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Improved managed variants, deprecation of Python 3.9 & More

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@northwestwitch northwestwitch released this 13 Nov 08:30
· 242 commits to main since this release
v4.106
d3f7f04
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[4.106]

Added

  • Bulk dismiss STR variants from variantS page (#5774)
  • Delete flag for update individual command (#5793)
  • Update report command, with a delete flag (#5793)
  • Display phase blocks gtf - new key on individuals, parsed from case load config or updated via CLI (#5822)
  • Validation of managed variants input (#5842)

Changed

  • Refactored variantS pages to share an intermediate template (#5774)
  • Removed ClinVar submissions instructions from case pages - it's still present on the ClinVar submissions page (#5806)
  • Render the case report's pedigree SVG to a temporary file without Cairo when exporting it to PDF (#5791)
  • Deprecate python 3.9 which has reached its EOL, default build to 3.14 (#5818)
  • Don't build in editable mode for Docker images (#5819)
  • Restored installation of chanjo-report from PyPI (#5820)
  • Export of managed variants to VCF is subject to validation. Variants failing validation will raise a warning instead of being included in the VCF file (#5813)
  • Reintroduced a link to ClinVar submissions page on variant page - now also for oncogenic variants (#5844)

Fixed

  • Filter f hotkey not working on cancer variantS pages (#5788)
  • IGV.js updated to v3.5.4 (#5790)
  • Broken ClinVar germline submission page when submission contains SVs (#5805)
  • Missing size_selector in old filters containing a size criterion, causing the variantS page to crash (#5817 and #5855)
  • Avoid backslash in f-strings, to preserve backwards compatibility with old python (#5818)
  • GnomAD links for the STR variant page (#5823)
  • get_gene_complete_coverage breaking for genes with no intervals on chanjo2, which is returning 'NA' instead of numerical stats (#5830)
  • Chromosome order for hg38 in IGV.js view (#5838)
  • Clinical filter for outlier variants (#5832)
  • Decipher query was treated as a primary - now secondary again (#5832)
  • Expansion support display on STR GT card (#5840)
  • Keep any active page filters alive when editing/removing managed variants (#5833 & #5836)
  • MIM diseases can have multiple descriptions - merge them instead of using the first (#5814)
  • Cytobands chrom select undefined at managed variants page load - js console warning cleanup (#5841)
  • Cancer case page not showing if a pinned variant is included in an oncogenic ClinVar submission (#5844)
  • 429 Client Error: Too Many Requests when updating the PanelApp GREEN panel using the command line (#5849)
  • Revert general POST redirect and introduce separate such for managed variants (#5857)
  • Prevent false positives in REF/ALT validation of managed variants (#5859)
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