def take(self, indices, axis=0, out=None, mode='raise', **kwargs): return take_genotypes(self, indices, axis=axis, wrap_axes={0, 1}, cls=type(self), take=_chunked.take, out=out, mode=mode, **kwargs) def subset(self, sel0=None, sel1=None, **kwargs): return subset_genotype_array(self, sel0, sel1, cls=type(self), subset=_chunked.subset, **kwargs) def concatenate(self, others, axis=0, **kwargs): return concatenate_genotypes(self, others, axis=axis, wrap_axes={0, 1}, cls=type(self), concatenate=_chunked.concatenate, **kwargs) # copy docstrings copy_method_doc(GenotypeChunkedArray.fill_masked, GenotypeArray.fill_masked) copy_method_doc(GenotypeChunkedArray.subset, GenotypeArray.subset) copy_method_doc(GenotypeChunkedArray.is_called, GenotypeArray.is_called) copy_method_doc(GenotypeChunkedArray.is_missing, GenotypeArray.is_missing) copy_method_doc(GenotypeChunkedArray.is_hom, GenotypeArray.is_hom) copy_method_doc(GenotypeChunkedArray.is_hom_ref, GenotypeArray.is_hom_ref) copy_method_doc(GenotypeChunkedArray.is_hom_alt, GenotypeArray.is_hom_alt) copy_method_doc(GenotypeChunkedArray.is_het, GenotypeArray.is_het) copy_method_doc(GenotypeChunkedArray.is_call, GenotypeArray.is_call) copy_method_doc(GenotypeChunkedArray.to_haplotypes, GenotypeArray.to_haplotypes) copy_method_doc(GenotypeChunkedArray.to_n_ref, GenotypeArray.to_n_ref) copy_method_doc(GenotypeChunkedArray.to_n_alt, GenotypeArray.to_n_alt) copy_method_doc(GenotypeChunkedArray.to_allele_counts, GenotypeArray.to_allele_counts) copy_method_doc(GenotypeChunkedArray.to_packed, GenotypeArray.to_packed) # TODO # copy_method_doc(GenotypeChunkedArray.from_packed, GenotypeArray.from_packed)
out = self.apply_method('to_gt', kwargs=dict(phased=phased, max_allele=max_allele), **storage_kwargs) return _chunked.ChunkedArray(out) def map_alleles(self, mapping, **storage_kwargs): def f(block, bmapping): return block.map_alleles(bmapping, copy=False) domain = (self, mapping) out = _chunked.apply(domain, f, **storage_kwargs) return GenotypeChunkedArray(out) # copy docstrings copy_method_doc(GenotypeChunkedArray.fill_masked, _ndarray.GenotypeArray.fill_masked) copy_method_doc(GenotypeChunkedArray.subset, _ndarray.GenotypeArray.subset) copy_method_doc(GenotypeChunkedArray.is_called, _ndarray.GenotypeArray.is_called) copy_method_doc(GenotypeChunkedArray.is_missing, _ndarray.GenotypeArray.is_missing) copy_method_doc(GenotypeChunkedArray.is_hom, _ndarray.GenotypeArray.is_hom) copy_method_doc(GenotypeChunkedArray.is_hom_ref, _ndarray.GenotypeArray.is_hom_ref) copy_method_doc(GenotypeChunkedArray.is_hom_alt, _ndarray.GenotypeArray.is_hom_alt) copy_method_doc(GenotypeChunkedArray.is_het, _ndarray.GenotypeArray.is_het) copy_method_doc(GenotypeChunkedArray.is_call,
kwargs=dict(phased=phased, max_allele=max_allele), **storage_kwargs) return _chunked.ChunkedArray(out) def map_alleles(self, mapping, **storage_kwargs): def f(block, bmapping): return block.map_alleles(bmapping, copy=False) domain = (self, mapping) out = _chunked.apply(domain, f, **storage_kwargs) return GenotypeChunkedArray(out) # copy docstrings copy_method_doc(GenotypeChunkedArray.fill_masked, _ndarray.GenotypeArray.fill_masked) copy_method_doc(GenotypeChunkedArray.subset, _ndarray.GenotypeArray.subset) copy_method_doc(GenotypeChunkedArray.is_called, _ndarray.GenotypeArray.is_called) copy_method_doc(GenotypeChunkedArray.is_missing, _ndarray.GenotypeArray.is_missing) copy_method_doc(GenotypeChunkedArray.is_hom, _ndarray.GenotypeArray.is_hom) copy_method_doc(GenotypeChunkedArray.is_hom_ref, _ndarray.GenotypeArray.is_hom_ref) copy_method_doc(GenotypeChunkedArray.is_hom_alt, _ndarray.GenotypeArray.is_hom_alt) copy_method_doc(GenotypeChunkedArray.is_het, _ndarray.GenotypeArray.is_het) copy_method_doc(GenotypeChunkedArray.is_call, _ndarray.GenotypeArray.is_call) copy_method_doc(GenotypeChunkedArray.to_haplotypes, _ndarray.GenotypeArray.to_haplotypes) copy_method_doc(GenotypeChunkedArray.to_n_ref, _ndarray.GenotypeArray.to_n_ref)
return self._method_drop_axis2('to_gt', phased=phased, max_allele=max_allele) def to_haplotypes(self): out = self.reshape(self.shape[0], -1) return view_subclass(out, HaplotypeDaskArray) def to_n_ref(self, fill=0, dtype='i1'): return self._method_drop_axis2('to_n_ref', fill=fill, dtype=dtype) def to_n_alt(self, fill=0, dtype='i1'): return self._method_drop_axis2('to_n_alt', fill=fill, dtype=dtype) # copy docstrings copy_method_doc(GenotypeDaskArray.fill_masked, _ndarray.GenotypeArray.fill_masked) copy_method_doc(GenotypeDaskArray.subset, _ndarray.GenotypeArray.subset) copy_method_doc(GenotypeDaskArray.is_called, _ndarray.GenotypeArray.is_called) copy_method_doc(GenotypeDaskArray.is_missing, _ndarray.GenotypeArray.is_missing) copy_method_doc(GenotypeDaskArray.is_hom, _ndarray.GenotypeArray.is_hom) copy_method_doc(GenotypeDaskArray.is_hom_ref, _ndarray.GenotypeArray.is_hom_ref) copy_method_doc(GenotypeDaskArray.is_hom_alt, _ndarray.GenotypeArray.is_hom_alt) copy_method_doc(GenotypeDaskArray.is_het, _ndarray.GenotypeArray.is_het) copy_method_doc(GenotypeDaskArray.is_call,