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Fix for dask to_allele_counts #266

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merged 4 commits into from May 31, 2019
Merged

Fix for dask to_allele_counts #266

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6e81b5f
Fix for dask to_allele_counts
May 30, 2019
9a33d47
fix long lines
alimanfoo May 31, 2019
4744b34
add #266 release note
alimanfoo May 31, 2019
b7da015
remove trailing whitespace
alimanfoo May 31, 2019
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11 changes: 6 additions & 5 deletions allel/model/dask.py
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Expand Up @@ -318,7 +318,7 @@ def __getitem__(self, item):
return index_genotype_array(self, item, array_cls=type(self),
vector_cls=GenotypeDaskVector)

def _method(self, method_name, chunks=None, drop_axis=None, dtype=None, **kwargs):
def _method(self, method_name, chunks=None, drop_axis=None, new_axis=None, dtype=None, **kwargs):
if chunks is None:
# no shape change
chunks = self.chunks
Expand All @@ -330,7 +330,7 @@ def f(block):
g = array_cls(block)
method = getattr(g, method_name)
return method(**kwargs)
out = da.map_blocks(f, self.values, drop_axis=drop_axis, dtype=dtype)
out = da.map_blocks(f, self.values, chunks=chunks, drop_axis=drop_axis, new_axis=new_axis, dtype=dtype)

else:
# map with mask
Expand All @@ -340,7 +340,7 @@ def f(block, bmask):
method = getattr(g, method_name)
return method(**kwargs)
m = self.mask[:, :, np.newaxis]
out = da.map_blocks(f, self.values, m, drop_axis=drop_axis, dtype=dtype)
out = da.map_blocks(f, self.values, m, chunks=chunks, drop_axis=drop_axis, new_axis=new_axis, dtype=dtype)

return out

Expand Down Expand Up @@ -439,8 +439,9 @@ def to_allele_counts(self, max_allele=None):
if max_allele is None:
max_allele = self.max().compute()[()]

chunks = (self.chunks[0], self.chunks[1], (max_allele + 1,))
out = self._method('to_allele_counts', chunks=chunks, max_allele=max_allele)
chunks = (self.chunks[0], self.chunks[1], (max_allele + 1, ))

out = self._method('to_allele_counts', chunks=chunks, max_allele=max_allele, drop_axis=2, new_axis=2)
out = GenotypeAlleleCountsDaskArray(out)
return out

Expand Down