Prepare bug with lowercase bases

[swarbred]

From memory we had a previous issue with lowercase bases in the input, if so then it has returned

The attached test.gtf has the following splice sites

NC_037283.1:200919-201095(-) gt ag
NC_037283.1:201282-201445(-) GT ag
NC_037283.1:201512-201775(-) gt ag
NC_037283.1:203421-203569(-) gt ag

i.e. all are canonical

however running mikado prepare on this gtf and attached NC_037283.1.fa file results in no transcripts in the prepare gtf, rerunning with --lenient and this model is output marked as having no canonical introns.

If the NC_037283.1.fa file is converted to uppercase then prepare functions correctly i.e. all introns are regarded as canonical so the issue is with having lowercase bases (commonly used for softmasking)

test.gtf.zip
NC_037283.1.fa.zip