Mark DePristo 817ece37a2 General infrastructure for ReadTransformers ... -- These are like read filters but can be applied either on input, on output, of handled by the walker -- Previous example of BAQ now uses the general framework -- Resulted in massive conceptual cleanup of SAMDataSource and ReadProperties! Yeah! -- BQSR now uses this framework. We can now do BQSR on input, on output, or within a walker -- PrintReads now handles all read transformers in the walker in map, enabling us to parallelize PrintReads with BAQ and BQSR -- Currently BQSR is excepting in parallel, which subsequent commit with fix -- Removed global variable setting in GenomeAnalysisEngine for BAQ, as command line parameters are cleanly handled by ReadTransformer infrastructure -- In principle ReadFilters are just a special kind of ReadTransformer, but this refactoring is larger than I can do. It's a JIRA entry -- Many files touched simply due to the refactoring and renaming of classes		2012-08-31 13:42:41 -04:00
..
config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	General infrastructure for ReadTransformers	2012-08-31 13:42:41 -04:00
test	I started to put together a set of unit tests for the PileupElement creation functionality of LocusIteratorByState and found pretty quickly that it's definitely still busted for indels. The data provider is nowhere near comprehensive yet, but I need to sit back and think about how to really test some of the functionality of LIBS. Committing what I have for now because at the very least it'll be helpful going forward (failing tests are commented out with TODO).	2012-08-30 22:49:13 -04:00