track config should take precedence of trackline

[paul-shannon]

With this config:

   var config = {format: "bed",
                 name: trackName,
                 url: url,
                 indexed:false,
                 displayMode: displayMode,
                 sourceType: "file",
                 color: color,
                 order: Number.MAX_VALUE,
		 height: trackHeight,
                 type: "annotation"};

and despite trackName being promoters I now see, when revisiting some old code, that the promoter track is always given the track label refGene. I cannot find any cause of this in my code (either R or javascript). Any ideas?

The string "refGene" does not appear in any of my code, neither in R nor Javascript.
I see it mentioned once in the igv.js code base, in featureParsers.js:

* Decode a UCSC "genePredExt" record.  refGene files are in this format

The track I display is (in my R class structure) a UCSCBedAnnotationTrack. So maybe it's not completely nuts for me to ask if featureParsers.js somehow substitutes "refGene" for my requested track name?

[jrobinso]

Does your bed file have a "track" line? Can you share one having this problem?

…

On Wed, Oct 9, 2019 at 7:00 PM Paul Shannon ***@***.***> wrote: With this config: var config = {format: "bed", name: trackName, url: url, indexed:false, displayMode: displayMode, sourceType: "file", color: color, order: Number.MAX_VALUE, height: trackHeight, type: "annotation"}; and despite trackName being promoters I now see, when revisiting some old code, that the promoter track is always given the track label refGene. I cannot find any cause of this in my code (either R or javascript). Any ideas? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#994?email_source=notifications&email_token=AAHD2HHRBD5UNRJWDTEAWE3QN2ECNA5CNFSM4I7G2D4KYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HQZPTSA>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHD2HFFTHZT4NJD24IVH4DQN2ECNANCNFSM4I7G2D4A> .

[paul-shannon]

@jrobinso That was it - thanks. An R library I use ("rtracklayer") uses an inherited track name when it exports an object to a file, creating a bed file track line with the default name. I now simply overwrite that name with the user's choice.

[jrobinso]

Im going to reopen this because I think the track config should take precedence over the track line.

[jrobinso]

This has been corrected, track config parameters now have precedence over track line parameters.