hanna 6d855041ec Oops...forgot to commit the changes that allow primitive VCF streaming. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4979 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-12 21:54:51 +00:00
..
AllLocusViewUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
CoveredLocusViewUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
LocusReferenceViewUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
LocusViewTemplate.java	Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.	2010-11-19 19:59:05 +00:00
ReadBasedReferenceOrderedViewUnitTest.java	Oops...forgot to commit the changes that allow primitive VCF streaming.	2011-01-12 21:54:51 +00:00
ReadReferenceViewUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
ReferenceOrderedViewUnitTest.java	Unit test fixed - Tribble codecs aren't designed to be stateless, but I was	2010-12-31 17:47:52 +00:00
ReferenceViewTemplate.java	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
ShardDataProviderUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00