oxbow.read_sam

oxbow.read_sam(src, region=None, index=None, fields=None, tag_defs=None, compressed=False)

Return Arrow IPC format from a SAM file.

Parameters:

• src (str or file-like) – The path to the source file or a file-like object.

• fields (str or list[str] or None, optional) – Standard SAM fields to project.

• tag_defs (list[tuple[str, str]], optional) – Tag definitions. None means no tags column.

• compressed (bool, optional [default: False]) – Whether the source is BGZF-compressed.

Returns:

Arrow IPC

Return type:

bytes