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Repo info
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  • 04:45

    garrettjstevens on issues22_23_24_GS

    Enable strictNullChecks in tsco… Don't use library-specific resp… Remove unnecessary try-catches and 4 more (compare)

  • Jan 14 05:57

    garrettjstevens on issues22_23_24_GS

    Add local test data Remove unused files Authenticate -> Authentication and 3 more (compare)

  • Jan 12 17:57

    garrettjstevens on apollo_entities

    Add getRefNames, make driver me… (compare)

  • Jan 12 16:42
    garrettjstevens assigned #31
  • Jan 12 16:42
    garrettjstevens opened #31
  • Jan 12 16:36
    garrettjstevens assigned #30
  • Jan 12 16:36
    garrettjstevens opened #30
  • Jan 12 01:55

    peterkxie on apollo_layout

    get boxes extending (compare)

  • Jan 11 16:27
    peterkxie assigned #29
  • Jan 11 16:27
    peterkxie labeled #29
  • Jan 11 16:27
    peterkxie opened #29
  • Jan 10 23:57

    peterkxie on apollo_layout

    add on mouse down px indicator … (compare)

  • Jan 10 03:43

    garrettjstevens on apollo_entities

    Add AnnotationFeature (compare)

  • Jan 08 01:08

    garrettjstevens on apollo_entities

    Initial Apollo entities classes… (compare)

  • Jan 07 17:11
    garrettjstevens assigned #28
  • Jan 07 17:11
    garrettjstevens assigned #27
  • Jan 07 17:11
    garrettjstevens assigned #16
  • Jan 07 17:11
    garrettjstevens assigned #16
  • Jan 07 17:03
    garrettjstevens opened #28
  • Jan 07 17:01
    garrettjstevens opened #27
Deepak
@deepakunni3
Awesome. So no more random break in integration tests.
Nathan Dunn
@nathandunn
basically when it pulls out a sequence alteration I am sorting it by its fmin . . . so if it fails .. it will consistently fail and vice versa
that is my hope :smile:
Deepak
@deepakunni3
but why would it fail sometimes and pass in other cases
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