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Alignment

pycyseq.Alignment dataclass

Wrapper class around a pysam alignment.

Parameters:

Name Type Description Default
pysam AlignedSegment

pysam.AlignedSegment object with the alignment information.

 required
direction: str property

Direction of the alignment of the read, can be 'fwd', 'rev' or 'none' if not aligned.

is_mapped: bool property

Return true if the alignment is mapped.

pysam: pysam.AlignedSegment property

The pysam.AlignmentSegment object for access to its methods. See https://pysam.readthedocs.io/en/stable/index.html for documentation.

__str__() -> str

Print the alignment coordinates and direction.