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lines changed Original file line number Diff line number Diff line change @@ -578,7 +578,16 @@ def parse_sa_tag(tag: str) -> List["SupplementaryAlignment"]:
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@classmethod
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def from_read (cls , read : pysam .AlignedSegment ) -> List ["SupplementaryAlignment" ]:
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- """Returns a list of SupplementaryAlignments for a given pysam.AlignedSegment."""
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+ """
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+ Construct a list of SupplementaryAlignments from the SA tag in a pysam.AlignedSegment.
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+
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+ Args:
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+ read: An alignment. The presence of the "SA" tag is not required.
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+
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+ Returns:
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+ A list of all SupplementaryAlignments present in the SA tag.
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+ If the SA tag is not present, or it is empty, an empty list will be returned.
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+ """
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if read .has_tag ("SA" ):
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sa_tag : str = cast (str , read .get_tag ("SA" ))
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return cls .parse_sa_tag (sa_tag )
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