3 Commits (6bb864da2a7941caaebb0de351cb488164b69a7c)

Author	SHA1	Message	Date
depristo	75b61a3663	Updated, optimized REadBackedPileup. Updated test that was breaking the build -- it created a pileup from reads without bases... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2169 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-25 23:30:39 +00:00
depristo	db40e28e54	ReadBackedPileup in all its glory. Documented, aligned with the output of LocusIteratorByState, and caching common outputs for performance ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2165 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-25 20:54:44 +00:00
depristo	03342c1fdd	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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2154 348d0f76-0448-11de-a6fe-93d51630548a	2009-11-25 03:51:41 +00:00