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unprocessedTranscriptColor is incompatible with NeatCanvasFeatures #1298

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billzt opened this Issue Dec 28, 2018 · 1 comment

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billzt commented Dec 28, 2018

Tring to use the unprocessedTranscriptColor attribute to fill the ncRNA gray while keeping others normal.

Give two configs as examples:

The first one uses normal CanvasFeatures:

      {
         "key" : "Test1",
         "storeClass" : "JBrowse/Store/SeqFeature/GFF3Tabix",
         "trackType" : "CanvasFeatures",
         "urlTemplate" : "test1.gff3.gz",
         "label" : "test1",
         "type" : "CanvasFeatures",
         "category" : "Feature Annotation",
         "subParts" : "CDS, UTR, five_prime_UTR, three_prime_UTR, exon",
         "noncodingType" : ["ncRNA"],
         "style" : {
            "unprocessedTranscriptColor" : "grey"
         }
      },

the result is OK
test1

The second one tried to use NeatCanvasFeatures:

      {
         "key" : "Test2",
         "storeClass" : "JBrowse/Store/SeqFeature/GFF3Tabix",
         "trackType" : "NeatCanvasFeatures/View/Track/NeatFeatures",
         "urlTemplate" : "test1.gff3.gz",
         "label" : "test2",
         "type" : "NeatCanvasFeatures/View/Track/NeatFeatures",
         "gradient": true,
         "category" : "Feature Annotation",
         "subParts" : "CDS, UTR, five_prime_UTR, three_prime_UTR, exon",
         "noncodingType" : ["ncRNA"],
         "style" : {
            "unprocessedTranscriptColor" : "grey"
         }
      },

the result is wrong and strange (the noncoding transcript is no longer spliced, and is no longer filled as the right color)
test2

@cmdcolin

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cmdcolin commented Dec 28, 2018

Thanks for finding this. I fixed it on the dev branch here 4f0576e

Pending release!

@cmdcolin cmdcolin closed this Dec 28, 2018

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