How to prevent abjoin from automatically filtering out trivial matches?

[ralgond]

I found stumpy has an option to enable "trivial match", so does the SCAMP has the similar options?

thank you.

[zpzim]

In SCAMP, abjoins do not filter out "trivial matches" by default because it is the assumption that an abjoin is running on two distinct sequences.

There is an option in the CLI to enable an exclusion zone for abjoins in the case that the sequences are not fully distinct: --aligned

https://scamp-docs.readthedocs.io/en/latest/cli.html#advanced-optional-arguments

This option is not exposed in pyscamp, but shouldn't be difficult to enable with a PR.