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