To prevent generation of empty *Counts-withNames.txt files, get_geneids.py should fallback to using whatever IDs are in the featureCounts CSV if the script fails to extract the the 'nice' IDs from the GTF/GFF. This way we always get a Degust-compatible counts file even if it doesn't have ideal transcript/gene names.
To prevent generation of empty
*Counts-withNames.txtfiles,get_geneids.pyshould fallback to using whatever IDs are in thefeatureCountsCSV if the script fails to extract the the 'nice' IDs from the GTF/GFF. This way we always get a Degust-compatible counts file even if it doesn't have ideal transcript/gene names.