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Return genotype probabilities and dosages #15
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tomwhite
approved these changes
Aug 25, 2020
sgkit_bgen/bgen_reader.py
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| @@ -107,15 +107,27 @@ def __getitem__(self, idx): | |||
| raise IndexError( # pragma: no cover | |||
| f"Indexer must be two-item tuple (received {len(idx)} slices)" | |||
| ) | |||
| if not all(isinstance(i, slice) or isinstance(i, int) for i in idx): | |||
| raise IndexError( # pragma: no cover | |||
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#13
This modifies
read_bento return both probabilities and dosages.It also includes a fix for the incorrect handling of scalar indexes (which happens if any chunk is of size 1) as well as fancy indexing (using
from_array(..., fancy=False)).FYI: The build won't work until https://github.com/pystatgen/sgkit/pull/137 goes through, but this is still ready for review.