gatk-3.8

Author	SHA1	Message	Date
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