malariagen_data.af1.Af1.snp_variants

Af1.snp_variants(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], site_mask: str | None = None, inline_array: bool = True, chunks: str | Tuple[int, ...] = 'native')

Access SNP sites and site filters.

Parameters

regionstr or Region or Mapping or list of str or Region or Mapping or tuple of str or Region or Mapping

Region of the reference genome. Can be a contig name, region string (formatted like “{contig}:{start}-{end}”), or identifier of a genome feature such as a gene or transcript. Can also be a sequence (e.g., list) of regions.

site_maskstr or None, optional

Which site filters mask to apply. See the site_mask_ids property for available values.

inline_arraybool, optional, default: True

Passed through to dask from_array().

chunksstr or tuple of int, optional, default: ‘native’

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. Also, can be a target size, e.g., ‘200 MiB’, or a tuple of integers.

Returns

A dataset containing SNP sites and site filters.