missing userfields options

[frederic-mahe]

As a follow-up on issue #545, here is a list of --userfields options available in usearch (see userfields), but not in vsearch.

Starting with the most important, in my opinion:

diffs 	  	Number of differences (gaps + mismatches).
mid 	  	Fraction of letter pairs that match.
qseq 	  	Full-length query sequence.
tseq 	  	Full-length target sequence.
qrowdots 	Aligned query segment with gaps and dots for matched positions.
trowdots 	Aligned target segment with gaps and dots for matched positions.

These other options are less important, or are specific to commands not yet available in vsearch:

abskew 	  	Abundance skew.
clusternr 	Cluster number.
qlor 	  	0-based query start coordinate.
qhir 	  	0-based query end coordinate.
tlor 	  	0-based target start coordinate.
thir 	  	0-based target end coordinate.
orflo 	  	Start coordinate of query ORF in nt sequence.
orfhi 	  	End coordinate of query ORF in nt sequence.
orfframe 	Frame of query ORF.

[gbbio]

Is this still on the roadmap? (Just curious to know)

[frederic-mahe]

Yes @gbbio this is still on the roadmap but with a low priority. If you miss a userfield in particular, please tell us which one. If it's easy to implement, maybe it can be included in the next vsearch release.

[gbbio]

For me it would be the full length sequences. The other ones are fairly easy to generate myself with some python code. Thanks for the reply!