depristo 20db00a3e8 Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4042 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-16 13:46:22 +00:00
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variantcontext	fix for a problem in readNextRecord() of BFS, where we'd go looking for the next record far into in the next contig because (f.getEnd() >= start) was never true once we cycled to a new conitg. Added a check for contig identity. Also, removed duplicate HW calculation classes in the GATK and Tribble.	2010-08-11 17:01:38 +00:00
AlignmentContext.java	A fix for the integration test I broke on Friday on my way out the door --	2010-07-17 22:22:44 +00:00
ReferenceContext.java	Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers.	2010-08-16 13:46:22 +00:00
StratifiedAlignmentContext.java	An initial fix for performance issues when filtering UG with new StratifiedAlignmentContext.	2010-07-07 01:07:46 +00:00