67656bab23
Add more logging to annotators, change loggers from info to warn Add comments to testStrandBiasBySample() Clarify comments in testStrandBiasBySample remove logic for not prcossing an indel if strand bias (SB) was not computed remove per variant warnings in annotate() Log warnings if using the wrong annotator or missing a pedgree file Log test failures once in annotate(), because HaplotypeCaller does not call initialize(). Avoid using exceptions Fix so only log once in annotate(), Hardey-Weinberg does not require pedigree files, fix test MD5s so pass Check if founderIds == null Update MD5s from HaplotypeCaller integrations tests and clean up code Change logic so SnpEff does not throw excpetions, change engine to utils in imports Update test MD5s, return immediately if cannot annotate in SnpEff.initialization() Post peer review, add more logging warnings Update MD5 for testHaplotypeCallerMultiSampleComplex1, return null if PossibleDeNovo.annotate() is not called by VariantAnnotator |
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| licensing | ||
| protected | ||
| public | ||
| settings/helpTemplates | ||
| .gitignore | ||
| README.md | ||
| ant-bridge.sh | ||
| intellij_example.tar.bz2 | ||
| pom.xml | ||