arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
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clarify autosomal_recessive naming/definition #774

Open jxchong opened 8 years ago

jxchong commented 8 years ago

This has been bugging me for the last 3 years but, technically the autosomal_recessive function is really doing a homozygous_recessive analysis. autosomal_recessive should equal comp_het + homozygous_recessive. I imagine it's probably too late to rename the function, but is there any way to reword the documentation to make this distinction clear and that the function is named this way for legacy reasons?

(In an ideal world an autosomal_recessive function would simultaneously identify candidate genes that contain either homozygous recessive variants or compound het variants).

jxchong commented 7 years ago

Or perhaps make an aliased command "homozygous_recessive" that runs autosomal_recessive?

brentp commented 7 years ago

I think the simplest thing is to clarify the docs.