agshumate/Liftoff

-f flag broken in v1.5.0?

Closed this issue · 2 comments

pkerpedjiev commented

I just upgraded to v1.5.0 but when I run the following command:

liftoff -g hg38.refGene.short.gtf.gz -f feature_types.txt chm13.draft_v1.0.fasta.bgz hg38.fa.bgz

I get a GFF does not contain any gene features. Use -f to provide a list of other feature types to lift over. error.

When I downgrade back to v1.4.2, it starts running as usual (albeit with the running time issue). Anything change related to that flag?

agshumate commented

Hi there, thanks for submitting this issue - it does look like the -f flag broke in 1.5.0 with gtf files only. i fixed the problem in 1.5.1 so you can upgrade to this version or use a gff3 file with 1.5.0

pkerpedjiev commented

Thank you for the quick response! And sorry about the duplicate issue. I must have hit submit and then gone back to edit the formatting and hit submit again.