Different score for insertion and deletion?

[y9c]

Is it possible to set different score for insertion and deletion?

[smarco]

I assume you are talking about gap-linear alignment? For the moment, no. The library is slowly incorporating all the features that are planned on the roadmap. If people ask for it, I will implement the asymmetrical version (it is an easy feature to provide).

[y9c]

Thank you for the reply. I would like to if this feature is on the roadmap?

[y9c]

Hi @smarco,

I would like to know if it is also not possible to set different score for insertion and deletion in gem3-mapper?

[smarco]

In that case, gap-affine is almost always formulated using {M,X,O,E}, where: M Match Score X Mismatch Penalty O Gap-Opening Penalty E Gap-Extension Penalty

So, again, it is symmetric. Sorry.

PS. It is possible, just not implemented.

[y9c]

Thanks. Will it be implemented in the future?

[smarco]

In the WFA, very likely (for gap-linear).

In the GEM, unlikely. At the moment, I don't have enough time to go back to GEM3 and re-implement that part. In the long term, it is very likely. I would love to use the WFA within the GEM.

[y9c]

cool. thanks

On Sun, Apr 3, 2022, 02:05 Santiago Marco-Sola @.***> wrote:

In the WFA, very likely (for gap-linear).

In the GEM, unlikely. At the moment, I don't have enough time to go back to GEM3 and re-implement that part. In the long term, it is very likely. I would love to use the WFA within the GEM.

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