--reference sometimes accepts filename and sometimes chrID

[mmokrejs]

Hi, I find it puzzling the --reference sometimes accepts ID of the reference record in the msa, I suggest the flag to be renamed. Other gofasta commands expect a filename after it so it is easy to misunderstand this.

$ ./gofasta variants -a 7-WU-FF1.gff -r 7-WU-FF1.fasta --msa 7-WU-FF.fa
Error: Couldn't find reference (7-WU-FF1.fasta) in msa
Usage:
  gofasta variants [flags]

Flags:
      --msa string          Multiple sequence alignment in fasta format (default "stdin")
  -r, --reference string    The ID of the reference record in the msa
  -a, --annotation string   Genbank or GFF3 format annotation file. Must have suffix .gb or .gff
  -o, --outfile string      Name of the file of variants to write (default "stdout")
      --start int           Only report variants after (and including) this position (default -1)
      --end int             Only report variants before (and including) this position (default -1)
      --aggregate           Report the proportions of each change
      --threshold float     If --aggregate, only report changes with a freq greater than or equal to this value
      --append-snps         Report the codon's SNPs in parenthesis after each amino acid mutation
  -t, --threads int         Number of threads to use (default 1)
  -h, --help                help for variants

$ ./gofasta variants -a 7-WU-FF1.gff -r 7-WU-FF --msa 7-WU-FF.fa
Error: Error parsing gff SeqID: 7-WU-FF
Usage:
  gofasta variants [flags]

Flags:
      --msa string          Multiple sequence alignment in fasta format (default "stdin")
  -r, --reference string    The ID of the reference record in the msa
  -a, --annotation string   Genbank or GFF3 format annotation file. Must have suffix .gb or .gff
  -o, --outfile string      Name of the file of variants to write (default "stdout")
      --start int           Only report variants after (and including) this position (default -1)
      --end int             Only report variants before (and including) this position (default -1)
      --aggregate           Report the proportions of each change
      --threshold float     If --aggregate, only report changes with a freq greater than or equal to this value
      --append-snps         Report the codon's SNPs in parenthesis after each amino acid mutation
  -t, --threads int         Number of threads to use (default 1)
  -h, --help                help for variants

[benjamincjackson]

I guess this was a bit silly in retrospect, but as gofasta is now at version > 1.0.0, I don't want to introduce breaking changes to the API.

[mmokrejs]

At least improving the parsing out would be helpful. Took me ages to realize the message was about ID name and not fasta filename. And still you can introduce --reference-filename and respect it in as many places as possible. How many users are there around the world?