chartl b42fc905e8 Added - new tests (Hapmap was re-added) ... Modified - Hapmap now takes a -q command to filter out variants by quality Modified - MathUtils - cumBinomialProbLog now uses BigDecimal to handle some numerical imprecisions Modified - PowerBelowFrequency - returns 0.0 if called with a negative number (can't be done from inside the walker itself, but since it's called elsewhere one can't be too careful) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2350 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-14 21:57:20 +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	CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads.	2009-12-14 21:52:30 +00:00
playground/gatk/walkers	Added - new tests (Hapmap was re-added)	2009-12-14 21:57:20 +00:00
utils	Refactored and generalized the VCF header info code.	2009-12-13 21:02:45 +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