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exact meaning of allowed_mismatches, if I read the code correctly, extension happens independently on either side of the k-mer match, and stops after allowed_mismatches in each direction. So if you specify allowed_mismatches = 1 the extended match will actually contain 2 mismatches, one on either side - which is not what one may expect at all.
whether output matches can overlap or not, if they don't overlap, will adjoining matches be merged or just border directly side-by-side?
The text was updated successfully, but these errors were encountered:
The following public function lacks a doc string:
rust-bio/src/alignment/sparse.rs
Line 398 in 43d198e
Some important questions to answer:
allowed_mismatches
, if I read the code correctly, extension happens independently on either side of the k-mer match, and stops afterallowed_mismatches
in each direction. So if you specifyallowed_mismatches = 1
the extended match will actually contain 2 mismatches, one on either side - which is not what one may expect at all.The text was updated successfully, but these errors were encountered: