# Copyright (C) 2023, Nick Conway
#
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'''
ssw.alignmenttuple
~~~~~~~~~~~~~~~~~~
Alignment data structure for ssw-py
NOTE: See this link for a info on the CIGAR format:
`What is a CIGAR? <http://genome.sph.umich.edu/wiki/SAM#What_is_a_CIGAR.3F>`_
'''
from typing import (
List,
NamedTuple,
Tuple,
)
[docs]class Alignment(NamedTuple):
'''Alignment namedtuple structure. Used for storing results of
:meth:`ssw.alignmentmgr.AlignmentMgr.align`
Attributes:
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
'''
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]]
def len_cigar(self) -> int:
'''
Returns:
Number of CIGAR pairs
'''
return len(self.cigar_pair_list)
def get_cigar_values(self, idx: int) -> Tuple[int, str]:
'''Fetch CIGAR value at an index in the CIGAR string
Args:
idx: Index to fetch
Returns:
Tuple of the form:
<CIGAR length>, <CIGAR code>
'''
return self.cigar_pair_list[idx]
def pprint(self):
print(
'Alignment(\n'
f' CIGAR={self.CIGAR}\n'
f' optimal_score={self.optimal_score}\n'
f' sub_optimal_score={self.sub_optimal_score}\n'
f' reference_start={self.reference_start}\n'
f' reference_end={self.reference_end}\n'
f' read_start={self.read_start}\n'
f' read_end={self.read_end}\n'
f' cigar_pair_list={self.cigar_pair_list}\n'
')',
)