Commit Graph

4 Commits (dbc2ed2887b974046a031ac8276916b341c11f3d)

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