-- Ensures that the posteriors remain within reasonable ranges. Fixed bug where normalization of posteriors = {-1e30, 0.0} => {-100000, 0.0} which isn't good. Now tests ensure that the normalization process preserves log10 precision where possible
-- Updated MathUtils to make this possible
-- Remove capability to truncate genotype likelihoods -- this wasn't used and isn't really useful after all
-- Added lots of contracts and docs, still more to come.
-- Created a default makeMaxLikelihoods function in ReferenceDiploidExactAFCalc and DiploidExactAFCalc so that multiple subclasses don't just do the default thing
-- Generalized reference bi-allelic model in IndependentAllelesDiploidExactAFCalc so that in principle any bi-allelic reference model can be used.
-- Fixed minor numerical stability issue in AFCalcResult
-- posterior of joint A/B/C is 1 - (1 - P(D | AF_b == 0)) x (1 - P(D | AF_c == 0)), for any number of alleles, obviously. Now computes the joint posterior like this, and then back-calculates likelihoods that generate these posteriors given the priors. It's not pretty but it's the best thing to do
-- Superceded by IndependentAFCalc
-- Added support to read in an ExactModelLog in AFCalcPerformanceTest and run the independent alleles model on it.
-- A few misc. bug fixes discovered during running the performance test
Added targets to build.xml to effectively 'mvn install' packaged GATK/Queue from ant.
TODO: Versions during 'mvn install' are hardcoded at 0.0.1 until a better versioning scheme that works with maven dependencies has been identified.
Modified the SAMFileWriterArgumentTypeDescriptor to accept output bam files that are null if they're not required (in the @Output annotation).
This change enables the nWayOut parameter for the IndeRealigner and ReduceReads to operate optionally while maintaining the original single way out.
[#DEV-10 transition:31 resolution:1]
For now, the het reduction should only be performed for diploids (n=2). We haven't really tested it for other ploidy so it should remain hidden until someone braves it out.
Pipeline runs end-to-end using example metadata and has been tested only for cases where everything is ideal.
Next step is to bring this to the cloud, test all different scenario (multiple tumors, single ended, missing parameters etc).
Parallel next step is to add QC metrics.
-- Before this branch, the EXACT calculation implementation was largely based on historical choices in the UnifiedGenotyper. The code was badly organized, there were no unit tests, and the Diploid EXACT calculation was super slow O(n.samples ^ n.alt.alleles)
-- Reorganized code into a single class AFCalc superclass that carries out the calculation and an AFCalcResult object that contains only the information we should expose to code users, and is well-validated.
-- Implement a new model for the multi-allelic exact calculation that sweeps for each alt allele B all likelihoods into a bi-allelic model XB where X is all alleles != B, and calls these all separately using the reference bi-allelic model. It produces identical quals for the bi-allelic case but slightly different results for multi-allelics due to a genuine model difference in that this Independent model doesn't penalize fully all genotype configurations as occurs in the Reference multi-allelic implementation. However, it seems after much debate that the reference model is doing the wrong thing, so in fact the Independent model seems correct. This code isn't the default implementation yet, simply because I want to do some cleanup and discuss with the methods group before enabling.
-- Constrained search model implemented, but will be deleted in a subsequent code cleanup
-- Massive (40K) suite of unit tests the exact models, which are passing for the reference and the independent alleles exact model.
-- Restored -- but isn't 100% hooked up -- the original clean bi-allelic model for Ryan to pass his optimized logless version on.
-- The only way to create these AFCalc objects is through an AFCalcFactory, which again validates its arguments. The AFCalcFactory.Calculation enum exposes calculations to the UG / HC as the AFModel.
-- Separated AFCalc from UG, into its own package that could in principle be pushed into utils now
-- Created a simple main[] function to run performance tests of the EXACT model.
-- Updating integration tests, confirming that results for the original EXACT model are as expected given our new more rigorous application of likelihoods, priors, and posteriors
-- Fix basic logic bug in AFCalcResult.isPolymorphic and UnifiedGenotypeEngine, where isNonRef really meant isRef. Not ideal. Finally caught by some tests, but good god it almost made it into the code
-- Now takes the Math.abs of the phred-scaled confidence so that we don't see -0.0
-- Massive new suite of unit tests to ensure that bi-allelic and tri-allele events are called properly with all models, and that the IndependentAllelesDiploidExactAFCalc calls events with up to 4 alt alleles correctly. ID'd some of the bugs below
-- Fix sort order bug in IndependentAllelesDiploidExactAFCalc caught by new unit tests
-- Fix bug in GeneralPloidyExactAFCalc where the AFCalcResult has meaningless values in the likelihoods when no there we no informative GLs.
-- UnifiedGenotyperEngine uses only the alleles used in genotyping, not the original alleles, when considering which alleles to include in output
-- AFCalcFactory has a more informative info message when looking for and selecting an exact model to use in genotyping
-- New capabilities in IndependentAllelesDiploidExactAFCalc to actually apply correct theta^n.alt.allele prior.
-- Tests that theta^n.alt.alleles is being applied correctly
-- Bugfix: keep in logspace when computing posterior probability in toAFCalcResult in AFCalcResultTracker.java
-- Bugfix: use only the alleles used in genotyping when assessing if an allele is polymorphic in a sample in UnifiedGenotyperEngine
-- AFCalcFactory is the only way to make AFCalcs now. There's a nice ordered enum there describing the models and their ploidy and max alt allele restrictions. The factory makes it easy to create them, and to find models that work for you given your ploidy and max alt alleles.
-- AFCalc no longer has UAC constructor -- only AFCalcFactory does. Code cleanup throughout
-- Enabling more unit tests, all of which almost pass now (except for IndependentAllelesDiploidExactAFCalc which will be fixed next)
-- It's now possible to run the UG / HC with any of the exact models currently in the system.
-- Code cleanup throughout the system, reorganizing the unit tests in particular
-- Continuing to get IndependentAllelesDiploidExactAFCalc working correctly. A long way towards the right answer now, but still not there
-- Restored (but not tested) OriginalDiploidExactAFCalc, the clean diploid O(N) version for Ryan
-- MathUtils.normalizeFromLog10 no longer returns -Infinity when kept in log space, enforces the min log10 value there
-- New convenience method in VariantContext that looks up the allele index in the alleles
Guillermo del Angel
Mark DePristo
Kristian Cibulskis
kshakir
Ryan Poplin
David Roazen
Mauricio Carneiro
Ami Levy Moonshine