Penalize indels more than mismatches #608
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Any updates on this PR? Love the way it penalizes different cases: I found CI fails and has not merged successfully. Is this because cutadapt has dropped support for python 3.6? |
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The algorithm isn’t quite finished. See the To Do above: It’s not guaranteed that the leftmost match is found if there are multiple occurrences of the adapter. Please have some patience. I will continue work on this when I have time. |
This changes the method for choosing the best alignment. While previously, only the number of matches in the alignment counted, with this change, the score of the alignment decides. Scores at the moment are: matches +1, mismatches -1, indels -2 Also, the leftmost alignment is now chosen somewhat more reliably. See #597 Closes #604
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This changes the method for choosing the best alignment (among those that are within the allowed error rate).
While previously, only the number of matches in the alignment counted, with this change, the score of the alignment decides.
Scores at the moment are: matches +1, mismatches -1, indels -2
See #597
Closes #604
To Do