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Features fusions #1114

Merged
merged 60 commits into from
Sep 16, 2024
Merged

Features fusions #1114

merged 60 commits into from
Sep 16, 2024

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acoffman
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Support a new Feature type in the data model: Transcript Fusions

acoffman and others added 30 commits March 27, 2024 11:27
@acoffman
initial migration of coordinates to their own table
6cdfba7
@acoffman
update gql queries to match new coordinate schema
c31c997
@acoffman
Merge branch 'features' into features-fusions
341ae16
@acoffman
Merge branch 'features' into features-fusions
b68e2dc
@acoffman
get coordinate display and form model working with new schema
527e34a
@acoffman
initial migration of coordinates to their own table
afc99c3
@acoffman
update gql queries to match new coordinate schema
63cf210
@acoffman
get coordinate display and form model working with new schema
4128418
@acoffman
Merge branch 'features-fusions' of github.com:griffithlab/civic-v2 in…
51e95f5 
…to features-fusions
@acoffman
revision suggestions working with variant coordinate model
e92ade0
@acoffman
wip: pull back multiple coordinate types for revisions
597ad2e
@acoffman
query the server for variant specific coordinate subtypes and ids on …
3ebef88 
…revisions page
@acoffman
wip add fusion models
b9f7d58
@susannasiebert
Add mutation for creating fusion feature
5b74e32
@acoffman
create fusions mutation working
2525460
@acoffman
display fusion features, alllow deprecation
0cd7238
@acoffman
intitial fusion select form logic/model
b747793
@acoffman
fusion select/create hooked up + validations
e6d9d48
@acoffman
fusion variant creation form working, mp name generation handles fusions
167ac64
@acoffman
fusion variant creation form is aware of gene partner status
8d96837
@acoffman
coordinate card working on fusion display
c592c28
@acoffman
fusions menu on gene feature pages
a18282d
@acoffman
remove hardcoded login
bc28f04
@acoffman
fix a couple of strings
56f7a64
@acoffman
attempt to backfill new coordinate type
bc31595
@acoffman
introduce exon coordinate type
14849fa
@susannasiebert
More updates to the backfill script
921e77c
@acoffman
background job to fill coordinates
b9d6afb
@acoffman
additional tweaks to fusion coordinate fill script
36b6e44
@susannasiebert
Display exon coordinates on fusion variant pages
5d6d61e
susannasiebert and others added 25 commits August 9, 2024 14:08
@susannasiebert
Implement fusion feature revision submission
242f541
@susannasiebert
Name representative variant for Fusions with an unknown fusion partne…
bcc644a 
…r "Rearrangement" instead of "Fusion"
@susannasiebert
Fix error with fusion feature creation due to usage of in_revision_va…
8af6477 
…lidation_context
@susannasiebert
Fix some bugs in the variant creation introduced with ExonCoordinate …
a3b2596 
…switch
@acoffman
retry fragment read with subtype on cache miss
e227cb9
@acoffman
validate transcript ids match expected ensembl format
edeca18
@acoffman
flag variants when there is an issue backfilling coordinates
d3cf584
@acoffman
stub in coordinate fields for default bucket fusions
2b6470c
@acoffman
fusion revision submission working
4de9386
@acoffman
remove hgvs and clinvar ids from fusion variant type
4a3b42e
@acoffman
remove clinvar ids from fusions on mp card
78f6ef8
@acoffman
accepting fusion coordinate revisions is working
68a43f7
@acoffman
add fusion filter to feature browse table
cb4c7b5
@acoffman
remove rearrangement fusion naming logic
48266d2
@acoffman
fix failing test case
76abf45
@acoffman
Merge branch 'main' into features-fusions
dc9544f
@acoffman
fix typo in tooltip message
bee7cd9
@acoffman
pass in representative fusion name
0d7e4f5
@acoffman
strip whitespace from transcript ids on input
236a0ce
@acoffman
update query example to work with new coordinate schema
e1534fd
@acoffman
update backfill script
5cec74a
@acoffman
remove hgvs/clinvar entry id validation until we determine what to do…
40af6e3 
… with it
@acoffman
pull back deprecated status in one more place
b2b5e9a
@acoffman
add open revision counts to the individual revision tabs
b39a1da
@acoffman
re-enable indexing on variants
00bf230
@acoffman acoffman added the new-feature PR Label for newly added features. Will appear in release notes. label Sep 16, 2024
@acoffman acoffman merged commit 91e451b into main Sep 16, 2024
4 checks passed
@acoffman acoffman deleted the features-fusions branch September 16, 2024 22:38
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@acoffman @susannasiebert