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If VCF header is very large, some weird behavior can occur #1139

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cmdcolin opened this Issue Jul 24, 2018 · 1 comment

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cmdcolin commented Jul 24, 2018

This was brought up in this issue that was closed with a workaround but I figure that it could be worth having an issue available for it #1049

I noticed the BAM code might have code to refetch for a larger header if this situation occurred

Specifically this code https://github.com/GMOD/jbrowse/blob/dev/src/JBrowse/Store/SeqFeature/BAM/File.js#L143-L151

@rbuels rbuels added the scalability label Jul 28, 2018

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cmdcolin Aug 1, 2018

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There is a large VCF header file in the repo now and an xit'd out test in the VCF jasmine test for checking the genotypes field (because currently the feature.get('genotypes') returns empty on files with very large VCF header)

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cmdcolin commented Aug 1, 2018

There is a large VCF header file in the repo now and an xit'd out test in the VCF jasmine test for checking the genotypes field (because currently the feature.get('genotypes') returns empty on files with very large VCF header)

@rbuels rbuels added this to the 1.15.4 milestone Sep 6, 2018

@rbuels rbuels self-assigned this Sep 19, 2018

@wafflebot wafflebot bot added the in progress label Sep 19, 2018

@rbuels rbuels added the has pullreq label Sep 19, 2018

@rbuels rbuels closed this Oct 2, 2018

@wafflebot wafflebot bot removed the in progress label Oct 2, 2018

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