group with `--per-contig` unnecessarily requires gene tags

[mfansler]

The --per-contig flag requires the --per-gene flag, and if outputting a TSV, ends up in this branch of the code:

https://github.com/CGATOxford/UMI-tools/blob/a5b348993cd220c32a524cf77155c8e42c89a3e1/umi_tools/group.py#L287-L291

This results in an error if there are no gene tags. I believe this is unnecessary because the --per-contig flag already entails that gene should be equated to the contig. Namely, we could instead handle the case like:

  if options.tsv:
    if options.per_gene:
      if options.per_contig:
        gene = read.reference_name
      else:
        gene = read.get_tag(gene_tag)
    else:
      gene = "NA"

[IanSudbery]

I agree. @TomSmithCGAT ?

[TomSmithCGAT]

Completely agree. From the commits, it looks this code section was not updated when the --per-contig option was added.

Thanks very much @mfansler. Do you want to issue a PR so your contribution is properly attributed?

[mfansler]

@TomSmithCGAT sounds good. Yes, happy to put a PR together.

[akmorrow13]

fixed with https://github.com/CGATOxford/UMI-tools/pull/577

[mfansler]

@akmorrow13 thanks! Lost track of this one 😬