ebanks b3f561710f Optimizations: ... 1. Only do calculations in UG for alternate allele with highest sum of quality scores (note that this also constitutes a bug fix for a precision problem we were having). 2. Avoid using Strings in DiploidGenotype when we can (it was taking 1.5% of my compute according to JProfiler) UG now runs in half the time for JOINT_ESTIMATE model. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2141 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-24 16:27:39 +00:00
..
alignment	Basic integration test for the aligner.	2009-11-23 23:08:05 +00:00
gatk	Optimizations:	2009-11-24 16:27:39 +00:00
playground/gatk/walkers	The old recalibrator is replaced with the refactored recalibrator. Added a version message to the logger output. These walkers start at version 2.0.0	2009-11-23 14:58:33 +00:00
utils	Updated recalibrator integration tests to use all three platforms as well as a bam with multi-platform reads intermingled. CountCovariates v2.0.1: Once again uses a read filter to filter out zero mapping quality reads. Added --sorted_output option to output the table recalibration file in sorted order	2009-11-23 19:51:36 +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	Added the capability to allow expressions in an integration test command (i.e. -filter 'foo') by escaping them in the command.	2009-11-24 02:34:48 +00:00