malariagen_data.ag3.Ag3.cnv_discordant_read_calls

Ag3.cnv_discordant_read_calls(contig: str | List[str] | Tuple[str, ...], sample_sets: Sequence[str] | str | None = None, sample_query: str | None = None, inline_array: bool = True, chunks: int | str | Tuple[int | str, ...] | Callable[[Tuple[int, ...]], int | str | Tuple[int | str, ...]] = 'ndauto0') → Dataset

Access CNV discordant read calls data.

Parameters

contigstr or list of str or tuple of str

Reference genome contig name. See the contigs property for valid contig names. Can also be a sequence (e.g., list) of contigs.

sample_setssequence of str or str or None, optional

List of sample sets and/or releases. Can also be a single sample set or release.

sample_querystr or None, optional

A pandas query string to be evaluated against the sample metadata, to select samples to be included in the returned data.

inline_arraybool, optional, default: True

Passed through to dask from_array().

chunksint or str or tuple of int or str or Callable[[typing.Tuple[int, …]], int or str or tuple of int or str], optional, default: ‘ndauto0’

If ‘auto’ let dask decide chunk size. If ‘native’ use native zarr chunks. If ‘ndauto’ let dask decide chunk size but only for arrays with more than one dimension. If ‘ndauto0’ as ‘ndauto’ but only vary the first chunk dimension. If ‘ndauto1’ as ‘ndauto’ but only vary the second chunk dimension. If ‘ndauto01’ as ‘ndauto’ but only vary the first and second chunk dimensions. Also, can be a target size, e.g., ‘200 MiB’, or a tuple of integers, or a callable which accepts the native chunks as a single argument and returns a valid dask chunks value.

Returns

Dataset

An xarray dataset of CNV alleles and genotypes.