malariagen_data.af1.Af1.haplotype_sites#

Af1.haplotype_sites(region: str | Region | Mapping | List[str | Region | Mapping] | Tuple[str | Region | Mapping, ...], field: str, analysis: str = 'default', inline_array: bool = True, chunks: str | Tuple[int, ...] | Callable[[Tuple[int, ...]], Tuple[int, ...]] = 'native') Array#

Access haplotype site data (positions or alleles).

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.

fieldstr

Name of array or column to access.

analysisstr, optional, default: ‘default’

Which haplotype phasing analysis to use. See the phasing_analysis_ids property for available values.

inline_arraybool, optional, default: True

Passed through to dask from_array().

chunksstr or tuple of int or Callable[[typing.Tuple[int, …]], 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 either SNP positions (“POS”), reference alleles (“REF”) or alternate alleles (“ALT”).