hanna fcb6a992c8 Switched IndexedFastaSequenceFile over to use memory mapping to load data rather than ... the loop-with-small block size. Performance improvements in loading refs are extreme; segments can be loaded in <1ms. chr1 in its entirety can be loaded in 1.5sec (down from 30sec). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1781 348d0f76-0448-11de-a6fe-93d51630548a		2009-10-08 00:07:15 +00:00
..
gatk	GELI_BINARY is now functional, and can be used as a variant type in SSG (-vf=GELI_BINARY). Also fixed the max mapping quality column in both GELI output formats, we haven't been correctly outputing up until now.	2009-10-07 18:20:34 +00:00
playground/gatk/walkers	changes to add VCF to the rod system, fix VCF output in VariantsToVCF, and some other minor changes	2009-09-24 15:16:11 +00:00
utils	Switched IndexedFastaSequenceFile over to use memory mapping to load data rather than	2009-10-08 00:07:15 +00:00
BaseTest.java	Added some code to change the instrumentation for tests.	2009-05-20 05:15:27 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	delete the integration test temp files when the test is over	2009-09-25 16:34:08 +00:00