e0c8c0ddcb
This is a temporary and hopefully short-lived solution. I've modified the FunctionalClass stratification to stratify by effect impact as defined by SnpEff annotations (high, moderate, and low impact) rather than by the silent/missense/nonsense categories. If we want to bring back the silent/missense/nonsense stratification, we should probably take the approach of asking the SnpEff author to add it as a feature to SnpEff rather than coding it ourselves, since the whole point of moving to SnpEff was to outsource genomic annotation. |
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| .. | ||
| arguments | ||
| datasources | ||
| executive | ||
| filters | ||
| iterators | ||
| refdata | ||
| report | ||
| traversals | ||
| walkers | ||
| EngineFeaturesIntegrationTest.java | ||
| GenomeAnalysisEngineUnitTest.java | ||
| WalkerManagerUnitTest.java | ||