kiran f3b38c0d3e Fixed a bug in my math where I assumed the genotype likelihoods were normalized to 1.0 when they in fact are not. *Now* genotypes get altered when a different genotype configuration leads to a more consistent answer with regards to inheritance constraints. There's the question of what to do when two configurations are almost equally likely - I should probably filter those events out. But currently there is no threshold on the transmission probability. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5901 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-27 22:08:05 +00:00
..
config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Fixed a bug in my math where I assumed the genotype likelihoods were normalized to 1.0 when they in fact are not. *Now* genotypes get altered when a different genotype configuration leads to a more consistent answer with regards to inheritance constraints. There's the question of what to do when two configurations are almost equally likely - I should probably filter those events out. But currently there is no threshold on the transmission probability.	2011-05-27 22:08:05 +00:00
test	We now skip over all covering RODs in the BQSR as intended instead of just those which can be converted into a VariantContext. All the integration tests change because of subtleties in how certain dbsnp rod records are being converted into VCs. Added integration test which uses a bed file as the list of known polymorphic sites.	2011-05-27 16:32:17 +00:00