delangel 653fb09bb7 a) Next iteration of context-dependent gap penalty model for new probabilistic alignment indel model. Actual model is now implemented, computes homopolymer run profile for candidate haplotypes and looks up in table gap penalties based on hrun length at each position. Initial penalty model is a very naive affine penalty model with each extra hrun increment decreasing Q2 the gap open penalty, until a minimum is reached. Still needs to be tuned and ideally get data from recalibration. ... b) small bug fix when setting debug arguments git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5446 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-15 16:46:28 +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	a) Next iteration of context-dependent gap penalty model for new probabilistic alignment indel model. Actual model is now implemented, computes homopolymer run profile for candidate haplotypes and looks up in table gap penalties based on hrun length at each position. Initial penalty model is a very naive affine penalty model with each extra hrun increment decreasing Q2 the gap open penalty, until a minimum is reached. Still needs to be tuned and ideally get data from recalibration.	2011-03-15 16:46:28 +00:00
test	A version of VQSRv2 that does contrastive clustering in two passes. The walkers will be renamed when they are moved to core.	2011-03-14 21:03:56 +00:00