Eric Banks 405f3c675d Fix for GSA-649: GenomeLocSortedSet.overlaps is crazy slow. Also improved GenomeLocSortedSet.sizeBeforeLoc.		2012-11-27 01:07:00 -05:00
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commandline	Refactored argument matching to support other plugins in addition to file lists.	2012-10-15 15:10:45 -04:00
gatk	I forget why I thought that the VariantAnnotator couldn't run multi-threaded because it works just fine. Now you can specify -nt with VA.	2012-11-26 11:34:59 -05:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Fix for GSA-649: GenomeLocSortedSet.overlaps is crazy slow. Also improved GenomeLocSortedSet.sizeBeforeLoc.	2012-11-27 01:07:00 -05:00
BaseTest.java	Extensive unit tests, contacts, and documentation for RecalDatum	2012-07-31 08:11:03 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
TestNGTestTransformer.java	Add custom TestNGTestTransformer that adds a maximum test runtime of 10 minutes to all testng tests	2012-11-01 15:34:12 -04:00
WalkerTest.java	Renaming -cnt to -nct for consistency	2012-09-05 21:13:19 -04:00