oxbow.from_bam

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oxbow.from_bam#

oxbow.from_bam(source: str | Path | Callable[[], IO[bytes] | str], compression: Literal['bgzf', None] = 'bgzf', *, fields: Literal['*'] | list[str] | None = '*', tag_defs: list[tuple[str, str]] | None = None, coords: Literal['01', '11'] = '11', regions: str | list[str] | None = None, index: str | Path | Callable[[], IO[bytes] | str] | None = None, batch_size: int = 131072) → BamFile#

Create a BAM file data source.

Changed in version 0.7.0: The tag_scan_rows parameter was removed and tag definitions are no longer discovered by default. The tag_defs parameter now defaults to omitting tag definitions (None). To perform tag discovery, use the with_tags() method on the returned data source, which accepts a scan_rows parameter to control how many records are scanned.

Parameters:

  • source (str, pathlib.Path, or Callable) – The URI or path to the BAM file, or a callable that opens the file as a file-like object.

  • compression (Literal["bgzf", None], default: "bgzf") – Compression of the source bytestream. By default, BAM sources are assumed to be BGZF-compressed. If None, the source is assumed to be uncompressed. For more custom decoding, provide a callable source instead.

  • fields (list[str] or "*", optional [default: "*"]) – Standard SAM fields to include. By default, all standard fields are included.

  • tag_defs (list[tuple[str, str]], optional [default: None]) – Definitions for tags to project. These will be nested in a “tags” column. If None, tag definitions are omitted. To discover tag definitions, use the with_tags() method on the returned data source.

  • regions (str | list[str], optional) – One or more genomic regions to query. Only applicable if an associated index file is available.

  • index (str, pathlib.Path, or Callable, optional) – An optional index file associated with the BAM file. If source is a URI or path, is BGZF-compressed, and the index file shares the same name with a “.tbi” or “.csi” extension, the index file is automatically detected.

  • batch_size (int, optional [default: 131072]) – The number of records to read in each batch.

Returns:

A data source object representing the BAM file.

Return type:

BamFile

Notes

Binary Alignment Map (BAM) is a binary representation of SAM files.

See also

from_sam

Create a SAM file data source.

from_cram

Create a CRAM file data source.

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