hanna 9db02059ac Fix for Ryan's issue: reads ending with indel distort the location of the ... pileup, resulting a two map() calls for the same locus (and no map call for the locus immediately following). Fixed bug and added comprehensive unit tests. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5067 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-24 19:49:39 +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	<key>=<value> tagging support for command-line arguments. Unfortunately, still	2011-01-21 00:22:42 +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	Fix for Ryan's issue: reads ending with indel distort the location of the	2011-01-24 19:49:39 +00:00
refdata	Oops...forgot to commit the changes that allow primitive VCF streaming.	2011-01-12 21:54:51 +00:00
traversals	<key>=<value> tagging support for command-line arguments. Unfortunately, still	2011-01-21 00:22:42 +00:00
walkers	Don't print out alt alleles for ref calls	2011-01-23 06:33:31 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00