allpairs_global option

[nhoffman]

Hello, very excited to see this project. If you are taking requests for usearch features, I would personally find the allpairs_global option useful. See http://www.drive5.com/usearch/manual/allpairs_global.html Thanks!

[torognes]

Thanks for your suggestion. We will consider adding this feature.

[torognes]

The new allpairs_global option is now implemented. It performs optimal global alignment of all pairs of sequences in the specified file. It uses no heuristics and is multi-threaded. It reports all alignments when the --acceptall option is specified, otherwise use the --id option and other accept/reject options.

[nhoffman]

Many thanks!

[torognes]

I hope it works as it should. As it performs an optimal alignment for all pairs of sequences it may be slower than usearch in some cases, but in return you are guaranteed the optimal alignment for all. Also, it's multi-threaded. Please report any problems you may encounter.

[frederic-mahe]

I've tested all options. Everything works correctly, except the --acceptall option:

vsearch --allpairs_global tmp.fas --acceptall --userout tmp.userout
vsearch v1.0.4_linux_x86_64, 15.6GB RAM, 4 cores

Fatal error: Specify either --acceptall or --id with an identity from 0.0 to 1.0

I've tried all possible combination of --acceptall and output options, none of them works.

I was also wondering if the --sizein option should be accepted too? It would shorten the sequence identifiers in output files.

[torognes]

Sorry for that bug. Resolved in 1.0.5.

[torognes]

How should the --sizein option work in this case. I do not understand.