Class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngineUnitTest

13

tests

0

failures

0

ignored

0.273s

duration

100%

successful

Tests

Test Duration Result
testAllAnnotations 0.040s passed
testAnnotationsHaveDescriptions 0.005s passed
testCombineAnnotations 0.001s passed
testCoverageAnnotationOnDBSNPAndOverlapSite 0.206s passed
testCoverageAnnotationOnDbSnpSite 0.006s passed
testCoverageAnnotationOnOverlapSite 0.005s passed
testCoverageAnnotationViaEngine 0.001s passed
testDBSNPONlyViaSpecialArg 0s passed
testEmpty 0s passed
testFinalizeAnnotations 0s passed
testMultipleAnnotations 0.001s passed
testNoNullInKeysAndDescriptions 0.008s passed
testNullFeatures 0s passed

Standard error

20:42:00.889 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
20:42:00.889 DEBUG GenomeLocParser -  1 (16000 bp)
20:42:00.889 DEBUG GenomeLocParser -  2 (16000 bp)
20:42:00.889 DEBUG GenomeLocParser -  3 (16000 bp)
20:42:00.889 DEBUG GenomeLocParser -  4 (16000 bp)
20:42:00.895 WARN  VariantAnnotatorEngine - Jumbo genotype annotations requested but fragment likelihoods or haplotype likelihoods were not given.
20:42:00.928 WARN  OriginalAlignment - One or more variant contexts is missing the 'TLOD' annotation, OCM will not be computed for these VariantContexts
20:42:00.928 WARN  TransmittedSingleton - Submitted pedigree has no trios. TransmittedSingleton annotation will not be calculated.
20:42:01.019 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
20:42:01.108 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine/one_entry_source.vcf
20:42:01.143 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
20:42:01.149 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf