730208133b
a) Utility class called Probability Vector that holds a log-probability vector and has the ability to clip ends that deviate largely from max value. b) Used this class to hold site error model, since likelihoods of error model away from peak are so far down that it's not worth computing with them and just wastes time. c) Expand unit tests and add an exhaustive test for ErrorModel class. d) Corrected major math bug in ErrorModel uncovered by exhaustive test: log(e^x) is NOT x if log's base = 10. e) Refactored utility functions that created artificial pileups for testing into separate class ArtificialPileupTestProvider. Right now functionality is limited (one artificial contig of 10 bp), can only specify pileups in one position with a given number of matches and mismatches to ref) but functionality will be expanded in future to cover more test cases. f) Use this utility class for IndelGenotypeLikelihoods unit test and for PoolGenotypeLikelihoods unit test (the latter testing functionality still not done). g) Linearized implementation of biallelic exact model (very simple approach, similar to diploid exact model, just abort if we're past the max value of AC distribution and below a threshold). Still need to add unit tests for this and to expand to multiallelic model. h) Update integration test md5's due to minor differences stemming from linearized exact model and better error model math |
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| .. | ||
| CNV | ||
| activeregionqc | ||
| annotator | ||
| beagle | ||
| bqsr | ||
| coverage | ||
| diagnostics | ||
| diffengine | ||
| fasta | ||
| filters | ||
| genotyper | ||
| indels | ||
| phasing | ||
| qc | ||
| recalibration | ||
| validation | ||
| varianteval | ||
| variantrecalibration | ||
| variantutils | ||
| BAQIntegrationTest.java | ||
| ClipReadsWalkersIntegrationTest.java | ||
| FlagStatIntegrationTest.java | ||
| PileupWalkerIntegrationTest.java | ||
| PrintReadsIntegrationTest.java | ||
| PrintReadsUnitTest.java | ||