args.aligner_choice error when running with -g option about sqanti2

[hvbakel]

After initializing args.aligner_choice to an empty string, sqanti_qc2.py will keep running, but it breaks again after cleaning the isoform IDs (which it should not do for a provided gtf file). It looks like the --gtf parameter is broken altogether.

[Magdoll]

Hi @hvbakel ,

You are right args.gtf is not implemented. I'll look into whether I should support it (it was supported in the original SQANTI) or I should remove the parameter. Thank you for notifying.

--Liz

[Magdoll]

I decided that for the moment I will not be supporting --gtf.

[hvbakel]

Ok understood. Will try to make our isoseq pipeline work with the isoform fasta instead.

Just a quick note, since yesterday's commit, the squanti2 pipeline is failing on "from BED import LazyBEDPointReader". I'm guessing it's a new function not yet committed in the cDNA_cupcake repo?

[Magdoll]

Thank you for pointing out the BED.py dependency failure. I have just updated the cDNA_Cupcake repo.