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Minor version 4.89 - advanced search, more OMICS load options, chanjo2 for MT report and user level request log
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@dnil dnil released this 26 Sep 13:38
· 68 commits to main since this release
v4.89
c5856ce
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Learn about vigilant mode.

[4.89]

Added

  • Button on SMN CN page to search variants within SMN1 and SMN2 genes
  • Options for selectively updating OMICS variants (fraser, outrider) on a case
  • Log users' activity to file by specifying USERS_ACTIVITY_LOG_PATH parameter in app config
  • Mean MT coverage, Mean chrom 14 coverage and Estimated mtDNA copy number on MT coverage file from chanjo2 if available
  • In ClinVar multistep form, preselect ACMG criteria according to the variant's ACMG classification, if available
  • Subject id search from caseS page (supporting multiple sample types e.g.) - adding indexes to speed up caseS queries
  • Advanced cases search to narrow down results using more than one search parameter
  • Coverage report available for any case with samples containing d4 files, even if case has no associated gene panels
  • RNA delivery reports

Changed

  • Documentation for OMICS variants and updating a case
  • Include both creation and deletion dates in gene panels pages
  • Moved code to collect MT copy number stats for the MT report to the chanjo extension
  • On the gene panelS page, show expanded gene panel version list in one column only
  • IGV.js WTS loci default to zoom to a region around a variant instead of whole gene
  • Refactored logging module
  • Case general report no longer shows ORPHA inheritance models. OMIM models are shown colored.
  • Chromosome alias tab files used in the igv.js browser, which now contain the alias for chromosome "M"
  • Renamed "Comment on clinical significance" to "Comment on classification" in ClinVar multistep form
  • Enable Gens CN button also for non-wgs cancer track cases

Fixed

  • Broken heading anchors in the documentation (admin-guide/login-system.md and admin-guide/setup-scout.md files)
  • Avoid open login redirect attacks by always redirecting to cases page upon user login
  • Stricter check of ID of gene panels to prevent file downloading vulnerability
  • Removed link to the retired SPANR service. SPIDEX scores are still parsed and displayed if available from variant annotation.
  • Omics variant view test coverage
  • String pattern escape warnings
  • Code creating Alamut links for variant genes without canonical_transcript set
  • Variant delete button in ClinVar submissions page
  • Broken search cases by case similarity
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