Class org.broadinstitute.hellbender.tools.walkers.annotator.VariantAnnotatorEngineUnitTest
Tests
| Test |
Duration |
Result |
| testAllAnnotations |
0.044s |
passed |
| testAnnotationsHaveDescriptions |
0.019s |
passed |
| testCombineAnnotations |
0.001s |
passed |
| testCoverageAnnotationOnDBSNPAndOverlapSite |
0.133s |
passed |
| testCoverageAnnotationOnDbSnpSite |
0.005s |
passed |
| testCoverageAnnotationOnOverlapSite |
0.004s |
passed |
| testCoverageAnnotationViaEngine |
0s |
passed |
| testDBSNPONlyViaSpecialArg |
0.001s |
passed |
| testEmpty |
0s |
passed |
| testFinalizeAnnotations |
0s |
passed |
| testMultipleAnnotations |
0.001s |
passed |
| testNoNullInKeysAndDescriptions |
0.017s |
passed |
| testNullFeatures |
0s |
passed |
Standard error
16:19:51.529 DEBUG GenomeLocParser - Prepared reference sequence contig dictionary
16:19:51.529 DEBUG GenomeLocParser - 1 (16000 bp)
16:19:51.529 DEBUG GenomeLocParser - 2 (16000 bp)
16:19:51.529 DEBUG GenomeLocParser - 3 (16000 bp)
16:19:51.529 DEBUG GenomeLocParser - 4 (16000 bp)
16:19:51.545 WARN VariantAnnotatorEngine - Jumbo genotype annotations requested but fragment likelihoods or haplotype likelihoods were not given.
16:19:51.571 WARN OriginalAlignment - One or more variant contexts is missing the 'TLOD' annotation, OCM will not be computed for these VariantContexts
16:19:51.572 WARN TransmittedSingleton - Submitted pedigree has no trios. TransmittedSingleton annotation will not be calculated.
16:19:51.688 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
16:19:51.699 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/walkers/annotator/VariantAnnotatorEngine/one_entry_source.vcf
16:19:51.727 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf
16:19:51.733 INFO FeatureManager - Using codec VCFCodec to read file file:///gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19.dbsnp135.chr1_1M.exome_intervals.vcf