class ApproximateMatcher:
def __init__(self, target):
self._text = target + '$'
self._bwt = BWT(self._text)
# return indices in target that contain
# matches of string pattern with up to d
# mismatches
def get_matches(self, pattern, d):
# initialze seed and check object
seed_checker = SeedChecker(pattern, d)
# for each seed k-mer in pattern
for seed, seed_index in seed_checker.enumerate():
# find exact matches of seed using BWT
indices = self._bwt.get_matches(seed)
# add candidate approximate matches based on
# seed exact matches
seed_checker.add_candidates(indices, seed_index)
# verify that candidate approximate matches are within
# minimum edit distance, and return final matches
matches = seed_checker.filter_candidates(self._text)
return matches
class ApproximateMatcher:
def __init__(self, target):
self._text = target + "$"
self._bwt = BWT(self._text)
# return indices in target that contain
# matches of string pattern with up to d
# mismatches
def get_matches(self, pattern, d):
# initialze seed and check object
seed_checker = SeedChecker(pattern, d)
# for each seed k-mer in pattern
for seed, seed_index in seed_checker.enumerate():
# find exact matches of seed using BWT
indices = self._bwt.get_matches(seed)
# add candidate approximate matches based on
# seed exact matches
seed_checker.add_candidates(indices, seed_index)
# verify that candidate approximate matches are within
# minimum edit distance, and return final matches
matches = seed_checker.filter_candidates(self._text)
return matches
