b8b139841d
- Merged Roger's metrics with Mauricio's optimizations
- Added Stats for DiagnoseTargets
- now has functions to find the median depth, and upper/lower quartile
- the REF_N callable status is implemented
- The walker now runs efficiently
- Diagnose Targets accepts overlapping intervals
- Diagnose Targets now checks for bad mates
- The read mates are checked in a memory efficient manner
- The statistics thresholds have been consolidated and moved outside of the statistics classes and into the walker.
- Fixed some bugs
- Removed rod binding
Added more Unit tests
- Test callable statuses on the locus level
- Test bad mates
- Changed NO_COVERAGE -> COVERAGE_GAPS to avoid confusion
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
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| .. | ||
| datasources | ||
| executive | ||
| filters | ||
| iterators | ||
| refdata | ||
| report | ||
| samples | ||
| traversals | ||
| walkers | ||
| EngineFeaturesIntegrationTest.java | ||
| GenomeAnalysisEngineUnitTest.java | ||
| WalkerManagerUnitTest.java | ||