oxbow.read_sam

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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.

  • region (str) – Genomic range string in the format “chr:start-end”, “chr:[start,end]” or “chr:[start,end)”.

  • 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

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