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15 Commits (ffdfdcde3ff3340d822693cb27efc8f7b6aaeeb4)

Author SHA1 Message Date
Mark DePristo a27641e1fc Cleaned up imports 2011-10-04 06:28:36 -07:00
Mark DePristo b20689ff55 No longer supports extraProperties 
-- the underlying data structure is still present, but until I decide what to do for the extensible system I've completely disabled the subsystem
-- Added code to merge Samples, so that a mostly full record can be merged with a consistent empty record.  If the two records are inconsistent, an error is thrown
-- addSample() in Sample.class now invokes mergeSample() when appropriate
-- Validation types are now only STRICT or SILENT
-- Validation code implemented in SampleDBBuilder
-- Extensive unit tests for SampleDBBuilder
 2011-10-03 19:20:33 -07:00
Mark DePristo 867a7476c1 Systematic unit tests for the sample object 2011-10-03 19:09:02 -07:00
Mark DePristo 2e3dc52088 Minor function renaming 2011-10-03 14:41:13 -07:00
Mark DePristo dd71884b0c On path to SampleDB engine integration 
-- PedReader tag parser
-- Separation of SampleDBBuilder from SampleDB (now immutable)
-- Removed old sample engine arguments
 2011-10-03 12:08:07 -07:00
Mark DePristo 89ac50e86e SampleDataSource -> SampleDB 2011-10-03 09:33:30 -07:00
Mark DePristo 93fba06cb5 Support for whitespace only lines 2011-10-03 09:30:10 -07:00
Mark DePristo 0604ce55d1 PedReader support for ; separated lines, not only newline 2011-10-03 09:19:58 -07:00
Mark DePristo 52f670c8b8 100% version of PedReader 
-- Passes all unit tests
-- Added unit tests for missing fields
 2011-10-03 06:12:58 -07:00
Mark DePristo dd75ad9f49 95% PedReader 
-- Passes significiant unit tests
-- Implicit sample creation for mom / dad when you create single samples
-- Continuing cleanup of Sample and SampleDataSource
 2011-09-30 18:03:34 -04:00
Mark DePristo 84160bd83f Reorganization of Sample 
-- Moved Gender and Afflication to separate public enums
-- PedReader 90% implemented
-- Improve interface cleanup to XReadLines and UserException
 2011-09-30 15:50:54 -04:00
Mark DePristo 5043d76c3d Removing more bad uses of SampleDataSource creation 2011-09-29 12:16:34 -04:00
Mark DePristo 5c9227cf5e Further cleanup of Sample database 
-- Removing more and more unnecessary code
-- Partial removal of type safe Sample usage.  On the road to SampleDB only
 2011-09-29 11:50:05 -04:00
Mark DePristo 2a0cd556d3 Further cleanup of Sample 
-- Cleaned up interface functions in GAE
-- Added Walker.getSampleDB() function which is an easier option for tools to get the samples db
 2011-09-29 10:34:51 -04:00
Mark DePristo e76f381628 Moved sample package from DataSources to gatk, and renamed it samples 
-- All associated changes to the codebase are just header updates
 2011-09-29 09:57:15 -04:00