-- Uses chi2 test for independences to determine if subcontext is worth representing. Give excellent visual results
-- Writes out analysis output file producing excellent results in R
-- Trivial reformatting of MathUtils
-- Reorganize functions in RecalDatum so that error rate can be computed indepentently. Added unit tests. Removed equals() method, which is a buggy without it's associated implementation for hashcode
-- New class RecalDatumTree based on QualIntervals that inherits from RecalDatum but includes the concept of sub data
-- VisualizeContextTree now uses RecalDatumTree and can trivially compute the penalty function for merging nodes, which it displays in the graph
-- Moved most of BQSR classes (which are used throughout the codebase) to utils.recalibration. It's better in my opinion to keep commonly used code in utils, and only specialized code in walkers. As code becomes embedded throughout GATK its should be refactored to live in utils
-- Removed unncessary imports of BQSR in VQSR v3
-- Now ready to refactor QualQuantizer and unit test into a subclass of RecalDatum, refactor unit tests into RecalDatum unit tests, and generalize into hierarchical recal datum that can be used in QualQuantizer and the analysis of adaptive context covariate
-- Update PluginManager to sort the plugins and interfaces. This allows us to have a deterministic order in which the plugin classes come back, which caused BQSR integration tests to temporarily change because I moved my classes around a bit.
-- Moved Datum, the now unnecessary superclass, into RecalDatum
-- Fixed some obviously dangerous synchronization errors in RecalDatum, though these may not have caused problems because they may not have been called in parallel mode
-- Check if a traversal error occurred in the last shard
-- Catch ExecutionException from the TreeReducer and throw as our HMS execption
-- ShardTraverser just throws the exception as formatted by the HMS, rather than wrapping it as a RuntimeException itself
-- EngineFeaturesIntegrationTests now uses public exampleFASTA (faster), and does 1000x iterations (slower)
-- Better error message when a traveral error occurs (a real bug)
-- EngineFeaturesIntegrationTest runs the multi-threaded error testing routines 50x times
-- A bit of cleanup in WalkerTest
We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything.
Tools can be hidden from GATKdocs with the @Hidden annotation
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
-- VariantFiltration now properly sets passFilters in VC
-- BCF2 writer now properly decodes lazy BCF genotype data that it uses. Improper use generated a horrible subtle bug but the good news is that the extra checks I put in (unnecessarily a few days ago) caught the bug!
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
-- Always decode genotypes block when writing out a BCF file. If the header changes (and we currently don't know this easily) then the dictionary keys used in the genotypes block may be invalid. Temporarily added a private static boolean that turns off writing of the blocks until Eric and his team rewrite the header.
Signed-off-by: Mark DePristo <depristo@broadinstitute.org>
GATKDocs looks for a key on gsa4, and updates the forum with new walker if it exists.
More changes were made to the GATKDocs. Works nicely with bootstrap on and offline.
Cleaned up the code as well
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Parameter wasn't working outside of the BQSR walker. It now takes the information on the recalibration report in other tools (PrintReads for example) and treats all reads as coming from the defined default platform.
* Did not touch archived walkers... those can be named whatever.
* Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...)
* Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
-- Heng wants to use 0x0? to represent any missing type value, which in our implementation was invalid. Updated our codebase to support this construct. Heng said he'll update the BCF2 quick reference.
-- Enabled integration test reading Heng's ex2.bcf file
-- GATK now only warns in the case where the END info field isn't the same (or +1 due to padding) as the getEnd() function as determined by the GATK. Turns out there's a single record in the 1000G SV call set that doesn't have the right length
-- VariantContextTestProvider now tests that X = Y where X -> writing -> reading -> writing -> reading = Y for a variety of variant context inputs X
-- Added integration test reading 1000G SV chr1 calls (from Chris)
-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status. This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF. The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
-- TODO: actually run integration tests when I have an internet connection
-- If eval has genotypes and comp has genotypes, then subset the genotypes of comp down to the samples being evaluated when considering TP, FP, FN, TN status. This is important in the case where you want to use this to assess, for example, the quality of calls on NA12878 but you have a CEU trio comp VCF. The previous version was counting sites polymorphic in mom against the calls in NA12878.
-- Added testdata VCF and integrationtests to ensure this behavior continues in the future
-- This actually proved to be a problem with Ion Torrent data where the base quality can be quite low, and so we need to include Q15 bases for calling effectively.
Ryan Poplin
Eric Banks
Guillermo del Angel
Mark DePristo
Mauricio Carneiro
Roger Zurawicki
Khalid Shakir
Christopher Hartl
Laurent Francioli