ssw.alignmenttuple

Alignment data structure for ssw-py

NOTE: See this link for a info on the CIGAR format: What is a CIGAR?

class ssw.alignmenttuple.Alignment(CIGAR: str, optimal_score: int, sub_optimal_score: int, reference_start: int, reference_end: int, read_start: int, read_end: int, cigar_pair_list: List[Tuple[int, str]])[source]

Alignment namedtuple structure. Used for storing results of ssw.alignmentmgr.AlignmentMgr.align()

CIGAR: The CIGAR string

optimal_score: The optimal alignment score (SSW primary score)

sub_optimal_score: The sub-optimal alignment score (SSW secondary score)

reference_start: The reference start index

reference_end: The reference end index

read_start: The read start index

read_end: The read end index

cigar_pair_list: Convenience list of cigar length code pairs