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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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hanna cba18116e4 A significant refactoring of the ROD system, done largely to simplify the process of 
streaming/piping VCFs into the GATK.  Notable changes:
- Public interface to RMDTrackBuilder is greatly simplified; users can use it only to build 
  RMDTracks and lookup codecs.
- RODDataSource and RMDTrack are no longer functionally at the same level; RODDataSources now
  manage RMDTracks on behalf of the GATK, and the only direct consumers of the RMDTrack class
  are the walkers that feel the need to access the ROD system directly.  (We need to stamp out
  this access pattern.
A few minor warts were introduced as part of this process, labeled with TODOs.  These'll be
fixed as part of the VCF streaming project.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4915 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-31 04:52:22 +00:00
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arguments A significant refactoring of the ROD system, done largely to simplify the process of 2010-12-31 04:52:22 +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 A significant refactoring of the ROD system, done largely to simplify the process of 2010-12-31 04:52:22 +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