delangel 8c262eb605 Initial commit of new likelihood model to evaluate indel quality. Principle is simple, a plain Pair HMM with affine gap penalties (in log space) that does quasi-local alignment between reads and candidate haplotypes and which in theory should be more solid and more reliable than the older Dindel-based model. It also allows to be easily extensible in the future if we decide to introduce either context-dependent and/or read-dependent gap penalties. ... Model is disabled by default and we're still using the old Dindel model until I'm more confident that new model is a definitive improvement, so right now this is enabled by hidden command line arguments, and it's not to be used yet. In detail: a) Several refactorings to share softMax() available to other modules, so its now part of MathUtils. b) Refactored a couple of read utilities and moved from BAQ to ReadUtils. c) New PairHMMIndelErrorModel class implementing new likelihood model d) Several new hidden debug arguments in UAC. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5389 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-07 15:31:58 +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	Initial commit of new likelihood model to evaluate indel quality. Principle is simple, a plain Pair HMM with affine gap penalties (in log space) that does quasi-local alignment between reads and candidate haplotypes and which in theory should be more solid and more reliable than the older Dindel-based model. It also allows to be easily extensible in the future if we decide to introduce either context-dependent and/or read-dependent gap penalties.	2011-03-07 15:31:58 +00:00
test	Added a boatload of new case-control association modules. Switched the U-test to use longs rather than ints (it just so happened that I overflowed and started getting negative U statistics. Not good.) Added the ALL association type for ease of specifying that we want to throw the book at something. Added an svn-commit.tmp~ because i can't get rid of it even with --force. Hopefully I can remove it after.	2011-03-06 21:58:12 +00:00