ebanks 08f2214f14 Stage 1 of massive Variation/Genotype refactoring. ... This stage consists only of the code originating in the Genotyper and flowing through to the genotype writers. I haven't finished refactoring the writers and haven't even touched the readers at all. The major changes here are that 1. Variations which are BackedByGenotypes are now correctly associated with those Genotypes 2. Genotypes which have an associated Variation can actually be associated with it (and then return it when toVariation() is called). The only integration tests which need to be updated are MSG-related (because the refactoring now made it easy for me to prevent MSG from emitting tri-allelic sites). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2269 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-06 03:12:41 +00:00
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alignment	Restructuring and interface change to ReadBackedPileup. We now lower support the Pileup interface, the BasicPileup static methods, and the ReadBackedPileup class. Now everything is a ReadBackedPileup and all methods to manipulate pileups are off of it. Also provides the recommended iterable() interface of pileup elements so you can use the syntax for (PileupElement p : pileup) and access directly from p.getBase() and p.getQual() and p.getSecondBase(). Only a few straggler walkers use the old style interface -- but those walkers will be retired soon. Documentation coming in the AM. Please everyone use the new syntax, it's safer, and will be more efficient as soon as the LocusIteratorByState directly emits the ReadBackedPileup for the Alignment context, as opposed to the current interface. In the process of the change over, discovered several bugs in the second-best base code due to things getting out of sync, but these changes were resolved manually. All other integrationtests passed without modification.	2009-11-25 03:51:41 +00:00
gatk	Stage 1 of massive Variation/Genotype refactoring.	2009-12-06 03:12:41 +00:00
playground/gatk/walkers	commenting out some broken integration tests, to be uncommented if needed.	2009-12-02 23:13:24 +00:00
utils	make sure we close the error log stream in CommandLineProgram if it's opened; unit tests and clean-up for BasicVariation	2009-12-03 06:59:27 +00:00
BaseTest.java	Added some code to change the instrumentation for tests.	2009-05-20 05:15:27 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.	2009-11-24 02:34:48 +00:00