-- 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
-- Added PartitionType.READ, and associated ReadScatterFunction. ReadScatterFunction is literally just ContigScatterFunction until someone wants to implement something better
-- LocusWalkers (and subclasses RodWalkers and RefWalkers) are by default PartitionType.LOCUS.
Bases that were excluded for MQ and BQ filters are now contributing to the MQ RMS (but not to consensus base counts and variant/not variant region triggers).
Reducing the reference bases to '=' results in an extra compression of 13% on average. The GATK is not ready to handle files with '=' bases, and the decision was to implement this a an engine support, not a part of ReduceReads.
These walkers should not be scatter gatherable. Annotating them accordingly so that Queue doesn't allow a less than knowledgeable user to try and scatter/gather VQSR.
-- 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
First, I'm sure there's a better way to do this, but I wanted to create a single commit summarizing the changes from my branch SamRecordFactory. What's the best way to do this? Rebase?
Now, on to the changes here:
-- Picard added a SamRecordFactory that is used to create instances the subclass SamRecord or BAMRecord. This factory allows us to have low-level picard readers (SamFileReader) create objects of type GATKSamRecord. The abomination of the extends and contains GATKSamRecord is now gone. GATKSamRecords are now produced by this factory, the GATK provides this factory to our SamFileReaders, and everything works with GATKSamRecord just extending BAMRecord. This results in up to a 2x performance improvement in writing BAMs and a ~10% improvement when reading BAMs files.
-- As a consequence of this, we no longer officially support SAM records. Attempting to create SAMRecord objects with the factory will throw a user exception.
-- Created a standard NGSPlatform enum, and GATKSamRecords support efficiently obtaining this value. The real BQSR (not the copy indel version) got the efficient code to use this. Please add all future platforms to this enum.
-- GATKSamRecord no longer supports using the OQ or defaultBaseQuality. This is performed in a wrapper iterator that's only added when these command line options are used.
-- ReducedRead code has been moved from ReadUtils until efficiency caching assessors in GATKSamRecord.
-- ArtificialSamUtils creates GATKSamRecords now, just SAMRecords. Added code here to create artifical pairs and using that code to create artificial ReadBackedPileups with specific properties
-- New smarter algorithm for FragmentPileup. This new code is up to 3x faster than the previous version, and is lazy so is more efficient when no overlapping pairs are actually in the pileup. Created extensive DataProvider driven UnitTest. Added Caliper-based benchmarking system to characterize the performance differences between the old and new algorithms. TODO still remains to make a efficient version that works for non-pileups for the HaplotypeCaller
Mark DePristo
Eric Banks
Mauricio Carneiro
David Roazen
Andrey Sivachenko
Guillermo del Angel
Khalid Shakir
Matt Hanna
Ryan Poplin