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Currently load_features in util.py looks for 'feature type' "CDS" and 'feature qualifier' "locus_tag" to get the gene name. For Zika this works as expected.
However, for TB, "CDS" does not contain "locus_tag" (or anything useful). Further, in "gene" (instead of CDS) the "locus_tag" is not the identifier commonly used for genes (ex: gene='dnaA' locus_tag='Rv0001').

For GFF files I have modified load_features (in 'vcf' branch) so that looks for 'gene' and 'gene' instead of 'CDS' and 'locus_tag'. However, for avian influenza Genbank files, the combination should be 'CDS' and 'gene' (this returns the expected PB2, HA, NA, etc).

We should probably either look to see if there is a general rule (or two) we can put in place to ensure we're always getting the common gene names, or we should consider turning this into an option of some kind for users to specify.

In util.py load_features, for VCF files, it now takes 'gene' as the name if it is specified, and 'locus_tag' if it is not. If no gene-list has been given by the user, this ensures that all genes are read. Similarly, if a gene-list has been specified, and user has named each gene by the 'gene' name if it has one (in the .gff file), and only used 'locus_tag' if it does not, this will find all genes.

However, if the user species a gene by 'locus_tag' even though it has a 'gene' name in the .gff file, it currently will not be included, as 'locus_tag' is only used if 'gene' is absent. If a gene list has been specified, we should check both fields so that users can specify either way.