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Arrowheads are not displayed for gene glyphs #454

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cmdcolin opened this Issue Mar 5, 2014 · 1 comment

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cmdcolin commented Mar 5, 2014

If I use an example GFF3 (volvox.gff3)

ctgA    exonerate       mRNA    17400   23000   .       +       .       ID=rna-Apple3;Name=Apple3;Note=mRNA with both CDSs and UTRs
ctgA    exonerate       UTR     17400   17999   .       +       .       Parent=rna-Apple3
ctgA    exonerate       CDS     18000   18800   .       +       0       Parent=rna-Apple3
ctgA    exonerate       CDS     19000   19500   .       +       1       Parent=rna-Apple3
ctgA    exonerate       CDS     21000   21200   .       +       2       Parent=rna-Apple3
ctgA    exonerate       UTR     21201   23000   .       +       .       Parent=rna-Apple3

And change this mRNA feature to have a gene parent

ctgA    exonerate       gene    17400   23000   .       +       .       ID=Apple3;Name=Apple3;
ctgA    exonerate       mRNA    17400   23000   .       +       .       ID=rna-Apple3;Name=Apple3;Parent=Apple3;Note=mRNA with both CDSs and UTRs
ctgA    exonerate       UTR     17400   17999   .       +       .       Parent=rna-Apple3
ctgA    exonerate       CDS     18000   18800   .       +       0       Parent=rna-Apple3
ctgA    exonerate       CDS     19000   19500   .       +       1       Parent=rna-Apple3
ctgA    exonerate       CDS     21000   21200   .       +       2       Parent=rna-Apple3
ctgA    exonerate       UTR     21201   23000   .       +       .       Parent=rna-Apple3

Then arrowheads won't be shown for this feature ( CanvasFeatures ).

jbrowse-ctga-12841-34320 2014-03-05 15-08-24

@rbuels rbuels added this to the Release 1.11.3 milestone Mar 5, 2014

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rbuels Mar 5, 2014

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cdiesh: yeah, pretty sure it's GFF3/Parser.js
cdiesh: well. so GFF3/Util.parse_feature doesn't change the strand to 1/-1
cdiesh: and it probably should
cdiesh: maybe try that and see?
cdiesh: would modify parse_feature in JBrowse/Util/GFF3.js

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rbuels commented Mar 5, 2014

cdiesh: yeah, pretty sure it's GFF3/Parser.js
cdiesh: well. so GFF3/Util.parse_feature doesn't change the strand to 1/-1
cdiesh: and it probably should
cdiesh: maybe try that and see?
cdiesh: would modify parse_feature in JBrowse/Util/GFF3.js

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