ebanks 8f38ebf98e Throw a user exception when using the clustered SNP filter in the presence of ref calls. It's unfortunate, but until we get a windowed ROD context this is just too much of a headache to support. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4537 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-21 02:44:10 +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	Throw a user exception when using the clustered SNP filter in the presence of ref calls. It's unfortunate, but until we get a windowed ROD context this is just too much of a headache to support.	2010-10-21 02:44:10 +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