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  • 01:18
    cmdcolin commented #2656
  • 01:02
    cmdcolin commented #2656
  • 01:02
    cmdcolin opened #2656
  • 01:02
    cmdcolin labeled #2656
  • 00:14
    codecov[bot] commented #2571
  • 00:03
    codecov[bot] commented #2571
  • 00:03
    cmdcolin synchronize #2571
  • 00:03

    cmdcolin on 607_stats_estimation_v3

    Minor fixes Misc (compare)

  • Jan 18 23:10
    codecov[bot] commented #2571
  • Jan 18 23:10
    cmdcolin synchronize #2571
  • Jan 18 23:10

    cmdcolin on 607_stats_estimation_v3

    Re-arrange Add BAM Rename method estimateGlobalSta… and 1 more (compare)

  • Jan 18 22:03
    cmdcolin labeled #2655
  • Jan 18 22:03
    cmdcolin unlabeled #2655
  • Jan 18 21:50
    codecov[bot] commented #2571
  • Jan 18 21:50
    cmdcolin synchronize #2571
  • Jan 18 21:50

    cmdcolin on 607_stats_estimation_v3

    Add a generic uniqBy function t… Fix lint Adjust label width on base feat… and 49 more (compare)

  • Jan 18 21:24

    cmdcolin on master

    Update CHANGELOG.md v1.1.10 (compare)

  • Jan 18 21:24

    cmdcolin on v1.1.10

    (compare)

  • Jan 18 20:40
    garrettjstevens assigned #33
  • Jan 18 20:40
    garrettjstevens review_requested #33
Robin Haw
@hawrobin
@scottcain I also took a look at the PAG abstract, made some suggestions
Colin Diesh
@cmdcolin
@bbimber if arbitrary header components want to be added to the react lgv we might be able to create an extra prop for that or similar
Colin Diesh
@cmdcolin
@bbimber possible helper here GMOD/jbrowse-components#2535
Garrett Stevens
@garrettjstevens
Another option could be to allow the user to specify their own ViewContainer, so they can e.g. match the styling on their page.
Colin Diesh
@cmdcolin
hmmm
could do that too
bbimber
@bbimber
Would customizing the ViewContainer allow us to increase the initial height? that's been a wish list item for us too
Colin Diesh
@cmdcolin
hmmm...maybe layout wise, but it might not have a bearing on the individual track heights
12 replies
Robin Haw
@hawrobin
@scottcain - i created an AACR 2022 folder in the Meetings folder on the Team drive
Robin Haw
@hawrobin
Lincoln is a member of AACR and I think he can be listed as a sponsor
bbimber
@bbimber
Another question: I see your docs on themes, which works well. However, are more public examples of specific color combinations people have figured out work well? For example, is there a stock jbrowse blue theme, red theme, etc? Or perhaps examples of what color sets people have used?
Colin Diesh
@cmdcolin
not too many examples of this yet i think, would be fun to make some more examples
Scott Cain
@scottcain
Category for JBrowse abstract. submit in which category? "Application of bioinformatics to cancer biology” or "New software tools for data analysis”? I feel like it should be the former, since it doesn’t really do “analysis”, it just helps users look at stuff to do their own analysis. Anybody want to disagree?
Also, sorry working on this so late: it’s been a busy day and I had to take the dog to the vet which has really messed up my schedule.
Colin Diesh
@cmdcolin
either probably fine
Scott Cain
@scottcain
I also have to pick keywords from a long, preexisting list. So far, the only one I’ve found that’s good is “genome"
Colin Diesh
@cmdcolin
such is the way when we step outside our normal conferences...
Scott Cain
@scottcain
yep
Robert Buels
@rbuels
@cmdcolin are you mostly out today with the moving?
Colin Diesh
@cmdcolin
yes
added to cal:)
Robert Buels
@rbuels
@peterkxie thoughts on #2541?
Shellfishgene
@Shellfishgene
Are csi indexes also supported for tabix (gff) files? I have a gff file that tabix won't do an tbi index for for some reason. When I use add-track with --indexFile=foo.gff.gz.csi it still tries to copy a (non existent) .tbi file.
Shellfishgene
@Shellfishgene
If I use inPlace and the csi index it works...
Colin Diesh
@cmdcolin
i think that add track works with indexFile and csi
$ jbrowse add-assembly test_data/volvox/volvox.fa --out t1 --load copy
Added assembly "volvox" to t1/config.json

$ jbrowse add-track test_data/volvox/volvox-sorted.bam --indexFile=test_data/volvox/volvox-sorted.bam.csi --out t1 --load copy
Added track "volvox-sorted" to t1/config.json

$ ls -1 t1
config.json
volvox.fa
volvox.fa.fai
volvox-sorted.bam
volvox-sorted.bam.csi
using jbrowse cli 1.5.1
Colin Diesh
@cmdcolin
some mega ucsc trackhubs/assembly hubs that could be cool to load
Shellfishgene
@Shellfishgene
Yes, it worked with my bam and cram files, but not with gff and csi.
Shellfishgene
@Shellfishgene
Colin Diesh
@cmdcolin
@Shellfishgene ah thanks much
this should get fixed
Colin Diesh
@cmdcolin
possible issue about estimating bytes downloaded, could be possibly a method for stats estimation GMOD/jbrowse-components#2251
Robert Buels
@rbuels
Oh that’s cool, you gonna go?
Colin Diesh
@cmdcolin
perhaps:)
it's free so why not
Robert Buels
@rbuels
Wonder if we can find some synergies between that working with crazy rearrangements
Colin Diesh
@cmdcolin
surely. even "non crazy"stuff benefits
bbimber
@bbimber
Hello - I'm hoping to get some advice. We're trying to make a plugin that filters variants in a VCF track based on whether specific samples are non-wild type. The logic is not hard (make sure the genotype of samples !== '"./." or "0/0"); however, has ~2500 samples. At least how we're doing this makes a very noticeable lag in loading. I experimented with pre-computing an array of the non-WT samples in the getFeatures() method of a custom VcfTabixAdapter; however, this code is called repeatedly whenever any rendering happens. Is there a place I could hook into the processing of VCF features that would let me efficiently pre-compute some information, and let that information persist? Alternately, is there another way I should think about approaching this problem?
Robert Buels
@rbuels
@bbimber I think a custom adapter is a good approach. What would probably help the performance of this a lot would be adding a cache of the features that your custom adapter is creating, so that the calls to getFeatures don't repeat the fetch/parse/filter steps
that cache would be in the custom adapter
bbimber
@bbimber
are there any existing examples of such a cache?
Robert Buels
@rbuels
i did some looking around just now, i don't see any good examples to template from
i can write an implementation sketch of it quickly, just a seec
bbimber
@bbimber
ok, thanks. is there anything particularly react or mobx-specific to this, vs. generic JS?
Robert Buels
@rbuels
no it's pretty generic js
38 replies
bbimber
@bbimber
@cmdcolin on #2554 you said something interesting I hope you could expand on here. you mention lazy parsing of genotypes. As noted above, we have a VCF with ~2400 samples. We previously never had code that did anything with samples until the details panel was opened. We are trying to implement code that lets the user filter sites based on specific samples having non-WT genotypes, and so we're starting to access genotype data much earlier and do this for all variants. What governs whether genotypes are parsed or not?