ebanks 91049269c2 Optimizations across the board, with help from Guillermo, Matt, and JProfiler. Too tired to give details now. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4535 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-20 20:47:41 +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	Optimizations across the board, with help from Guillermo, Matt, and JProfiler. Too tired to give details now.	2010-10-20 20:47:41 +00:00
test	ReadBackedPhasing now uses a SortedVCFWriter to simplify, and has the ability to merge phased SNPs into MNPs on the fly [turned off by default]; MergeSegregatingPolymorphismsWalker can also do this as a post-processing step; Integration tests for MergeSegregatingPolymorphismsWalker were also added	2010-10-20 20:27:10 +00:00