14 Commits (5f8264dddb0ded5f0e039bc50c02fb2a2c8cfbb2)

Author	SHA1	Message	Date
Mark DePristo	e36994e36b	Refactored a FeatureManager class from RMDTrackBuilder ... New class handles (vastly more cleanly) the db of tribble codecs, features, and names for use throughout the GATK. Added SelfScopingFeatureCodec interface that allows a FeatureCodec to examine a file and determine if the file can be parsed. This is the first step towards allowing the GATK to dynamically determine the type of a RodBinding.	2011-08-08 14:04:46 -04:00
Mark DePristo	8f696c7731	Continuing progress towards RodBinding 1.0 ... -- Cleaning up old interface to RMDT, docs and contracts added -- Proper type checking for RodBinding for cases where the Tribble type isn't found or is the wrong type	2011-08-03 17:19:28 -04:00
Mark DePristo	800bb97f0b	Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser ... Updated all walkers that used the now deleted methods.	2011-08-03 16:04:51 -04:00
Mark DePristo	b25140db83	Contracts and documentation for some of RefMetaDataTracker ... Continuing to fix integration tests that don't pass / run	2011-08-03 13:34:20 -04:00
Mark DePristo	d9bc673ff2	Fixed bad constructor in RMDTUnitTest	2011-08-03 09:42:43 -04:00
Mark DePristo	83891271b5	--variants throughout integrationtests	2011-08-02 20:28:47 -04:00
Mark DePristo	e4a67f3df1	RefMetaDataTracker has complete set of get() functions for List<RodBinding<T>> ... Including unit tests	2011-08-02 14:28:35 -04:00
Mark DePristo	03741fb640	Merge branch 'master' into rodRefactor ... Conflicts: public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java	2011-08-02 14:21:58 -04:00
Mark DePristo	7b07c4e04e	RefMetaDataTracker now has get() methods accepting RodBindings ... 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.	2011-07-30 15:34:11 -04:00
Mark DePristo	3b799db61a	RefMetaDataTracker cleanup and unit tests ... You know have to provide an explicit list of RODRecordLists upfront to the constructor. RefMetaDataTracker is now immutable. Changes in engine to incorporate these differences Extensive UnitTests for RefMetaDataTracker now.	2011-07-29 13:23:17 -04:00
Mark DePristo	2a51543693	Actually should have been gone...	2011-07-25 13:27:42 -04:00
Mark DePristo	ebfd8df06c	Restoring accidentially deleted unit test	2011-07-25 13:25:30 -04:00
Mark DePristo	f3049fba63	refdata directory cleanup ... Removing unused files RODRecordIterator, ReferenceOrderedData, QueryableTrack, RMDTrackCreationException, GATKFeatureIterator, ReferenceOrderedDataUnitTest Refactored dbSNP and refseq utilities to be closer to the other files implementing these features	2011-07-25 13:21:52 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, ... removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00