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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

Commits on Mar 27, 2024

  1. initial migration of coordinates to their own table

    @acoffman
    acoffman committed Mar 27, 2024
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Commits on Mar 28, 2024

  1. update gql queries to match new coordinate schema

    @acoffman
    acoffman committed Mar 28, 2024
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  2. Merge branch 'features' into features-fusions

    @acoffman
    acoffman committed Mar 28, 2024
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Commits on Mar 29, 2024

  1. Merge branch 'features' into features-fusions

    @acoffman
    acoffman committed Mar 29, 2024
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  2. get coordinate display and form model working with new schema

    @acoffman
    acoffman committed Mar 29, 2024
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  3. initial migration of coordinates to their own table

    @acoffman
    acoffman committed Mar 29, 2024
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  4. update gql queries to match new coordinate schema

    @acoffman
    acoffman committed Mar 29, 2024
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  5. get coordinate display and form model working with new schema

    @acoffman
    acoffman committed Mar 29, 2024
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Commits on Apr 2, 2024

  1. Merge branch 'features-fusions' of github.com:griffithlab/civic-v2 in… 

    …to features-fusions
    @acoffman
    acoffman committed Apr 2, 2024
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  2. revision suggestions working with variant coordinate model

    @acoffman
    acoffman committed Apr 2, 2024
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Commits on Apr 17, 2024

  1. wip: pull back multiple coordinate types for revisions

    @acoffman
    acoffman committed Apr 17, 2024
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Commits on Apr 24, 2024

  1. query the server for variant specific coordinate subtypes and ids on … 

    …revisions page
    @acoffman
    acoffman committed Apr 24, 2024
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Commits on May 15, 2024

  1. wip add fusion models

    @acoffman
    acoffman committed May 15, 2024
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Commits on Jun 14, 2024

  1. Add mutation for creating fusion feature

    @susannasiebert
    susannasiebert committed Jun 14, 2024
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Commits on Jun 17, 2024

  1. create fusions mutation working

    @acoffman
    acoffman committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. display fusion features, alllow deprecation

    @acoffman
    acoffman committed Jun 18, 2024
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Commits on Jun 19, 2024

  1. intitial fusion select form logic/model

    @acoffman
    acoffman committed Jun 19, 2024
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Commits on Jun 20, 2024

  1. fusion select/create hooked up + validations

    @acoffman
    acoffman committed Jun 20, 2024
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Commits on Jul 3, 2024

  1. fusion variant creation form working, mp name generation handles fusions

    @acoffman
    acoffman committed Jul 3, 2024
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Commits on Jul 8, 2024

  1. fusion variant creation form is aware of gene partner status

    @acoffman
    acoffman committed Jul 8, 2024
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Commits on Jul 9, 2024

  1. coordinate card working on fusion display

    @acoffman
    acoffman committed Jul 9, 2024
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  2. fusions menu on gene feature pages

    @acoffman
    acoffman committed Jul 9, 2024
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Commits on Jul 18, 2024

  1. remove hardcoded login

    @acoffman
    acoffman committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. fix a couple of strings

    @acoffman
    acoffman committed Jul 19, 2024
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Commits on Jul 26, 2024

  1. attempt to backfill new coordinate type

    @acoffman
    acoffman committed Jul 26, 2024
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  2. introduce exon coordinate type

    @acoffman
    acoffman committed Jul 26, 2024
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Commits on Aug 6, 2024

  1. More updates to the backfill script

    @susannasiebert
    susannasiebert committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. background job to fill coordinates

    @acoffman
    acoffman committed Aug 7, 2024
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  2. additional tweaks to fusion coordinate fill script

    @acoffman
    acoffman committed Aug 7, 2024
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  3. Display exon coordinates on fusion variant pages

    @susannasiebert
    susannasiebert committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. initial fusions revision form

    @acoffman
    acoffman committed Aug 8, 2024
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  2. Display VICC compliant name

    @susannasiebert
    susannasiebert committed Aug 8, 2024
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  3. Add a few more TODOs to the port_fusion_coords script

    @susannasiebert
    susannasiebert committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. Implement fusion feature revision submission

    @susannasiebert
    susannasiebert committed Aug 9, 2024
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Commits on Aug 12, 2024

  1. Name representative variant for Fusions with an unknown fusion partne… 

    …r "Rearrangement" instead of "Fusion"
    @susannasiebert
    susannasiebert committed Aug 12, 2024
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  2. Fix error with fusion feature creation due to usage of in_revision_va… 

    …lidation_context
    @susannasiebert
    susannasiebert committed Aug 12, 2024
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  3. Fix some bugs in the variant creation introduced with ExonCoordinate … 

    …switch
    @susannasiebert
    susannasiebert committed Aug 12, 2024
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  4. retry fragment read with subtype on cache miss

    @acoffman
    acoffman committed Aug 12, 2024
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  5. validate transcript ids match expected ensembl format

    @acoffman
    acoffman committed Aug 12, 2024
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  6. flag variants when there is an issue backfilling coordinates

    @acoffman
    acoffman committed Aug 12, 2024
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  7. stub in coordinate fields for default bucket fusions

    @acoffman
    acoffman committed Aug 12, 2024
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  8. fusion revision submission working

    @acoffman
    acoffman committed Aug 12, 2024
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  9. remove hgvs and clinvar ids from fusion variant type

    @acoffman
    acoffman committed Aug 12, 2024
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  10. remove clinvar ids from fusions on mp card

    @acoffman
    acoffman committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. accepting fusion coordinate revisions is working

    @acoffman
    acoffman committed Aug 13, 2024
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  2. add fusion filter to feature browse table

    @acoffman
    acoffman committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. remove rearrangement fusion naming logic

    @acoffman
    acoffman committed Aug 14, 2024
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  2. fix failing test case

    @acoffman
    acoffman committed Aug 14, 2024
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Commits on Sep 14, 2024

  1. Merge branch 'main' into features-fusions

    @acoffman
    acoffman committed Sep 14, 2024
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Commits on Sep 16, 2024

  1. fix typo in tooltip message

    @acoffman
    acoffman committed Sep 16, 2024
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  2. pass in representative fusion name

    @acoffman
    acoffman committed Sep 16, 2024
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  3. strip whitespace from transcript ids on input

    @acoffman
    acoffman committed Sep 16, 2024
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  4. update query example to work with new coordinate schema

    @acoffman
    acoffman committed Sep 16, 2024
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  5. update backfill script

    @acoffman
    acoffman committed Sep 16, 2024
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  6. remove hgvs/clinvar entry id validation until we determine what to do… 

    … with it
    @acoffman
    acoffman committed Sep 16, 2024
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  7. pull back deprecated status in one more place

    @acoffman
    acoffman committed Sep 16, 2024
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  8. add open revision counts to the individual revision tabs

    @acoffman
    acoffman committed Sep 16, 2024
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  9. re-enable indexing on variants

    @acoffman
    acoffman committed Sep 16, 2024
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  10. fix typos to make codespell happy

    @acoffman
    acoffman committed Sep 16, 2024
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  11. coordinates are revisable

    @acoffman
    acoffman committed Sep 16, 2024
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