-- Now only includes leaf nodes in the summary, i.e., summaries of the form "*.*....*.X", which are really the most valuable to see. This calculation can be accomplished in linear time for N differences, rather than the previous O(n^2) algorithm
-- Now computes the max number of elements to read correctly. Counts now the size of the entire element tree, not just the count of the roots, which was painful because the trees vary by orders of magnitude in size.
-- Because of this we can enforce a meaningful, useful value for the max elements in MD5 or 100K, and this works well.
-- Added integration test for new leaf and old pairwise calculations
-- Bugfix for Utils.join(sep, int[]) that was eating the first element of the AD, PL fields
-- Created a new Genotype interface with a more limited set of operations
-- Old genotype object is now SlowGenotype. New genotype object is FastGenotype. They can be used interchangable
-- There's no way to create Genotypes directly any longer. You have to use GenotypeBuilder just like VariantContextBuilder
-- Modified lots and lots of code to use GenotypeBuilder
-- Added a temporary hidden argument to engine to use FastGenotype by default. Current default is SlowGenotype
-- Lots of bug fixes to BCF2 codec and encoder.
-- Feature additions
-- Now properly handles BCF2 -> BCF2 without decoding or encoding from scratch the BCF2 genotype bytes
-- Cleaned up semantics of subContextFromSamples. There's one function that either rederives or not the alleles from the subsetted genotypes
-- MASSIVE BUGFIX in SelectVariants. The code has been decoding genotypes always, even if you were not subsetting down samples. Fixed!
-- Not hooked up yet, so the output of VariantEval should be the same as before
-- Implemented a VariantEvalUnitTest that tests the low level strat / eval combinatorics and counting routines
-- Better docs throughout
*** WAY FASTER ***
-- 3x performance for multiple sample analysis with 1000 samples
-- Analyzing 1MB of the ESP call set (3100 samples) takes 40 secs, compared to several minutes in the previous version
-- According to JProfiler all of the runtime is now spent decoding genotypes, which will only get better when we move to BCF2
-- Remove the TableType system, as this was way too complex. No longer possible to embed what were effectively multiple tables in a single Evaluator. You now have to have 1 table per eval
-- Replaced it with @Molten, which allows an evaluator to provide a single Map from variable -> value for analysis. IndelLengthHistogram is now a @Molten data type. GenotypeConcordance is also.
-- No longer allow Evaluators to use private and protected variables at @DataPoints. You get an error if you do.
-- Simplified entire IO system of VE. Refactored into VariantEvalReportWriter.
-- Commented out GenotypePhasingEvaluator, as it uses the retired TableType
-- Stratifications are all fully typed, so it's easy for GATKReports to format them.
-- Removed old VE work around from GATKReportColumn
-- General code cleanup throughout
-- Updated integration tests
Pulled out the functionality from Indel Realigner and Table Recalibrator into Utils.setupWriter to make everyone else's life's easier if they want to include the PG tag in their walkers.
* expanded the systematic cigar string space test framework Roger wrote to all tests
* moved utility functions into Utils and ReadUtils
* cleaned up unused classes
-- scatterLocusIntervals master utility
-- Moved around some general functionality from GenomeLocSortedSet to GenomeLoc
-- Util function for reversing a list (List<T> -> List<T>, unlike Collections version)
-- DoC is PartitionType.INTERVAL
-- Significant unit tests on new functionality (all passing)
-- Ready for real-world testing, as soon as I can get LocusScatterFunction.scala to actually work
initial size for a Java hash table (HashMap, HashSet, etc.) given an expected
maximum number of elements. The optimum size is the smallest size that's
guaranteed not to result in any rehash / table-resize operations.
Example Usage:
Map<String, Object> hash = new HashMap<String, Object>(Utils.optimumHashSize(expectedMaxElements));
I think we're paying way too heavy a price in unnecessary rehash operations across
the GATK. If you don't specify an initial size, you get a table of size 16 that gets
completely rehashed and doubles in size every time it becomes 75% full. This means you
do at least twice as much work as you need to in order to populate your table:
(n + n/2 + n/4 + ... 16 ~= (1 + 1/2 + 1/4...) * n ~= 2 * n
Mark DePristo
Eric Banks
Mauricio Carneiro
Khalid Shakir
David Roazen