* Includes tests that include HardClip to Read and Reference Coords.
* Changed ReadUtils.HardClipByReferenceCoordinates from private to protected to allow for testing
-- UnitTests for key functions on reduced reads
-- PileupElement calls static functions in ReadUtils
-- Simple routine that takes a reduced read and fills in its quals with its reduced qual
b) Change md5 to reflect records that are now merged correctly.
c) Change unit merge alleles test to reflect the fact that a null non-variant vc object is not valid and not supported because there's no way to codify such object in a vcf. The code correctly converts this to a non-variant single-base event with whatever the reference is at that location.
-- Old code required qual to be <64, which isn't strictly necessary. Now uses the Picard SAMUtils.MAX_PHRED_SCORE constant
-- Unittest to enforce this behavior
-- Previously, on the fly indices didn't have dictionary set on the fly, so the GATK would read, add dictionary, and rewrite the index. This is now fixed, so that the on the fly index contains the reference dictionary when first written, avoiding the unnecessary read and write
-- Added a GenomeAnalysisEngine and Walker function called getMasterSequenceDictionary() that fetches the reference sequence dictionary. This can be used conveniently everywhere, and is what's written into the Tribble index
-- Refactored tribble index utilities from RMDTrackBuilder into IndexDictionaryUtils
-- VCFWriter now requires the master sequence dictionary
-- Updated walkers that create VCFWriters to provide the master sequence dictionary
-- No functional changes (my algorithm wouldn't work)
-- Major structural cleanup (returning more basic data structures that allow us to development new algorithm)
-- Unit tests for the efficiency of interval partitioning
-Rewrote SnpEff support in VariantAnnotator to support the latest SnpEff release (version 2.0.2)
-Removed support for SnpEff 1.9.6 (and associated tribble codec)
-Will refuse to parse SnpEff output files produced by unsupported versions (or without a version tag)
-Correctly matches ref/alt alleles before annotating a record, unlike the previous version
-Correctly handles indels (again, unlike the previous version
VariantEval module CountVariants is corrected and an additional column is added so that we log mixed events and complex indels separately (before they were being conflated).
VariantEval module IndelStatistics is considerably simplified as the sample stratification was wrong and redundant, now it should work with the VE-generic Sample stratification. Several columns are renamed or removed since they're not really useful
Mark DePristo
Mauricio Carneiro
Roger Zurawicki
Guillermo del Angel
Eric Banks
David Roazen