kiran 1861ca90fc A change to the definition of CpG sites (is now, from 5' to 3' a CG dinucleotide in the reference, and the CpG site is at the C, rather than either at the C or a G). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5373 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-04 15:36:07 +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 checkpoint commit of two BAM reading projects going on simultaneously. These two projects	2011-02-25 17:50:32 +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	More descriptive error when VerifyingSamIterator hits an inconsistent alignment. Also updated	2011-03-03 03:55:24 +00:00
refdata	Oops...forgot to commit the changes that allow primitive VCF streaming.	2011-01-12 21:54:51 +00:00
traversals	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
walkers	A change to the definition of CpG sites (is now, from 5' to 3' a CG dinucleotide in the reference, and the CpG site is at the C, rather than either at the C or a G).	2011-03-04 15:36:07 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00