Feature binary traits

[HolEv]

dense_gt.py:

• don't transform phenotypes if there are only two distinct values (i.e., it's a binary phenotype because association testing functions cannot handle the transformed values).

deeprvat/associate.py:

• run ScoretestNoK on quantitative traits (!= 2 distinct y values) and ScoretestLogit on binary traits (2 distinct y values).
• Account for the fact that ScoretestLogit doesn't return betas

seed_gene_discovery/seed_gene_discovery.py:

• run ScoretestNoK on quantitative traits (!= 2 distinct y values) and ScoretestLogit on binary traits (2 distinct y values).
• Account for the fact that ScoretestLogit doesn't return betas
• fix in recording of timing
• fix in dropping of duplicates of exploded annotations data frame (reset index (variant id) before dropping duplicates)
• implement and use collapsing of ultra rare variants in SKAT tests

seed_gene_discovery/seed_gene_discovery.snakefile:

• distinct roules for regression of missense/plof tests to optimise resource usage