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Add v4 CNVs #1176

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Add v4 CNVs #1176

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5e65538
cnv notebook draft
elissa-alarmani Sep 14, 2023
46ad865
inital pipelines and task creation
elissa-alarmani Sep 21, 2023
d0103d8
create cnv resolvers
elissa-alarmani Sep 27, 2023
0110036
create cnv queries
elissa-alarmani Sep 27, 2023
a9adba5
create cnv graphql types
elissa-alarmani Sep 27, 2023
2d3959a
create cnvs pipeline and tasks
elissa-alarmani Sep 27, 2023
549d1fe
add cnv dataset as an enum dataset-id
elissa-alarmani Oct 3, 2023
12ad7ad
add cnv to gene type
elissa-alarmani Oct 3, 2023
eef8cfc
add cnvs to query type
elissa-alarmani Oct 3, 2023
a1f257a
add cnvs to region type
elissa-alarmani Oct 3, 2023
72853ba
add cnv resolvers to schema
elissa-alarmani Oct 3, 2023
282385e
update singular and plural naming
elissa-alarmani Oct 3, 2023
197ab86
python black formatter
elissa-alarmani Oct 3, 2023
52dad61
wip resolvers and queries
elissa-alarmani Oct 3, 2023
36dae00
minor pipeline edits
elissa-alarmani Oct 4, 2023
cfcf644
add CNVDatasetId to Gene, Query, Region types
elissa-alarmani Oct 4, 2023
affe4bb
fix resolver and query errors
elissa-alarmani Oct 4, 2023
526191b
add cnvs to dataset
elissa-alarmani Oct 6, 2023
57a511e
add textOrMissingTextWarning
elissa-alarmani Oct 6, 2023
634c724
add gnomad_cnv_r4 to search dataset
elissa-alarmani Oct 6, 2023
26f85b6
add gnomad_cnv_r4 to metadata
elissa-alarmani Oct 6, 2023
f8d54b8
create cnv populations table
elissa-alarmani Oct 6, 2023
bdd1fa1
add cnv page to variant page router
elissa-alarmani Oct 6, 2023
094ad47
WIP cnv page
elissa-alarmani Oct 6, 2023
5d72c96
WIP cnv attribute list
elissa-alarmani Oct 6, 2023
d3d2e61
add cnv coverage track for percent callable
elissa-alarmani Oct 12, 2023
8cef11d
fix datasetselector oraganization for cnvs
elissa-alarmani Oct 13, 2023
66875e4
add variantfeedback spec tests
elissa-alarmani Oct 13, 2023
13fbc27
create cnv reference list
elissa-alarmani Oct 13, 2023
548e0d4
add v4 and cnv v4 to metadata
elissa-alarmani Oct 13, 2023
4b2a345
add CNV info to gene page display
elissa-alarmani Oct 13, 2023
390ca74
update cnv pop table labels
elissa-alarmani Oct 13, 2023
9e89be3
WIP variant cnv page
elissa-alarmani Oct 13, 2023
62139f1
create cnv types ts
elissa-alarmani Oct 13, 2023
287f00a
update attribute list
elissa-alarmani Oct 13, 2023
c111e15
add filter zoom region for cnvs
elissa-alarmani Oct 13, 2023
e618553
update graphql types
elissa-alarmani Oct 13, 2023
abcf5a9
create tests
elissa-alarmani Oct 18, 2023
6ccf5e6
create cnv factories
elissa-alarmani Oct 18, 2023
a091f0d
add exome only coverage for cnvs
elissa-alarmani Oct 19, 2023
d28db68
add param to only display exome coverage for cnvs
elissa-alarmani Oct 19, 2023
eaa2939
add cnv type
elissa-alarmani Oct 19, 2023
999689d
add format prettier
elissa-alarmani Oct 23, 2023
db258fe
draft track callable coverage
elissa-alarmani Oct 25, 2023
9446351
add cnv coverage bin type
elissa-alarmani Oct 25, 2023
f2376ea
update metadata and sample counts
elissa-alarmani Oct 26, 2023
1092789
add final graphql edits
elissa-alarmani Oct 26, 2023
9fb2d64
fix pipeline edits
elissa-alarmani Oct 26, 2023
fa08958
Final Gene and Region Page edits for CNV
elissa-alarmani Oct 26, 2023
a603ced
eslint pass
elissa-alarmani Oct 26, 2023
b1fabcd
remove inital coverage files
elissa-alarmani Oct 26, 2023
004ba1e
coverage edits
elissa-alarmani Oct 26, 2023
84fea62
Add snapshot test updates
elissa-alarmani Oct 27, 2023
4dc9495
add page changes
elissa-alarmani Oct 29, 2023
2b16f07
add formatting
elissa-alarmani Oct 29, 2023
f709675
update dataset selection
elissa-alarmani Oct 29, 2023
9aa35bc
remove console.log
elissa-alarmani Oct 29, 2023
407263b
finalize testing files
elissa-alarmani Oct 29, 2023
aa51e93
add new vcf file path
elissa-alarmani Oct 29, 2023
6b5a687
add chromosome to variant table position
elissa-alarmani Oct 29, 2023
c4180e2
fix variant table broke search
elissa-alarmani Oct 29, 2023
dfff177
eslint fix
elissa-alarmani Oct 29, 2023
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186 changes: 120 additions & 66 deletions browser/src/CopyNumberVariantPage/__snapshots__/CopyNumberVariantPage.spec.tsx.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D
>
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_or_cnv_dataset"
data-item="current_sv_dataset"
Copy link
Contributor

@phildarnowsky-broad phildarnowsky-broad Oct 29, 2023 •
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I'm not clear on what this commit is about either. nvm, it was late and I was tired and now it's pretty clear.

href="/?dataset=gnomad_cnv_r4"
onBlur={[Function]}
onClick={[Function]}
Expand Down Expand Up @@ -74,80 +74,97 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D
<div
className="DatasetSelector__GroupedNav-sc-1p2fxbn-7 cJJZPz"
>
GRCh37
GRCh38
</div>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_sv_r2_1"
href="/?dataset=gnomad_sv_r2_1"
data-item="gnomad_sv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD SVs v2.1
gnomAD SVs v4
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
10,847 samples
63,046 samples
</div>
</a>
</li>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_sv_r2_1_non_neuro"
href="/?dataset=gnomad_sv_r2_1_non_neuro"
data-item="gnomad_cnv_r4"
href="/?dataset=gnomad_cnv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD SVs v2.1 (non-neuro)
gnomAD exome CNVs v4.0
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
8,342 samples
464,566 samples
</div>
</a>
</li>
</li>
<li>
<div
className="DatasetSelector__GroupedNav-sc-1p2fxbn-7 cJJZPz"
>
GRCh37
</div>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_sv_r2_1_controls"
href="/?dataset=gnomad_sv_r2_1_controls"
data-item="gnomad_sv_r2_1"
href="/?dataset=gnomad_sv_r2_1"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD SVs v2.1 (controls)
gnomAD SVs v2.1
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
5,192 samples
10,847 samples
</div>
</a>
</li>
</li>
<li>
<div
className="DatasetSelector__GroupedNav-sc-1p2fxbn-7 cJJZPz"
>
GRCh38
</div>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_cnv_r4"
href="/?dataset=gnomad_cnv_r4"
data-item="gnomad_sv_r2_1_non_neuro"
href="/?dataset=gnomad_sv_r2_1_non_neuro"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD exome CNVs v4.0
gnomAD SVs v2.1 (non-neuro)
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
464,566 samples
8,342 samples
</div>
</a>
</li>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_sv_r2_1_controls"
href="/?dataset=gnomad_sv_r2_1_controls"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD SVs v2.1 (controls)
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
5,192 samples
</div>
</a>
</li>
Expand Down Expand Up @@ -237,14 +254,6 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D
0.3565
</dd>
</div>
<div>
<dt>
Quality score
</dt>
<dd>
99
</dd>
</div>
<div>
<dt>
Position
Expand Down Expand Up @@ -422,6 +431,24 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D
</tfoot>
</table>
</section>
<div
className="CopyNumberVariantPage__Wrapper-sc-1ase2rg-0 elCRDU"
>
<section
className="CopyNumberVariantPage__ResponsiveSection-sc-1ase2rg-1 lfHhrQ"
>
<h2>
Consequences
</h2>
<p>
This variant has consequences in
0
gene
s
.
</p>
</section>
</div>
</div>
`;

Expand Down Expand Up @@ -458,7 +485,7 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D
>
<a
className="DatasetSelector__TopLevelNavigationLink-sc-1p2fxbn-1-Link eggTrD"
data-item="current_sv_or_cnv_dataset"
data-item="current_sv_dataset"
href="/?dataset=gnomad_cnv_r4"
onBlur={[Function]}
onClick={[Function]}
Expand Down Expand Up @@ -499,80 +526,97 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D
<div
className="DatasetSelector__GroupedNav-sc-1p2fxbn-7 cJJZPz"
>
GRCh37
GRCh38
</div>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_sv_r2_1"
href="/?dataset=gnomad_sv_r2_1"
data-item="gnomad_sv_r4"
href="/?dataset=gnomad_sv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD SVs v2.1
gnomAD SVs v4
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
10,847 samples
63,046 samples
</div>
</a>
</li>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_sv_r2_1_non_neuro"
href="/?dataset=gnomad_sv_r2_1_non_neuro"
data-item="gnomad_cnv_r4"
href="/?dataset=gnomad_cnv_r4"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD SVs v2.1 (non-neuro)
gnomAD exome CNVs v4.0
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
8,342 samples
464,566 samples
</div>
</a>
</li>
</li>
<li>
<div
className="DatasetSelector__GroupedNav-sc-1p2fxbn-7 cJJZPz"
>
GRCh37
</div>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_sv_r2_1_controls"
href="/?dataset=gnomad_sv_r2_1_controls"
data-item="gnomad_sv_r2_1"
href="/?dataset=gnomad_sv_r2_1"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD SVs v2.1 (controls)
gnomAD SVs v2.1
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
5,192 samples
10,847 samples
</div>
</a>
</li>
</li>
<li>
<div
className="DatasetSelector__GroupedNav-sc-1p2fxbn-7 cJJZPz"
>
GRCh38
</div>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_cnv_r4"
href="/?dataset=gnomad_cnv_r4"
data-item="gnomad_sv_r2_1_non_neuro"
href="/?dataset=gnomad_sv_r2_1_non_neuro"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD exome CNVs v4.0
gnomAD SVs v2.1 (non-neuro)
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
464,566 samples
8,342 samples
</div>
</a>
</li>
<li>
<a
className="DatasetSelector__SubNavigationLink-sc-1p2fxbn-5-Link gbnrKe"
data-item="gnomad_sv_r2_1_controls"
href="/?dataset=gnomad_sv_r2_1_controls"
onBlur={[Function]}
onClick={[Function]}
onKeyDown={[Function]}
>
gnomAD SVs v2.1 (controls)
<div
className="DatasetSelector__ItemDescription-sc-1p2fxbn-6 hlVhHR"
>
5,192 samples
</div>
</a>
</li>
Expand Down Expand Up @@ -662,14 +706,6 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D
0.3565
</dd>
</div>
<div>
<dt>
Quality score
</dt>
<dd>
99
</dd>
</div>
<div>
<dt>
Position
Expand Down Expand Up @@ -847,5 +883,23 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D
</tfoot>
</table>
</section>
<div
className="CopyNumberVariantPage__Wrapper-sc-1ase2rg-0 elCRDU"
>
<section
className="CopyNumberVariantPage__ResponsiveSection-sc-1ase2rg-1 lfHhrQ"
>
<h2>
Consequences
</h2>
<p>
This variant has consequences in
0
gene
s
.
</p>
</section>
</div>
</div>
`;
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