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Save track data fractional coordinates #4029

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scottcain opened this issue Oct 31, 2023 · 1 comment
Closed

Save track data fractional coordinates #4029

scottcain opened this issue Oct 31, 2023 · 1 comment
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@scottcain
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Describe the bug

I was recently asked how to save the sequence of a "random" location in JBrowse 2 (that is, not the sequence of feature like a gene). While the "save track data" option available on the git branch of the same name sort of works, it has problems in this instance. Given this location:

https://wormbase.org/tools/genome/jbrowse2/?session=share-YtcgDU0zgF&password=zju5Q

(that is, C. elegans N2, V:13707382..13707915)

and selecting "save track data" from the track ... menu, I get a dialog to save. GFF and BED don't really make sense in this context, so select GenBank (fasta would be a good option here too). The result looks like this:

Screenshot 2023-10-31 at 12 28 38 PM

Note the fractional coordinates: V:13707382.014586711..13707915.014586711. In some cases while look at this bug, I found that it also got the starting base wrong if the fraction was a little less than the starting coordinate (like it's doing a int of the coordinate, which is not terribly unreasonable, but would be wrong in this case).

Version:

JBrowse 2.6.3 (haven't had a chance to test with newer version yet) in Firefox

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@scottcain scottcain added the bug Something isn't working label Oct 31, 2023
@cmdcolin
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moving this just as a link into the save track data PR

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