malariagen_data.af1.Af1.site_filters

Af1.site_filters(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], mask: str, field: str = 'filter_pass', inline_array: bool = True, chunks: str | Tuple[int, ...] = 'native') → Array

Access SNP 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.

maskstr

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

fieldstr, optional, default: ‘filter_pass’

Name of array or column to access.

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

Array

An array of boolean values identifying sites that pass the filters.