We can't have a public test that depends on both public and private
code/data -- the new release system needs to do public-only tests,
and will catch this sort of thing.
-- Changes associated code throughout the codebase
-- Updated necessary (but minimal) UnitTests to reflect new behavior
-- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC
classloading of bcel*.jar/ant-apache-bcel*.jar. Switching instead to manually
specifying a minimal set of packages/classes to include in the vcf.jar via
build.xml, and adding a unit test which creates a limited classloader
only aware of vcf.jar and tribble.jar and tries to use it to load the core
classes in the vcf jar.
Hopefully third time's the charm.
* 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
Eric Banks
David Roazen
Mark DePristo
Matt Hanna
Mauricio Carneiro
Roger Zurawicki
Guillermo del Angel