delangel e6e8a20a1e 1) Fix MyHaplotypeScore to ignore 454 reads, since all those pathological non-existing indels make some sites' score blow up. If a site is only covered by 454 reads, we (hopefully) detect this graciously and just emit a score of 0.0 for the site. ... 2) New annotation SByDepth = log10(-StrandBias/Depth) (non-standard annotation, key name = "SBD"). If StrandBias/Depth happens to be positive (very rare but can happen), annotation gets value=-1000. 3) Abstracted out new class AnnotationByDepth so that QD and SBD can share code. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3930 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-04 15:23:08 +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	1) Fix MyHaplotypeScore to ignore 454 reads, since all those pathological non-existing indels make some sites' score blow up. If a site is only covered by 454 reads, we (hopefully) detect this graciously and just emit a score of 0.0 for the site.	2010-08-04 15:23:08 +00:00
test	VariantEval now uses the "standard" modules only by default. You can add other modules with the -E argument and not use all of the standard ones with -noStandard (they can be added back individually with -E).	2010-08-03 16:51:10 +00:00