fromer 798955b006 After discussing with Mark, revert to "Master merging" of phase information from VCFs. This has the advantage of creating minimal phased VCFs from RBP, from which phase info is merged into the original "master VCF". Also, updated Genotype.sameGenotype() to be simpler and NOT REVERSE the ignorePhase flag in comparing Allele lists/sets ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5167 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-01 19:50:15 +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	After discussing with Mark, revert to "Master merging" of phase information from VCFs. This has the advantage of creating minimal phased VCFs from RBP, from which phase info is merged into the original "master VCF". Also, updated Genotype.sameGenotype() to be simpler and NOT REVERSE the ignorePhase flag in comparing Allele lists/sets	2011-02-01 19:50:15 +00:00
test	Pulled out CpG stratification in test results at Kiran's suggestion.	2011-02-01 18:36:09 +00:00