sketch ... --name is not documented in CLI help

[mr-eyes]

sourmash sketch dna --help, does not have --name parameter to give a specific name to the signature. Probably with other sketching modes.

[ctb]

well, sort of? -h shows:

File handling options:
  -f, --force           recompute signatures even if the file exists
  -o OUTPUT, --output OUTPUT
                        output computed signatures to this file
  --merge FILE, --name FILE
                        merge all input files into one signature file with the
                        specified name

it's caused confusion in the past as well, so maybe we can improve things, but it is there :)

It's also in the sourmash sketch docs -

First, you can use --name/--merge to build
a single (named) sketch out of multiple input files:

sourmash sketch dna -p k=31 sample_R1.fq.gz sample_R2.fq.gz \
    --name "sample" -o sample.zip

Here you need to specify a name because sourmash does not pick a default
name when given multiple files; you also need to provide an output file
name because sourmash doesn't pick a default output name in this situation.

Second, you can stream the input files into sourmash sketch via stdin:

gunzip -c sample_R?.fq.gz | sourmash sketch dna -p k=31 - \
    -o sample.zip

As above, you need to specify an output filename because sourmash
can't guess a good default for streaming input. The --name option
can still be specified if you want to name the output sketch something
other than -.

Thoughts as to how to improve things -

• we could put --name before --merge in the argparse output;
• we could add a section in the sourmash sketch docs that is explicitly about naming sketches;
• we could also add something to the internals document talking about how signature names are output by the sourmash CLI;

[ctb]

as of today's release of sourmash v4.8.9, --name is more prominent in sourmash sketch CLI help.