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Variants load speedup, delete RNA command + other improvements and fixes

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@northwestwitch northwestwitch released this 13 Jan 09:58
· 209 commits to main since this release
v4.107
3ab66e2
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Learn about vigilant mode.

[4.107]

Added

  • On cases page, print a RNA label whenever WGS or WES cases have associated RNA data (#5886)
  • Save and display maintainer/institutes for managed variants (#5890)
  • Link to VuTR at the transcript level from the variant page (#5893)
  • Filter germline ClinVar submission IDs by ClinVar ID (#5907)
  • Link to ACMG classification form on SV page - with warnings (#5891)
  • scout delete rna -c <case-id> command to remove all RNA-related data from a case (#5916)
  • Chromograph ideograms for hg38 (#5883)

Changed

  • A case becomes inactive whenever there is a change to any VCF or RNA-associated file (#5888)
  • Enhance variants filters by allowing selection of individual soft filters (#5897)
  • On ACMG classification form, move Submit button at the bottom and ClinGen gene links to the top (#5876)
  • Search panels by gene only within user’s institutes (#5902)
  • A more compact gene panels page with panel search options (#5913)
  • Extra space for sequencing type badges on cases page (#5920)
  • Support multi-value REVEL scores when parsing each transcript (#5923)
  • Update GitHub workflows (#5935)
  • IGV.js to version 3.7.1 (#5931)
  • Refactored code for collecting and displaying STR variants, which now shares same routines as SV and MEI variants (#5895)
  • Deprecate reupload_sv (#5933)
  • Dual locus IGV view for BNDs with breaks on different chromosomes (#5939)
  • Lazier checking of variant load criteria: most costly query last (#5924)
  • Caching variant load criteria queries for considerable speedup for large variant files (#5924)

Fixed

  • Fix PanelApp fetch failures caused by 429 responses - Retry-After support (#5864)
  • Parsing of REVEL rank score field for LRS from all transcript of a LRS variant (#5860)
  • Tests for cli command to update VCF files not running (#5888)
  • Gene in panels search results broken layout - overflow when a panel has many panel versions containing the gene (#5899)
  • ACMG evaluation PDF export, both style and colors (#5879)
  • Genotype query for singletons when not selecting include only in unaffected (#5914)
  • Restored Analysis type label on verified/causatives view (#5915)
  • Start to end interval search for managed variants (#5917)
  • Export causatives from CLI when variant id or quality is unset (#5929)
  • Add color to inheritance tags under "Gene annotations", on variant page (#5940)
  • STR allele sequences no longer printed in full on general report (#5928)
  • gDNA overview in IGV.js undefined loci (#5948)
  • ClinGen Criteria Specifications links (CSPEC) on previously submitted ACMG classifications (#5949)
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