def to_allele_counts(self, alleles=None, **storage_kwargs):
# determine alleles to count
if alleles is None:
m = self.max()
alleles = list(range(m + 1))
out = self.apply_method('to_allele_counts',
kwargs=dict(alleles=alleles),
**storage_kwargs)
return _chunked.ChunkedArray(out)
def mask(self, mask):
# check input
if not hasattr(mask, 'shape'):
mask = np.asarray(mask)
if mask.shape != self.shape[:2]:
raise ValueError('mask has incorrect shape')
# store
self._mask = _chunked.ChunkedArray(mask)
def is_doubleton(self, allele=1, **storage_kwargs):
out = self.apply_method('is_doubleton',
kwargs=dict(allele=allele),
**storage_kwargs)
return _chunked.ChunkedArray(out)
def is_non_segregating(self, allele=None, **storage_kwargs):
out = self.apply_method('is_non_segregating',
kwargs=dict(allele=allele),
**storage_kwargs)
return _chunked.ChunkedArray(out)
def is_segregating(self, **storage_kwargs):
out = self.apply_method('is_segregating', **storage_kwargs)
return _chunked.ChunkedArray(out)
def is_non_variant(self, **storage_kwargs):
out = self.apply_method('is_non_variant', **storage_kwargs)
return _chunked.ChunkedArray(out)
def max_allele(self, **storage_kwargs):
out = self.apply_method('max_allele', **storage_kwargs)
return _chunked.ChunkedArray(out)
def allelism(self, **storage_kwargs):
out = self.apply_method('allelism', **storage_kwargs)
return _chunked.ChunkedArray(out)
def to_frequencies(self, fill=np.nan, **storage_kwargs):
out = self.apply_method('to_frequencies',
kwargs=dict(fill=fill),
**storage_kwargs)
return _chunked.ChunkedArray(out)
def to_gt(self, phased=False, max_allele=None, **storage_kwargs):
out = self.apply_method('to_gt',
kwargs=dict(phased=phased,
max_allele=max_allele),
**storage_kwargs)
return _chunked.ChunkedArray(out)
def to_packed(self, boundscheck=True, **storage_kwargs):
out = self.apply_method('to_packed',
kwargs=dict(boundscheck=boundscheck),
**storage_kwargs)
return _chunked.ChunkedArray(out)
def to_n_alt(self, fill=0, dtype='i1', **storage_kwargs):
out = self.apply_method('to_n_alt',
kwargs=dict(fill=fill, dtype=dtype),
**storage_kwargs)
return _chunked.ChunkedArray(out)
