ebanks 848977678d No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime... ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4913 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-29 22:06:19 +00:00
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arguments	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
contexts/variantcontext	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
datasources	Push command-line expansions, such as BAM list unpacking and -B tag parsing, out	2010-12-22 19:00:17 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	Final version of BAQ calculation. default gap open is 1e-4, a good sensitive value. Useful timer class SimpleTimer added. BAQ is now live.	2010-12-10 19:35:12 +00:00
refdata	Fixed a bug in UnitTest	2010-12-17 19:44:35 +00:00
traversals	Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns.	2010-12-05 18:29:39 +00:00
walkers	No reason to convert the GLs to a String for formatting when they're just going to be converted to PLs later. That was 5% of the UG runtime...	2010-12-29 22:06:19 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00