Class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngineUnitTest
Tests
| Test |
Duration |
Result |
| testAllAnnotations |
0.039s |
passed |
| testAnnotationsHaveDescriptions |
0.014s |
passed |
| testCombineAnnotations |
0.002s |
passed |
| testCoverageAnnotationOnDBSNPAndOverlapSite |
0.187s |
passed |
| testCoverageAnnotationOnDbSnpSite |
0.006s |
passed |
| testCoverageAnnotationOnOverlapSite |
0.007s |
passed |
| testCoverageAnnotationViaEngine |
0.002s |
passed |
| testDBSNPONlyViaSpecialArg |
0s |
passed |
| testEmpty |
0s |
passed |
| testFinalizeAnnotations |
0s |
passed |
| testMultipleAnnotations |
0s |
passed |
| testNoNullInKeysAndDescriptions |
0.029s |
passed |
| testNullFeatures |
0s |
passed |
Standard error
22:11:37.181 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
22:11:37.182 DEBUG GenomeLocParser - 1 (16000 bp)
22:11:37.182 DEBUG GenomeLocParser - 2 (16000 bp)
22:11:37.182 DEBUG GenomeLocParser - 3 (16000 bp)
22:11:37.182 DEBUG GenomeLocParser - 4 (16000 bp)
22:11:37.198 WARN VariantAnnotatorEngine - Jumbo genotype annotations requested but fragment likelihoods or haplotype likelihoods were not given.
22:11:37.220 WARN OriginalAlignment - One or more variant contexts is missing the 'TLOD' annotation, OCM will not be computed for these VariantContexts
22:11:37.220 WARN TransmittedSingleton - Submitted pedigree has no trios. TransmittedSingleton annotation will not be calculated.
22:11:37.378 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:11:37.392 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine/one_entry_source.vcf
22:11:37.427 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:11:37.433 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
22:11:37.469 DEBUG ContextCleaner - Got cleaning task CleanShuffle(15)
22:11:37.469 DEBUG ContextCleaner - Cleaning shuffle 15
22:11:37.470 DEBUG BlockManagerStorageEndpoint - removing shuffle 15
22:11:37.470 DEBUG ContextCleaner - Cleaned shuffle 15
22:11:37.470 DEBUG ContextCleaner - Got cleaning task CleanShuffle(10)
22:11:37.470 DEBUG ContextCleaner - Cleaning shuffle 10