Update STR page allele size histogram to show colors based on genotype quality or other values#1649
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phildarnowsky-broad merged 18 commits intomainfrom Mar 20, 2025
Merged
Update STR page allele size histogram to show colors based on genotype quality or other values#1649phildarnowsky-broad merged 18 commits intomainfrom
phildarnowsky-broad merged 18 commits intomainfrom
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rileyhgrant
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Looks good to me!
Really nice work.
I left a few comments in line, one about typing, two very minor things, and one "nice one" for reuse of the your sorting hook.
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@rileyhgrant this latest should address all your feedback |
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Thanks for addressing those so promptly, I just left one minor comment about two !s being (possibly) mistakenly dropped.
After double checking that, LGTM!
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| repeatUnitsByClassification.pathogenic && | ||
| repeatUnitsByClassification.pathogenic.length === 1 && | ||
| repeatUnitsByClassification.benign && | ||
| repeatUnitsByClassification.unknown |
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It looks like the ! may have been mistakenly dropped from these last two conditions:
before:
(repeatUnitsByClassification as any).pathogenic &&
(repeatUnitsByClassification as any).pathogenic.length === 1 &&
!(repeatUnitsByClassification as any).benign &&
!(repeatUnitsByClassification as any).unknown
after:
repeatUnitsByClassification.pathogenic &&
repeatUnitsByClassification.pathogenic.length === 1 &&
repeatUnitsByClassification.benign &&
repeatUnitsByClassification.unknown
Just wanted to flag this in case it was unintentional!
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Major changes here are: * Instead of a single `reference_region`, STRs now have a list of `reference_regions` with a single one designated the `main_reference_region` * Allele size distributions and genotype distributions were previously represented with an attempt to represent multidimensional data with a number of nested structs, which was serviceable when there were only one or two dimensions we might want to filter on, but was getting increasingly convoluted. Since this new data expands the number of dimensions further, rather than build on the former schema and confuse things more, these distributions are now represented with a flattened list of structs each of which represents a single subset of the distribution.
Key changes: * Allele size distribution plot can now show, by use of stacked bars, breakdown of each bucket by population, quality, or sex. This also involved replacing some of our custom logic with calls to the visx family of libraries. * More options for y-scaling of allele size distribution plot. * Assorted refactoring, type specifying, and similar cleanup
This indicates intergenic loci, which aren't associated with a gene.
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remaining TODOs: