provide sensible default signature names for sourmash sig intersect

[ctb]

right now, many of the sig subcommands don't explicitly name the output signatures. Maybe this should change where sensible names can be inferred?

see discussion in #1171 (comment)

[taylorreiter]

could we add the --name parameter to the command line? I don't dislike the default name, but it would be nice to set the name manually.

[ctb]

two or three thoughts -

sure, it's easy enough :). but why not use sourmash sig merge ... | sourmash sig rename?

Probably part of the problem is that --name isn't part of the set of options that work by default across all of the sourmash sig commands. If we put in the effort to add it to sourmash sig merge we should consider (a) what other good default options there should be and (b) implementing them in a "standard" way for all of the sig subcommands, somewhat like we've done with -q/--quiet, -k, and the molecule ypes.

Another part of the problem is that the default naming scheme is kinda not good here; it just names it the md5sum. Maybe instead of choosing the default we could print out something helpful like naming it default; use --name to set the name.

[taylorreiter]

I was mostly just surprised that I got an error with --name using sourmash sig intersect; seems like there is more to consider than just adding the param. I guess rename is fine for this, a little annoying to have two steps but better then not having any options :)

[ctb]

Diving into this a little - some fun facts.

• sig merge takes --name as an argument to name the merged signature.
• sig extract, sig filter, and sig flatten take --name arguments that select the signatures to operate on. I don't know if we've ever used this. Might be good to change it up to use some of the other sig selection mechanisms (but, major version change) or eliminate it since sig grep supports a more flexible signature selection mechanism anyway;
• I think sig inflate, sig filter, sig downsample, and sig flatten keep the signature name from the signature they're operating on; double check this and make sure it's tested!

So candidates for a --name or --rename argument (joining sig merge) are:

• sig intersect
• sig subtract

which is frankly much simpler than I was expecting.

[ctb]

sig intersect and sig subtract support --set-name as of today's release of sourmash v4.8.9.