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Penalize indels more #604

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marcelm opened this issue Mar 4, 2022 · 0 comments · Fixed by #608
Closed

Penalize indels more #604

marcelm opened this issue Mar 4, 2022 · 0 comments · Fixed by #608

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@marcelm
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marcelm commented Mar 4, 2022

Indels are enabled by default, but cost the same as mismatches. This often leads to unexpected results, typically longer sequences being trimmed than expected, see #597.

We could penalize indels more, but should also re-consider whether optimizing the number of matches is the best thing to do.
marcelm added a commit that referenced this issue Mar 18, 2022
@marcelm
Penalize indels more than mismatches
cd65032 
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

See #597
Closes #604
@marcelm marcelm mentioned this issue Mar 18, 2022
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marcelm added a commit that referenced this issue Mar 23, 2022
@marcelm
Penalize indels more than mismatches
5bbdf88 
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
marcelm added a commit that referenced this issue Mar 23, 2022
@marcelm
Penalize indels more than mismatches
98e540c 
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
@arteymix arteymix mentioned this issue May 10, 2022
Closed
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Penalize indels more than mismatches marcelm/cutadapt
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@marcelm