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  • Jan 28 21:42

    garrettjstevens on change_manager

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  • Jan 28 21:41

    garrettjstevens on main

    Initial Apollo entities classes… Add AnnotationFeature Add getRefNames, make driver me… and 22 more (compare)

  • Jan 28 21:41
    garrettjstevens closed #35
  • Jan 28 21:41
    garrettjstevens closed #27
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  • Jan 28 21:33

    garrettjstevens on apollo-shared_package

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  • Jan 28 21:33

    garrettjstevens on change_manager

    Add apollo-shared package Move shared code to apollo-shar… Merge pull request #37 from GMO… (compare)

  • Jan 28 21:33
    garrettjstevens closed #37
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  • Jan 28 17:41
    garrettjstevens commented #34
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    kyostiebi on FileDownloadAndUpload

    added test/data -subfolder to g… (compare)

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    Ready for 2nd review (compare)

  • Jan 27 02:49
    garrettjstevens assigned #37
  • Jan 27 02:49
    garrettjstevens opened #37
Nathan Dunn
@nathandunn
test chat message
Deepak
@deepakunni3
Message received
Nathan Dunn
@nathandunn
great . .. FYI, I just pushed a change so that the integration tests are more consistent
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