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Speedups and Clinical SV filter change

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@dnil dnil released this 28 Apr 12:17
· 1305 commits to main since this release
ccf742c

[4.67]

Added

  • Prepare to filter local SV frequency

Changed

  • Speed up instituteS page loading by refactoring cases/institutes query
  • Clinical Filter for SVs includes splice_polypyrimidine_tract_variant as a severe consequence
  • Clinical Filter for SVs includes local variant frequency freeze ("old") for filtering, starting at 30 counts
  • Speed up caseS page loading by adding status to index and refactoring totals count
  • HPO file parsing is updated to reflect that HPO have changed a few downloadable file formats with their 230405 release.

Fixed

  • Page crashing when a user tries to edit a comment that was removed
  • Warning instead of crashed page when attempting to retrieve a non-existent Phenopacket
  • Fixed StJude ProteinPaint gene link (URL change)
  • Freeze of werkzeug library to version<2.3 to avoid problems resulting from the consequential upgrade of the Flask lib
  • Huge list of genes in case report for megabases-long structural variants.
  • Fix displaying institutes without associated cases on institutes page
  • Fix default panel selection on SVs in cancer case report