- Added an optional argument to BaseRecalibrator to produce sorted GATKReport Tables
- Modified BSQR Integration Tests to include the optional argument. Tests now produce sorted tables
The weird part is that the comments claimed it was doing what it was supposed to, but it didn't actually do it.
Now we maintain the last header element of the consensus (but without bases and quals) if it adjoins an element with an insertion.
Added the user's test file as an integration test.
This is an intermediate commit so that there is a record of these changes in our
commit history. Next step is to isolate the test classes as well, and then move
the entire package to the Picard repository and replace it with a jar in our repo.
-Removed all dependencies on org.broadinstitute.sting (still need to do the test classes,
though)
-Had to split some of the utility classes into "GATK-specific" vs generic methods
(eg., GATKVCFUtils vs. VCFUtils)
-Placement of some methods and choice of exception classes to replace the StingExceptions
and UserExceptions may need to be tweaked until everyone is happy, but this can be
done after the move.
Reads that are soft-clipped off the contig (before the beginning of the contig) were being soft-clipped to position 0 instead of 1 because of an off-by-one issue. Fixed and included in the integration test.
-- Uses high-performance local writer backed by byte array that writes the entire VCF line in some write operation to the underlying output stream.
-- Fixes problems with indexing of unflushed writes while still allowing efficient block zipping
-- Same (or better) IO performance as previous implementation
-- IndexingVariantContextWriter now properly closes the underlying output stream when it's closed
-- Updated compressed VCF output file
-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.
As reported by Menachem Fromer: a critical bug in AFCalcResult:
Specifically, the implementation:
public boolean isPolymorphic(final Allele allele, final double log10minPNonRef) {
return getLog10PosteriorOfAFGt0ForAllele(allele) >= log10minPNonRef;
}
seems incorrect and should probably be:
getLog10PosteriorOfAFEq0ForAllele(allele) <= log10minPNonRef
The issue here is that the 30 represents a Phred-scaled probability of *error* and it's currently being compared to a log probability of *non-error*.
Instead, we need to require that our probability of error be less than the error threshold.
This bug has only a minor impact on the calls -- hardly any sites change -- which is good. But the inverted logic effects multi-allelic sites significantly. Basically you only hit this logic with multiple alleles, and in that case it'\s including extra alt alleles incorrectly, and throwing out good ones.
Change was to create a new function that properly handles thresholds that are PhredScaled quality scores:
/**
* Same as #isPolymorphic but takes a phred-scaled quality score as input
*/
public boolean isPolymorphicPhredScaledQual(final Allele allele, final double minPNonRefPhredScaledQual) {
if ( minPNonRefPhredScaledQual < 0 ) throw new IllegalArgumentException("phredScaledQual " + minPNonRefPhredScaledQual + " < 0 ");
final double log10Threshold = Math.log10(QualityUtils.qualToProb(minPNonRefPhredScaledQual));
return isPolymorphic(allele, log10Threshold);
}
ReduceReads now co-reduces bams if they're passed in toghether with multiple -I. Co-reduction forces every variant region in one sample to be a variant region in all samples.
Also:
* Added integrationtest for co-reduction
* Fixed bug with new no-recalculation implementation of the marksites object where the last object wasn't being removed after finalizing a variant region (updated MD5's accordingly)
DEV-200 #resolve #time 8m
-- The logic for determining active regions was a bit broken in the HC when intervals were used in the system
-- TraverseActiveRegions now uses the AllLocus view, since we always want to see all reference sites, not just those covered. Simplifies logic of TAR
-- Non-overlapping intervals are always treated as separate objects for determing active / inactive state. This means that each exon will stand on its own when deciding if it should be active or inactive
-- Misc. cleanup, docs of some TAR infrastructure to make it safer and easier to debug in the future.
-- Committing the SingleExomeCalling script that I used to find this problem, and will continue to use in evaluating calling of a single exome with the HC
-- Make sure to get all of the reads into the set of potentially active reads, even for genomic locations that themselves don't overlap the engine intervals but may have reads that overlap the regions
-- Remove excessively expensive calls to check bases are upper cased in ReferenceContext
-- Update md5s after a lot of manual review and discussion with Ryan
The MD5s for these tests were changed in commit 87435f1074615b2cd016f042980109fd53962c8d
to match the output of a broken version of BaseRecalibration. With the patch in
commit c397102ecc1fd1d2cd8f209a8f358ab4a60b50a7, the output once again matches the
*original* MD5s for these tests, and does not vary as you increase -nct.
Final resolution to GSA-632
-- I'm committing because there's some kind of fundamental problem with the ReadCovariates cache, in that historical data isn't being cleared / computed properly, and I'd rather it fail for a while than leave it in JIRA.
-- The integration tests test the -nct with PrintReads to get 1, 2, 4 and the 4 fails. But that's because of this incorrect calculation
-- Updating GATKPerformanceOverTime with the new @ClassType annotation
The old BaseRecalibrator walker is and never will be thread-safe, since it's a
LocusWalker that uses read attributes to track state.
ONLY the newer DelocalizedBaseRecalibrator is believed likely to be thread-safe
at this point. It is safe to run the DelocalizedBaseRecalibrator with -nct > 1
for testing purposes, but wait for further testing to be done before using it
for production purposes in multithreaded mode.
Bringing in the following relevant changes:
* Fixes the indel realigner N-Way out null pointer exception DEV-10
* Optimizations to ReduceReads that bring the run time to 1/3rd.
Conflicts:
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
DEV-10 #resolve #time 2m
-- Updated StandardCallerArgumentCollection to remove MaxAltAllelesForIndels. Previous argument is deprecated with meaningful doc message for people to use maxAltAlleles
-- All constructores, factory methods, and test builders and their users updated to provide just a single argument
-- Updating MD5s for integration tests that change due to genotyping more alleles
-- Adding more alleles to genotyping results in slight changes in the QUAL value for multi-allelic loci where one or more alleles aren't polymorphic. That's simply due to the way that alternative hypotheses contribute as reference evidence against each true allele. The effect can be large (new qual = old qual / 2 in one case here).
-- If we want more precision in our estimates we could decide (Eric, should we discuss?) to actually separately do a discovery phase in the genotyping, eliminate all variants not considered polymorphic, and then do a final round of calling to get the exact QUAL value for only those that are segregating. This would have the value of having the QUAL stay constant as more alleles are genotyped, at the cost of some code complexity increase and runtime. Might be worth it through
-- Created a JIRA ticket https://jira.broadinstitute.org/browse/GSA-623 for Guillermo to look at the differences as the multi-allelic nature of many sites seems to change with the new more protected infrastructure. This may be due to implementation issues in the pooled caller, problems with my interface, or could be a genuine improvement.
-- Potentially a very fast implementation (it's very clean) but restricted to the biallelic case
-- A starting point for future bi-allelic only optimized (logless) or generalized (bi-allelic general ploidy) implementations
-- Added systematic unit tests covering this implementation, and comparing it to others
-- Uncovered a nasty normalization bug in StateTracker that was capping our likelihoods at 0, even after summing up multiple likelihoods, which is just not safe to do and was causing us to lose likelihood in some cases
-- Removed the restriction that a likelihood be <= 0 in StateTracker, and the protection for these cases in GeneralPloidyExactAFCalc which just wasn't right
-- Changed UG / HC to use this one via the StandardCallerArgumentCollection
-- Update the AFCalcFactory.Calculation to have a getDefault() value instead of having a duplicate entry in the enums
-- GeneralPloidyExactAFCalc turns -Infinity values into -Double.MAX_VALUE, so our calculations pass unit tests
-- Bugfix for GeneralPloidyGenotypeLikelihoodsCalculationModel, return a null VC when the only allele we get from our final alleles to use method is the reference base
-- Fix calculation of reference posteriors when P(AF == 0) = 0.0 and P(AF == 0) = X for some meaningful value of X. Added unit test to ensure this behavior is correct
-- Fix horrible sorting bug in IndependentAllelesDiploidExactAFCalc that applied the theta^N priors in the wrong order. Add contract to ensure this doesn't ever happen again
-- Bugfix in GLBasedSampleSelector, where VCs without any polymorphic alleles were being sent to the exact model
--
-- These two classes were really the same, and now they are actually the same!
-- Cleanuped the interfaces, removed duplicate data
-- Added lots of contracts, some of which found numerical issues with GeneralPloidyExactAFCalc (which have been patched over but not fixed)
-- Moved goodProbability and goodProbabilityVector utilities to MathUtils. Very useful for contracts!
The CompressionStash is now responsible for keeping track of all intervals that must be kept uncompressed by all samples. In general this is a list generated by a tumor sample that will enforce all normal samples to abide.
- Updated ReduceReads integration tests
- Sliding Window is now using the CompressionStash (single sample).
DEV-104 #resolve #time 3m
-- 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.
-- 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
-- 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.
-- 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
-- AFCalcResult now sports a isPolymorphic and getLog10PosteriorAFGt0ForAllele functions that allow you to ask individually whether specific alleles we've tried to genotype are polymorphic given some confidence threshold
-- Lots of contracts for AFCalcResult
-- Slowly killing off AFCalcResultsTracker
-- Fix for the way UG checks for alt alleles being polymorphic, which is now properly conditioned on the alt allele
-- Change in behavior for normalizeFromLog10 in MathUtils: now sets the log10 for 0 values to -10000, instead of -Infinity, since this is really better to ensure that we don't have -Infinity values traveling around the system
-- ExactAFCalculationModelUnitTest now checks for meaningful pNonRef values for each allele, uncovering a bug in the GeneralPloidy (not fixed, related to Eric's summation issue from long ago that was reverted) in that we get different results for diploid and general-ploidy == 2 models for multi-allelics.
-- All of the code now uses the AFCalc object, not the not package protected AFCalcResultTracker. Nearly all unit tests pass (expect for a contract failing one that will be dealt with in subsequent commit), due to -Infinity values from normalizeLog10.
-- Changed the way that UnifiedGenotyper decides if the best model is non-ref. Previously looked at the MAP AC, but the MAP AC values are no longer provided by AFCalcResult. This is on purpose, because the MAP isn't a meaningful quantity for the exact model (i.e., everything is going to go to MLE AC in some upcoming commit). If you want to understand why come talk to me. Now uses the isPolymorphic function and the EMIT confidence, so that if pNonRef > EMIT then the site is poly, otherwise it's mono.
-- Renamed old class AFCalcResultTracker. This object is now allocated by the AFCalc itself, since it is heavy-weight and was badly optimized in the UG with a thread-local variable. Now, since there's already a AFCalc thread-local there, we get that optimization for free.
-- Removed the interface to provide the AFCalcResultTracker to getlog10PNonRef.
-- Wrote new, clean but unused AFCalcResult object that will soon replace the tracker as the external interface to the AFCalc model results, leaving the tracker as an internal tracker structure. This will allow me to (1) finally test things exhaustively, as the contracts on this class are clear (2) finalize the IndependentAllelesDiploidExactAFCalc class as it can work with a meaningfully defined result across each object
-- This model separates each of N alt alleles, combines the genotype likelihoods into the X/X, X/N_i, and N_i/N_i biallelic case, and runs the exact model on each independently to handle the multi-allelic case. This is very fast, scaling at O(n.alt.alleles x n.samples)
-- Many outstanding TODOs in order to truly pass unit tests
-- Added proper unit tests for the pNonRef calculation, which all of the models pass
-- Now contained in a package called afcalc
-- Extracted standard alone classes from private static classes in ExactAF
-- Most fields are now private, with accessors
-- Overall cleaner organization now
-- Now there's no duplication between exact old and constrained models. The behavior is controlled by an overloaded abstract function
-- No more static function to access the linear exact model -- you have to create the surrounding class. Updated code in the system
-- Everything passes unit tests
-- walks over the genotypes in VC, and computes for each alt allele the maximum AC we need to consider in that alt allele dimension. Does the calculation based on the PLs in each genotype g, choosing to update the max AC for the alt alleles corresponding to that PL. Only takes the first lowest PL, if there are multiple genotype configurations with the same PL value. It takes values in the order of the alt alleles.
-- Added a true base class that only does truly common tasks (like manage call logging)
-- This base class provides the only public method (getLog10PNonRef) and calls into a protected compute function that's abstract
-- Split ExactAF into superclass ExactAF with common data structures and two subclasses: DiploidExact and GeneralPloidyExact
-- Added an abstract reduceScope function that manages the simplification of the input VariantContext in the case where there are too many alleles or other constraints require us to only attempt a smaller computation
-- All unit tests pass
-- For the pooled caller we were writing diploid no-calls even when other samples were haploid. Changed maxPloidy function to return a defaultPloidy, rather than 0, in the case where all samples are missing.
-- VCF/BCF Writers now create missing genotypes with the ploidy of other samples, or 2 if none are available at all.
-- Updating integration tests for general ploidy, as previously we wrote ./. even when other calls were 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/1/1/1/1/1, but now we write ./././././././././././././././././././././././. (ugly but correct)
-- Includes header page
-- Table of arguments (Arguments)
-- Summary of counts (RecalData0)
-- Summary of counts by qual (RecalData1)
-- Fixed bug in output that resulted in covariates list always being null (updated md5s accordingly)
-- BQSR.R loads all relevant libaries now, include gplots, grid, and gsalib to run correctly
Tad Jordan
Ryan Poplin
Eric Banks
David Roazen
Mauricio Carneiro
Mark DePristo
Guillermo del Angel
Yossi Farjoun