Mark DePristo 3414ecfe2e Restored serial version of reader initialization. Serial mode is default, as the performance gains aren't so huge. ... -- Serial version can be re-enabled with a static boolean, if we decide to return to the serial version -- Comparison of serial and parallel reader with cached and uncached files: Initialization time: serial with 500 fully cached BAMs: 8.20 seconds Initialization time: serial with 500 uncached BAMs : 197.02 seconds Initialization time: parallel with 500 fully cached BAMs: 30.12 seconds Initialization time: parallel with 500 uncached BAMs : 75.47 seconds		2011-12-16 09:22:10 -05:00
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R	scales=free shows variance within analysis better	2011-12-07 14:09:32 -05:00
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	Restored serial version of reader initialization. Serial mode is default, as the performance gains aren't so huge.	2011-12-16 09:22:10 -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	Support for NT testing (default up to 4) for CC and UG	2011-12-14 18:45:00 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00