delangel 71bfb1ee35 First redesign of HaplotypeScore - now, a different approach is taken to build possible haplotypes at a site: first, all possible haplotypes consistent with reads are formed (reference is not used). After this list has been formed, it is ranked according to the number of reads that are consistent with it and the two most popular haplotypes are chosen. ... this reduces to the old method in typical cases, but it builds haplotypes correctly if there are two variants close by within a context window. Annotation is temporarily named MyHaplotypeScore so it can be run in parallel with old one, soon it will be renamed after some more testing. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3885 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-27 10:54:56 +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	First redesign of HaplotypeScore - now, a different approach is taken to build possible haplotypes at a site: first, all possible haplotypes consistent with reads are formed (reference is not used). After this list has been formed, it is ranked according to the number of reads that are consistent with it and the two most popular haplotypes are chosen.	2010-07-27 10:54:56 +00:00
test	Archiving	2010-07-27 02:47:18 +00:00