ebanks 717eb1de96 - Depth annotation now includes MQ0 reads ... - Removed MQ0 annotation - Updated RMS MQ annotation to use new pileup - UG now outputs all of its arguments as key/value pairs in the header (for VCF) - Cleaned up VCFGenotypeWriterAdapter interface a bit git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2288 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-09 02:53:00 +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	- Depth annotation now includes MQ0 reads	2009-12-09 02:53:00 +00:00
playground/gatk/walkers	Stage 3 of Variation refactoring:	2009-12-08 21:43:28 +00:00
utils	Stage 3 of Variation refactoring:	2009-12-08 21:43:28 +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