depristo cc78027bd3 Two optimizations. Even more aggressive printProgress meter optimization to only even consider doing work once every 1000 cycles through the engine. Second, GenomeLocParser now uses a single indirection around the contigInfo variable. This class uses a last used cache to retrieve efficiently contig information instead of always returning to the underlying SAMSequenceDictionary hashmap to make genome locs. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5670 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-21 01:31:26 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Two optimizations. Even more aggressive printProgress meter optimization to only even consider doing work once every 1000 cycles through the engine. Second, GenomeLocParser now uses a single indirection around the contigInfo variable. This class uses a last used cache to retrieve efficiently contig information instead of always returning to the underlying SAMSequenceDictionary hashmap to make genome locs.	2011-04-21 01:31:26 +00:00
test	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00