bamstats not working with Ensembl GTF (with "gene_biotype" attribute)

[usergsc]

Ensembl GTFs have "gene_biotype", instead of "gene_type", attribute.
ftp://ftp.ensembl.org/pub/release-102/gtf/homo_sapiens.

This affects the calculation of fraction_rrna in the bamstats program, if nothing else.

[emi80]

Hi @usergsc,

thanks for reporting this.

A possible fix would be using a list of attributes when detecting rRNA genes in the annotation. The list would include both gene_type and gene_biotype (in order) and use the first one available from each entry.

Best,
Emilio

[usergsc]

Hi Emilio,

It would be helpful if the list of expected GTF attributes are listed in the README file, so users are aware of the requirements, and can update their GTF files if necessary.