95b5f99feb
Problem: -Downsamplers were treating reduced reads the same as normal reads, with occasionally catastrophic results on variant calling when an entire reduced read happened to get eliminated. Solution: -Since reduced reads lack the information we need to do position-based downsampling on them, best available option for now is to simply exempt all reduced reads from elimination during downsampling. Details: -Add generic capability of exempting items from elimination to the Downsampler interface via new doNotDiscardItem() method. Default inherited version of this method exempts all reduced reads (or objects encapsulating reduced reads) from elimination. -Switch from interfaces to abstract classes to facilitate this change, and do some minor refactoring of the Downsampler interface (push implementation of some methods into the abstract classes, improve names of the confusing clear() and reset() methods). -Rewrite TAROrderedReadCache. This class was incorrectly relying on the ReservoirDownsampler to preserve the relative ordering of items in some circumstances, which was behavior not guaranteed by the API and only happened to work due to implementation details which no longer apply. Restructured this class around the assumption that the ReservoirDownsampler will not preserve relative ordering at all. -Add disclaimer to description of -dcov argument explaining that coverage targets are approximate goals that will not always be precisely met. -Unit tests for all individual downsamplers to verify that reduced reads are exempted from elimination |
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