Split variant flags #1623
Split variant flags #1623
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@rileyhgrant I've decided to put the VA/VRS-related fixes in the other VA topic branch I've been working on, which I'll rebase on top of this, hence this PR doesn't include VA fixes. |
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LGTM, very nicely done, I especially like the care taken to the testing, and to a neatly organized series of commits.
Just one minor comment about the naming of a common region flag (based on the docs, it might be named "non_par", rather than "par", but I wasn't quite sure and wanted to double check).
Nice one!
| const baseExomeFlags = variant.exome?.flags || [] | ||
| const baseGenomeFlags = variant.genome?.flags || [] | ||
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| const regionalFlags = ['par', 'segdup', 'lcr'].filter( |
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Based on the hail tables help text, it appears as though the par flag might be named "non_par"?
I did a quick grep and didn't see any place where we rename this flag in our pipeline, so just wanted to check, this flag seems to potentially differ in meaning from in the SV datasets where there is a "par" flag.
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The v4 data pipeline does address this,
, but it would be smart for me to double-check that it's correct.There was a problem hiding this comment.
Ah whoops, I naively only grepped for "non_par", my bad for not finding that, and nice catch!
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This updates the API and frontend to support flags both on a variant generally, or on the exome and/or genome specifically, and fixes a number of related bugs related to display of flags.
fixes #1614