Replace all missing query with mostly all missing query in get_examples_haploid

astheeggeggs / lshmm

code to run Li and Stephens

MIT License

4 stars 3 forks source link

Replace all missing query with mostly all missing query in get_examples_haploid #46

Closed szhan closed 4 months ago

szhan commented 4 months ago

In get_examples_haploid in lsbase.py, the example query query_miss_all in which the entire query is MISSING is not added to the list queries, which is output and passed to tests. It should a quick and easy fix.

szhan commented 4 months ago

I think it is better to replace this pathological case of a query consisted of only MISSING with a less pathological case where all except one site is MISSING.

astheeggeggs commented 4 months ago

I agree - we should throw an error if the entirety of the query sequence is missing values too.