no structure annotation in stockholm file with 2.0.0RC8

[klamkiew]

Hi there,

when using mlocarna --stockholm <INPUT> with version 2.0.0RC8, the final stockholm alignment does not have the #=GC SS_cons annotation. I did the same command with version 1.9.2.1 and 1.9.2.3, and in both cases the annotation line was present.

For 2.0.0RC8, I have to explicitly call mlocarna --stockholm --consensus-structure alifold <INPUT> in order to get the same behavior. I was not able to see from the release note / manual, whether this is intended, thus I created this issue.

Greetings from Jena!
Kevin

[s-will]

Thanks for pointing this out. I intentionally deactivated the computation by default, since it can take significant time especially for large alignments. Unfortunately, this info is 'hidden' in the ChangeLog. Indeed, --consensus-structure alifold gets the annotation back.