gatk-3.8

Author	SHA1	Message	Date
Matt Hanna	e923a2e512	Revving Picard to incorporate final version of ReadWalker performance improvements.	2012-01-10 12:12:33 -05:00
Matt Hanna	3642a73c07	Performance improvements for dynamically merging BAMs in read walkers. This change and my previous change have dropped runtime when dynamically merging 2k BAM files from 72.6min/1M reads to 46.8sec/1M reads. Note that many of these changes are stopgaps -- the real problem is the way ReadWalkers interface with Picard, and I'll have to work with Tim&Co to produce a more maintainable patch.	2011-12-16 09:37:44 -05:00
Matt Hanna	8bb4d4dca3	First pass of the asynchronous block loader. Block loads are only triggered on queue empty at this point. Disabled by default (enable with nt:io=?).	2011-11-18 15:02:59 -05:00
Mark DePristo	f3ad4ec94b	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
David Roazen	3c9497788e	Reorganized the codebase beneath top-level public and private directories, removing the playground and oneoffprojects directories in the process. Updated build.xml accordingly.	2011-06-28 06:55:19 -04:00