-- Sorting of ArgumentSources now done in GATKDoclet, not in the ParsingEngine, as the system depends on the LinkedTreeMap
-- Fixed broken exception throwing in the case where a file's type could not be determined
-- ArgumentSources are now sorted by case insensitive names, so arguments are shown in alphabetical order (Ryan)
-- @Advanced annotation can be used to indicate that an argument is an advanced option and should be visually deemphasized in the GATKs. There's now an advanced section. Mauricio or Ryan -- could you figure out how to make this section less prominent in the style.css?
-- Allowed values for RodBinding<T> are displayed in the GATKDocs
-- Longest name up to 30 characters is chosen for main argument list (suggested by Ryan/Mauricio)
-- Features are listed in alphabetical order
-- Moved useful getParameterizedType() function to JVMUtils
-- Tests of these features in the Documentation Test
-- RefSeqCodec bug: getFeatureClass() returned RefSeqCodec.class, not RefSeqFeature.class. Really should change this in Tribble to require Class<T extends Feature> to get compile time type checking
-- Better error messages that actually list the available tribble types, when there's a type error
-- Verified now to be correct at runtime
-- UnitTest covers this
-- createTypeDefault now takes a Type, not a Class, so that parameterized classes can have their parameter fetched in the defaults.
-- DocString function for types that create default outputs "stdout"
-- RodBinding now creates a makeUnbound default value automatically for you if your RodBinding isn't required
-- Removed warning about sparse help from TextFormattingUtils
-- CombineVariants now uses the new RodBinding syntax, -V / --variants. Passed all integration tests on first run
-- Exposed gapping bug in the List<RodBinding<T>> system now fixed. ParserEngine now has a addRodBinding() that is called by RodBindingArgumentTypeDescriptor when it encounters each RodBinding. This allows the system to work with collection types that are recursively parsed by the system.
-- support for explicit naming of bindings (-X:name,type x)
-- support for automatic naming of bindings in lists (-X:vcf foo.vcf -X:vcf bar.vcf will generate internal names X and X2)
-- ParserEngineUnitTest expanded to cover all of the Rodbinding cases
-- RodBindingUnitTest tests all of the low-level accessors
-- Parsing engine throws UserExceptions when bad bindings are provided on the command line
RodBinding no longer duplicates the get() methods in RMDT. This is just an object now that connects the command line system to the RMDT.
Updated programs to use new style
Added UnitTests for the RodBinding accessors.
On the path towards converging getVariantContext() and getValues() in tracker so that we can have a single approach to get values from RODs with the new RodBinding() types
Problem is that Novelty sees multiple records at a site (SNP, INDEL) to calculate whether a site is novel, but VariantEvalWalker makes an arbitrary decision which to use for analysis and CompOverlap may not see a comp record of the same type as eval. So you get lines where the stratification is known but there are 10 novel sites!
It's no longer possible to provided allowed types, as this was a very rarely used feature in the engine. These get methods have been removed and local uses replaced with tests directly in their code. This simplified the RefMetaDataTracker significantly
VariantContextRodBinding now forwards along all of the RefMetaDataTracker methods, so it is possible to create a full equivalent VariantContextRodBinding now as a walker field variable.
All walkers updated to the new RefMetaDataTracker function call style
Renamed many functions to more clearly state what they are actually doing
Removed unnecessary / unused functionality, reducing interface complexity
Updated all uses of this code in GATK
Added generic, type-safe accessors to RefMetaDataTracker such as public <T> List<T> getValues(final String name, Class<T> clazz)
Added standard refMetaDataTracker accessors to RodBinding, so you can do everything you can for generic rods with the tracker directly with with the RodBinding
Initial version of RodBinding class.
Flow from walker Rodbinding @Arguments -> RMDTriplet (old system) -> GATK engine (standard). Will need refactoring.
Eric Banks
Khalid Shakir
Mark DePristo
Matt Hanna