genomicsdb-use-bcf-codec], /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta)
• GnarlyGenotyperIntegrationTest. testUsingGenomicsDB[9]([Ljava.io.File;@2f228a1, src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/noGTCount.expected.chr20snippet.vcf, null, [chr20:1-2147483647], [], /home/runner/work/gatk/gatk/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz)

Classes