Matt Hanna 15533e08df Fixed issue with RODWalker parallelization. ... Turns out that someone previously upped the declared size of a ROD shard to 100M bases, making each ROD shard larger than the size of chr20. Why didn't we see this in Stable? Because the ShardStrategy/ShardStrategyFactory mechanism was dutifully ignoring the shard size specification. When I rolled the ShardStrategy/ShardStrategyFactory mechanics back into the DataSources as part of the async I/O project, I inadvertently reenabled this specifier.		2011-12-07 11:55:42 -05:00
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R	Compacting pdfs when running under R 2.13+.	2011-10-27 14:51:56 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Fixed issue with RODWalker parallelization.	2011-12-07 11:55:42 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Use optional() instead of required() to construct javaMemoryLimit argument in JavaCommandLineFunction	2011-12-05 14:06:00 -05:00
testdata	Testdata for IntervalStratification	2011-11-10 11:08:34 -05:00