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Saving HTMLVariants track to GFF3 #1309

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dionnezaal opened this Issue Feb 4, 2019 · 3 comments

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dionnezaal commented Feb 4, 2019

We were very excited to see the fix for exporting to GFF3 in the latest version of JBrowse (1.16.2). It works perfectly with the CanvasFeatures track. Thank you!

We were also happy to see that we could now save HTMLVariants tracks to GFF3 files. We only found a small bug. The annotation column of the GFF3 does contain some fields like description, reference_allele, name which are exported correctly, but some fields like alternative_alleles are exported as the following:

alternative_alleles=[object Object];
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cmdcolin commented Feb 4, 2019

Thanks for reporting, that can be verified. Some aspects of this can be verified far back even to much older versions, I saw this in 1.12.5 for example. We'll take a look at it. In some sense it would be nice to simply get VCF export back also, is that something of interest?

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dionnezaal commented Feb 5, 2019

Thank you! Returning a VCF export will indeed make more sense for the HTML Variants track.

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cmdcolin commented Feb 15, 2019

I created a workaround that simply dumps json into the value field. This is a little weird by gff standards but gff doesn't seem to have a notion of nested values so that seemed reasonable.

We'll keep VCF export on the horizon but hopefully this helps somewhat

@cmdcolin cmdcolin closed this Feb 15, 2019

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