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v4.50 - individual OMIM, more links, fixes and refactoring
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@dnil dnil released this 09 Mar 07:00
· 2415 commits to main since this release
v4.50
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Learn about vigilant mode.

[4.50]

Added

  • Individual-specific OMIM terms
  • OMIM disease descriptions in ClinVar submission form
  • Add a toggle for melter rerun monitoring of cases
  • Add a config option to show the rerun monitoring toggle
  • Add a cli option to export cases with rerun monitoring enabled
  • Add a link to STRipy for STR variants; shallow for ARX and HOXA13
  • Hide by default variants only present in unaffected individuals in variants filters
  • OMIM terms in general case report
  • Individual-level info on OMIM and HPO terms in general case report
  • PanelApp gene link among the external links on variant page
  • Dashboard case filters fields help
  • Filter cases by OMIM terms in cases and dashboard pages

Fixed

  • A malformed panel id request would crash with exception: now gives user warning flash with redirect
  • Link to HPO resource file hosted on http://purl.obolibrary.org
  • Gene search form when gene exists only in build 38
  • Fixed odd redirect error and poor error message on missing column for gene panel csv upload
  • Typo in parse variant transcripts function
  • Modified keys name used to parse local observations (archived) frequencies to reflect change in MIP keys naming
  • Better error handling for partly broken/timed out chanjo reports
  • Broken javascript code when case Chromograph data is malformed
  • Broader space for case synopsis in general report
  • Show partial causatives on causatives and matching causatives panels
  • Partial causative assignment in cases with no OMIM or HPO terms
  • Partial causative OMIM select options in variant page

Changed

  • Slightly smaller and improved layout of content in case PDF report
  • Relabel more cancer variant pages somatic for navigation
  • Unify caseS nav links
  • Removed unused add_compounds param from variant controllers function
  • Changed default hg19 genome for IGV.js to legacy hg19_1kg_decoy to fix a few problematic loci
  • Reduce code complexity (parse/ensembl.py)
  • Silence certain fields in ClinVar export if prioritised ones exist (chrom-start-end if hgvs exist)
  • Made phenotype non-mandatory when marking a variant as partial causative
  • Only one phenotype condition type (OMIM or HPO) per variant is used in ClinVar submissions
  • ClinVar submission variant condition prefers OMIM over HPO if available
  • Use lighter version of gene objects in Omim MongoDB adapter, panels controllers, panels views and institute controllers
  • Gene-variants table size is now adaptive
  • Remove unused file upload on gene-variants page
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