-- Added unit tests for combining RecalibrationTables. As a side effect now has serious tests for incrementDatumOrPutIfNecessary
-- Removed unnecessary enum.index system from RecalibrationTables.
-- Moved what were really static utility methods out of RecalibrationEngine and into RecalUtils.
-- Added unit tests for EventType and ReadRecalibrationInfo
-- Simplified interface of EventType. Previously this enum carried an index with it, but this is redundant with the enum.ordinal function. Now just using that function instead.
-- With the newer, faster BQSR, scaling was limited by the NestedIntegerArray. The solution to this is to make the entire table thread-local, so that each nct thread has its own data and doesn't have any collisions.
-- Removed the previous partial solution of having a thread-local quality score table
-- Added a new argument -lowMemory
- Made few small modifications to code
- Replaced the two arguments in GATKReportTable constructor with an enum used to specify way of sorting the table
This isn't hooked up yet with BQSR; it's just a static method used in my testing walker. I'll hook this into BQSR after more testing and the addition of unit tests.
Most of the changes in this commit are actually documentation-related.
-- AdvancedRecalibrationEngine now uses a thread-local table for the quality score table, and in finalizeData merges these thread-local tables into the final table. Radically reduces the contention for RecalDatum in this very highly used table
-- Refactored the utility function to combine two tables into RecalUtils, and created UnitTests for this function, as well as all of RecalibrationTables. Updated combine in RecalibrationReport to use this table combiner function
-- Made several core functions in RecalDatum into final methods for performance
-- Added RecalibrationTestUtils, a home for recalibration testing utilities
- 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
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.
-- Refactor calculation so that upfront constant values are pre-computed, and cached, and their values just looked up during application
-- Trivial comment on how we might use BAQ better in BaseRecalibrator
-- Cleaned up code in updateDataForRead so that constant values where not computed in inner loops
-- BaseRecalibrator doesn't create it's own fasta index reader, it just piggy backs on the GATK one
-- ReadCovariates <init> now uses a thread local cache for it's int[][][] keys member variable. This stops us from recreating an expensive array over and over. In order to make this really work had to update recordValues in ContextCovariate so it writes 0s over base values its skipping because of low quality base clipping. Previously the values in the ReadCovariates keys were 0 because they were never modified by ContextCovariates. Now these values are actually zero'd out explicitly by the covariates.
-- No longer computes at each update the overall read group table. Now computes this derived table only at the end of the computation, using the ByQual table as input. Reduces BQSR runtime by 1/3 in my test
numbers larger than 999 in the Errors column were printed out with commas (which looks like a separate column).
This wasn't caught earlier because there are no integration tests covering the csv. I'll add one into unstable in a sec.
Caching and reusing ReadCovariates instances across reads sounds good in theory, but:
-it doesn't work unless you zero out the internal arrays before each read
-the internal arrays must be sized proportionally to the maximum POSSIBLE
recalibrated read length (5000!!!), instead of the ACTUAL read lengths
By contrast, creating a new instance per read is basically equivalent to doing an
efficient low-level memset-style clear on a much smaller array (since we use the actual
rather than the maximum read length to create it). So this should be faster than caching
instances and calling clear() but slower than caching instances and not calling clear().
Credit to Ryan to proposing this approach.
-- 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 ReadGroupCovariate class was not thread-safe. This led to horrible race conditions
in multithreaded runs of the BQSR where (for example) the same read group could get
inserted into the reverse lookup table twice with different IDs.
Should fix the intermittent crash reported in GSA-492.
-- In the process uncovered two strange things
1 -- qualityScoreByFullCovariateKey was created but never used. Seems like a cache?
2 -- Discovered nasty bug in BaseRecalibrator: https://jira.broadinstitute.org/browse/GSA-534
-- These are like read filters but can be applied either on input, on output, of handled by the walker
-- Previous example of BAQ now uses the general framework
-- Resulted in massive conceptual cleanup of SAMDataSource and ReadProperties! Yeah!
-- BQSR now uses this framework. We can now do BQSR on input, on output, or within a walker
-- PrintReads now handles all read transformers in the walker in map, enabling us to parallelize PrintReads with BAQ and BQSR
-- Currently BQSR is excepting in parallel, which subsequent commit with fix
-- Removed global variable setting in GenomeAnalysisEngine for BAQ, as command line parameters are cleanly handled by ReadTransformer infrastructure
-- In principle ReadFilters are just a special kind of ReadTransformer, but this refactoring is larger than I can do. It's a JIRA entry
-- Many files touched simply due to the refactoring and renaming of classes
-- I'm seeing a lot of people trying to use BinaryTagCovariate in the community. They really shouldn't do this, so I moved it to private.
-- Throw an exception if its required bintag argument is missing
-- Check explicitly if user is requesting DinucCovariate and tell them that its been retired in favor of ContextCovariate
-- Show the type (Required, Experimental, Standard) of the covariates when running --list
-- 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
-- Added bonferroni corrected p-value pruning, so you tell it how significant of a different you are willing to collapse in the tree, and it prunes the tree down to this maximum threshold
-- Penalty is now a phred-scaled p-value not the raw chi2 value
-- Split command line arguments in VisualizeContextTree into separate arguments for each type of pruning
Eric Banks
Mark DePristo
Tad Jordan
David Roazen
Ryan Poplin
Menachem Fromer