Update likelihood code to handle non-uniform allelic mixtures

hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly

Apache License 2.0

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Update likelihood code to handle non-uniform allelic mixtures #571

Closed arahuja closed 7 years ago

arahuja commented 7 years ago

This PR contains the following changes:

Misc updates from the code review on #568
Changes Genotype from a collection of alleles to a map of Allele -> Allele Fraction
Updates Likelihood.scala and LikelihoodSuite.scala to handle this

This change is

coveralls commented 7 years ago

Coverage increased (+0.4%) to 75.589% when pulling 0dedb7ef408d40871abb7811e3d8f236d3826fd9 on somatic-standard-upgrades into 5924d60efc0ac6cf28c0486ef628ffbd5e4c7b5d on master.

ryan-williams commented 7 years ago

lgtm modulo adding a comment per above, and also some tweaks I sent in #574, which you can incorporate here or which I can pull out as a separate PR, uty!

coveralls commented 7 years ago

Coverage increased (+0.4%) to 75.545% when pulling c79d6150214e741af6be669b92669208428366f3 on somatic-standard-upgrades into ec529d58eece5d93445be772cb7b36d2425cf887 on master.

coveralls commented 7 years ago

Coverage increased (+0.4%) to 75.545% when pulling c79d6150214e741af6be669b92669208428366f3 on somatic-standard-upgrades into ec529d58eece5d93445be772cb7b36d2425cf887 on master.