Use Signac with annotation from gtf file

[lldelisle]

Dear Signac developpers,
I realized that signac requires that the Annotation slot gets the transcript ids stored into tx_id. While it is the case for the annotations from GetGRangesFromEnsDb, it is not the case from the import from file.
I don't know if the best place is in the code of signac or in the vignettes and/or in the man for CreateChromatinAssay but would be good to introduce a:

if (is.null(annotation$tx_id)) {
  annotation$tx_id <- annotation$transcript_id
}

I would be happy to write a PR if you tell me where you prefer.

[timoast]

If you'd like to take a shot at adding this to the gene annotation setter function I'd be happy to incorporate something like this into Signac

signac/R/objects.R

Line 862 in 0b33b11

} else if (layer == "annotation") {

[lldelisle]

See #1797