search

Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
Other
182 stars 23 forks source link

Allow lowercase bases in Refiner? #181

Open mcfrith opened 1 year ago

mcfrith commented 1 year ago

If I run Refiner (in RepeatModeler-2.0.3) like this:

./Refiner myseqs.fa I get this error message:

MultAln::buildConsensusFromArray: Matrix alphabet doesn't include
three-way IUB codes: A -> c
 at ./Refiner line 523.

This happens if there are lowercase bases in the input sequences. How about allowing lowercase (e.g. convert to uppercase on reading), or else an error message saying that uppercase is needed?

rmhubley commented 1 year ago

Good point! Thanks Martin, this will make it into the next release.