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  • Jan 25 22:22
    cmdcolin commented #35
  • Jan 25 22:21
    cmdcolin commented #35
  • Jan 25 19:42
    garrettjstevens ready_for_review #35
  • Jan 25 19:39
    garrettjstevens synchronize #35
  • Jan 25 19:39

    garrettjstevens on change_manager

    Fix dependency version (compare)

  • Jan 25 19:37
    garrettjstevens synchronize #35
  • Jan 25 19:37

    garrettjstevens on change_manager

    Use updated yarn install comman… (compare)

  • Jan 25 19:24
    garrettjstevens synchronize #35
  • Jan 25 19:24

    garrettjstevens on change_manager

    Regsiter change with the change… (compare)

  • Jan 25 03:59
    garrettjstevens assigned #35
  • Jan 25 03:59
    garrettjstevens opened #35
  • Jan 25 03:55

    garrettjstevens on change_manager

    Initial Apollo entities classes… Add AnnotationFeature Add getRefNames, make driver me… and 14 more (compare)

  • Jan 25 03:47

    garrettjstevens on apollo_entities

    Add simple Apollo View that wra… Add some volvox test data to te… Load GFF3 from Apollo view and 5 more (compare)

  • Jan 24 15:27
    kyostiebi review_requested #34
  • Jan 24 15:27
    kyostiebi opened #34
  • Jan 24 15:22

    kyostiebi on FileDownloadAndUpload

    work in progress temp commit New branch now contains file an… (compare)

  • Jan 20 19:23

    garrettjstevens on apollo_entities

    AnnotationFeatures -> Annotatio… Add missing "await" Add abstract fromJSON, update c… (compare)

  • Jan 20 18:32

    rbuels on apollo_entities

    add a type registry for change … (compare)

  • Jan 20 15:08

    kyostiebi on EnvAndResponseChanges

    backup save only (compare)

  • Jan 20 10:57

    kyostiebi on EnvAndResponseChanges

    work in progress (compare)

Nathan Dunn
@nathandunn
I'm sure there is some random assortment of sequence alterations that when combined create this error. . . that or you can't combine them randomly
either way you want a consistent result
Nathan Dunn
@nathandunn
BTW, what is status of #458?
Deepak
@deepakunni3
#458 is up for review. It should be fixed with the commits made in the pull request
Nathan Dunn
@nathandunn
I see . . is this for @monicacecilia to review?
or did I already merge it? (sorry long weekend)
it looks like I did in #472 . . this should be marked as ready then and put up?
Deepak
@deepakunni3
yeah. I wanted your opinion on it. if it looks good then we can put it up for testing.
Nathan Dunn
@nathandunn
yeah, I looked over it, but if you want to walk me through it that would be great
Deepak
@deepakunni3
sure. skype?
Nathan Dunn
@nathandunn
sure
Nathan Dunn
@nathandunn
@deepakunni3 This was the alternate codes one I was talking about: GMOD/Apollo#95
anyway . . . not sure what the priority is
Deepak
@deepakunni3
ah, yes. We should add this to the agenda for Thursday
Nathan Dunn
@nathandunn
agreed
Robert Buels
@rbuels
@nathandunn oh this channel exists!
Nathan Dunn
@nathandunn
I here
Dan Keith
@DoctorBud
I'm just a fly on the wall here... Pay me no mind.
Nathan Dunn
@nathandunn
He’s on to us!
Nathan Dunn
@nathandunn
Apropos @DoctorBud the genome feature widget is bein refactored to not have any react components in the test or the demo, so hopefully will clean things up
Robert Buels
@rbuels
@nathandunn @deepakunni3 OK if I configure Gitter to watch the GMOD/Apollo repo and issues for activity messages
?
commits and whatnot
Deepak
@deepakunni3
@rbuels Yes, that would be useful to keep track of development :+1:
Robert Buels
@rbuels
ok done. events in the GMOD/Apollo repo should appear in the sidebar now
Nathan Dunn
@nathandunn
Please!
Yating Liu
@Yating-L
@nathandunn I removed the gene lines from GFF3 and generated GFF3Tabix track. But there are a few CDS do not show. Is this a known issue? Or it has been solved?
Screen Shot 2018-04-05 at 9.57.24 AM.png
Nathan Dunn
@nathandunn
@Yating-L I’m not sure. If the CDS parent is the exon or the gene instead of the mRNA that could be a problem. Mostly it depends on how its created. Can you send your samples before and after?
I’m assuming this is just for the HTML version?
Yating Liu
@Yating-L
HTMLFeatures, yes
Yating Liu
@Yating-L
@nathandunn here are the gene prediction output file, before and after filtering gene lines
Nathan Dunn
@nathandunn
@Yating-L there are no exons (which is fine). Are you saying that it is not showing some of the specified CDS’s?
Robert Buels
@rbuels
@nathandunn is this the use case you're working on in your gff3tabix pull req so that it works out of the box?
Nathan Dunn
@nathandunn
@rbuels I thiknk so
Yating Liu
@Yating-L
@nathandunn yes, some CDSs are not showing
Nathan Dunn
@nathandunn
@Yating-L this is with the HTMLFeatures?
I’m guess it is
so, the answer to your question is yes @rbuels
Yating Liu
@Yating-L
@nathandunn I think so. I tested on two GFF3. Canvas renders correctly
but HTML missing some subfeatures
Robert Buels
@rbuels
which data store were both tests using? GFF3Tabix?
Yating Liu
@Yating-L
"JBrowse/Store/SeqFeature/GFF3Tabix"
Nathan Dunn
@nathandunn
yeah, they both use the same store. The difference is when the Canvas redners, they just render one on top of another and it works. With HTMLFeatures, you can’t do that with divs and so it blocks the other one out
Yating Liu
@Yating-L
is this solvable?
Robert Buels
@rbuels
is there a reason that you guys can't just use canvasfeatures? i've been hoping since 2013 to deprecate htmlfeatures
is it cause of apollo needing to drag the features around
Nathan Dunn
@nathandunn
@rbuels Part of it is dragging the features, an important feature of Apollo. The other reason is highlighting edges.