Custom alpha best support in meme-4.11.0 -- Implications/Regression

[Saket Choudhary]

With the version 4.11.0, it seems MEME supports custom alphabets as motifs.

However, this creates a distinct regression from previous meme releases, in the context of repeat-masked sequences.

The Changelog does indicate support for custom alphabets.

However, I guess it would help to clarify that the masked sequences now appear as it is.

In the previous versions, the masked repeats were converted to uppercase IUPAC unambiguous DNA.

Here is a relevant diff, that broke my tests:

https://gist.github.com/anonymous/d704ae94235af7aa874f