46edab6d6a
-Switch back to the old implementation, if needed, with --use_legacy_downsampler -LocusIteratorByStateExperimental becomes the new LocusIteratorByState, and the original LocusIteratorByState becomes LegacyLocusIteratorByState -Similarly, the ExperimentalReadShardBalancer becomes the new ReadShardBalancer, with the old one renamed to LegacyReadShardBalancer -Performance improvements: locus traversals used to be 20% slower in the new downsampling implementation, now they are roughly the same speed. -Tests show a very high level of concordance with UG calls from the previous implementation, with some new calls and edge cases that still require more examination. -With the new implementation, can now use -dcov with ReadWalkers to set a limit on the max # of reads per alignment start position per sample. Appropriate value for ReadWalker dcov may be in the single digits for some tools, but this too requires more investigation. |
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