-- Performance optimizations
-- Tables now are cleanly formatted (floats are %.2f printed)
-- VariantSummary is a standard report now
-- Removed CompEvalGenotypes (it didn't do anything)
-- Deleted unused classes in GenotypeConcordance
-- Updates integration tests as appropriate
-- Updating MD5s for UG to reflect that what was previously called ./.:.:10:0,0,0 is now just ./. Eric will fix long-standing bug in QD observed from this change
-- VFW MD5s restored to their old correct values. There was a bug in my implementation to caused the genotypes to not be parsed from the lazy output even through the header was incorrect.
This syntax predates the ability to have multiple -L arguments, is
inconsistent with the syntax of all other GATK arguments, requires
quoting to avoid interpretation by the shell, and was causing
problems in Queue.
A UserException is now thrown if someone tries to use this syntax.
-- Now you provide a LazyParsing object
-- LazyGenotypesContext now knows nothing about the VCF parser itself. The parser holds all of the necessary data to parse the VCF genotypes when necessarily, and the LGC only has a pointer to this object
-- Using new interface added LazyGenotypesContext to unit tests with a simple lazy version
-- Deleted VCFParser interface, as it was no longer necessary
-- With our GenotypesContext class we can naturally create a LazyGenotypesContext subclass that does the on-demand loading.
-- This new class was replaced all of the old, complex functionality
-- Better still, there were many cases were the genotypes were being loaded unnecessarily, resulting in efficiency. This was detected because some of the integration tests changed as the genotypes were no longer being parsing unnecessarily
-- Misc. bug fixes throughout the system
-- Bug fixes for PhaseByTransmission with new GenotypesContext
-- We should no longer have md5s changing because of hashmaps changing their sort order on us
-- Added GenotypeLikelihoodsUnitTests
-- Refactored ExactAFCaclculation to put the PL -> QUAL calculation in the GenotypeLikelihoods class to avoid the code copy.
-- New approach to making VariantContexts modeled on StringBuilder
-- No more modify routines -- use VariantContextBuilder
-- Renamed isPolymorphic to isPolymorphicInSamples. Same for mono
-- getChromosomeCount -> getCalledChrCount
-- Walkers changed to use new VariantContext. Some deprecated new VariantContext calls remain
-- VCFCodec now uses optimized cached information to create GenotypesContext.
-- Major change to how chromosomeCounts is computed. Now NO_CALL alleles are always excluded. So ChromosomeCounts(A/.) is 1, the previous result would have been 2.
-- Naming changes for getSamplesNameInOrder()
-- Compares performance across a bunch of common operations with GATK 1.3 version of VariantContext and GATK 1.4
-- 1.3 VC and associated utilities copied wholesale into test directory under v13
-Modified the SnpEff parser to work with the SnpEff 2.0.4 VCF output format
-Assigning functional classes and effect impacts now handled directly
by SnpEff rather than the GATK
-Removed support for SnpEff 2.0.2, as we no longer trust the output of that
version since it doesn't exclude effects associated with certain nonsensical
transcripts. These effects are excluded as of 2.0.4.
-Updated unit and integration tests
This support is based on a *release-candidate* of SnpEff 2.0.4, and so is subject
to change between now and the next GATK release.
compressed the representation of the reduce reads counts by offset results in 17% average compression in final BAM file size.
Example compression -->
from : 10, 10, 11, 11, 12, 12, 12, 11, 10
to: 10, 0, 1, 1,2, 2, 2, 1, 0
-- I have no idea why I named this InferredGeneticContext, a totally meaningless term
-- Renamed to CommonInfo.
-- Made package protected, as no one should use this outside of VariantContext and Genotype
-- UGEngine was using IGC constant, but it's now using the public one in VariantContext.
-- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples
-- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type.
-- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous. Now everything uses GenotypeMap with a specific ordering of samples (by name)
-- Integrationtests updated and all pass
* Generalized the concept of a synthetic read to cread both running consensus and a synthetic reads of filtered data.
* Synthetic reads can now have deletions (but not insertions)
* New reduced read tag for filtered data synthetic reads *(RF)*
* Sliding window header now keeps information of consensus and filtered data
* Synthetic reads are created simultaneously, new functionality is controlled internally by addToSyntheticReads
The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...).
* No tools should create SAMRecord anymore, use GATKSAMRecord instead *
-- 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
-- Supports ReadBackedPileup -> FragmentCollection as before
-- Added support for List<SAMRecord> -> FragmentCollection for Ryan's haplotype caller
-- General cleanup, renaming, move to separate package, more extensive unit tests, etc.
-- Added toFragment() function to ReadBackedPileup interface
Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
-- removed intermiate functions. Now only original version and best optimized new version remain
-- Moved general artificial read backed pileup creation code into ArtificialSamUtils
Ryan Poplin
Mark DePristo
Mauricio Carneiro
David Roazen
Matt Hanna
Khalid Shakir
Eric Banks
Laurent Francioli
Roger Zurawicki