v4.91 - PanelApp extension, Dashboard advanced search, fixing ClinVar conflicting classifications and more

This release notably contains

• A new PanelApp extension, using the newer PanelApp API, allows more control building PanelApp "Green" aggregate panels.
• The Dashboard statistics now also uses the advanced caseS search.
• ClinVar category 8 had changed to "Conflicting classifications of pathogenicity" instead of "interpretations", causing many conflicting classifications to be presented as CLNSIG "other" on the variantS page. This is fixed for new cases.
• Some fixes related to the Balsamic 16 release, e.g. prioritising FORMAT.AF over AD for VAF and more accessible display of variant caller on variantS pages.
• Some LRS related fixes to variant export, and alignment display (IGV v3.0.9).
• Some fixes to ClinVar submission support.

A special thank you to contributors @molucorner (for Franklin links) and @Jakob37 (for WTS Outlier coordinate copy buttons)!

[4.91]

Added

• Variant link to Franklin in database buttons (different depending on rare or cancer track)
• MANE badges on list of variant's Genes/Transcripts/Proteins table, this way also SVs will display MANE annotations
• Export variant type and callers-related info fields when exporting variants from variantS pages
• Cases advanced search on the dashboard page
• Possibility to use only signed off panels when building the PanelApp GREEN panel

Changed

• On genes panel page and gene panel PDF export, it's more evident which genes were newly introduced into the panel
• WTS outlier position copy button on WTS outliers page
• Update IGV.js to v3.0.9
• Managed variants VCF export more verbose on SVs
• /api/v1/hpo-terms returns pymongo OperationFailure errors when provided query string contains problematic characters
• When parsing variants, prioritise caller AF if set in FORMAT over recalculation from AD
• Expand the submissions information section on the ClinVar submissions page to fully display long text entries
• Jarvik et al for PP1 added to ACMG modification guidelines
• Display institute _id + display name on dashboard filters
• ClinVar category 8 has changed to "Conflicting classifications of pathogenicity" instead of "interpretations"
• Simplify always loading ClinVar CLNSIG P, LP and conflicting annotations slightly
• Increased visibility of variant callers's "Pass" or "Filtered" on the following pages: SNV variants (cancer cases), SV variants (both RD and cancer cases)
• Names on IGV buttons, including an overview level IGV MT button
• Cases query no longer accepts strings for the name_query parameter, only ImmutableMultiDict (form data)
• Refactor the loading of PanelApp panels to use the maintained API - Customised PanelApp GREEN panels
• Better layout for Consequence cell on cancer SNVs page
• Merged Qual and Callers cell on cancer SNVs page

Fixed

• Empty custom_images dicts in case load config do not crash
• Tracks missing alignment files are skipped on generating IGV views
• ClinVar form to accept MedGen phenotypes
• Cancer SV variantS page spinner on variant export
• STRs variants export (do not allow null estimated variant size and repeat locus ID)
• STRs variants page when one or more variants have SweGen mean frequency but lack Short Tandem Repeat motif count
• ClinVar submission enquiry status for all submissions after the latest
• CLI scout update type hint error when running commands using Python 3.9
• Missing alignment files but present index files could crash the function creating alignment tracks for IGV display
• Fix missing "Repeat locus" info on STRs export

What's Changed

• On genes panel page, make more evident which genes are new after the panel is updated by @northwestwitch in #4957
• Fix #4970 - empty custom images dict does not crash on load by @dnil in #4971
• Fix #4974 - crash on missing aln file for one of the inds by @dnil in #4975
• WTS outlier copy to clipboard by @Jakob37 in #4981
• Fix #4977 - update IGV.js to 3.0.9 by @dnil in #4978
• Fix #4969 - adress the VCF output of given managed variants by @dnil in #4973
• /api/v1/hpo-terms handles pymongo OperationFailure errors by @northwestwitch in #4984
• Triallelic cancer VAF by @dnil in #4994
• Fix ClinVar form to accept MedGen phenotypes by @northwestwitch in #4998
• Expand ClinVar submission description section to display full info by @northwestwitch in #5000
• add form validate for cancer svs by @dnil in #5014
• Fix STRs variant export by @northwestwitch in #5015
• Fix #5001 - Jarvik for ACMG PP1 modification by @dnil in #5010
• Add MANE badges to the long list of transcripts on variant page by @northwestwitch in #5009
• Display institute _id + display name on dashboard filters by @northwestwitch in #5019
• Fix #5017 - ClinVar classifications of pathogenicity by @dnil in #5020
• Increased visibility of variant callers's "Pass" or "Filtered" on SNVs and SVs variants pages (both RD and cancer variants) by @northwestwitch in #5016
• Fix broken ClinVar submission status enquiry for all submissions after the latest by @northwestwitch in #5022
• Missing track item pt2 by @dnil in #5027
• Fix #4958 - IGV button names and IGV MT overview link by @dnil in #4976
• Advanced cases search on dashboard page by @northwestwitch in #4985
• Fix #5017 pt2 - swings and merry-go-rounds by @dnil in #5028
• Fix typing error when using python 3.9 by @northwestwitch in #5033
• Fix STRs export - part 2 by @northwestwitch in #5035
• Refactor PanelApp panels loading to use the correct PanelApp API by @northwestwitch in #5025
• Better layout for Consequence cell in cancer SNVs page by @northwestwitch in #5040
• Fix STRs variants view by @northwestwitch in #5038
• Franklin variant link by @dnil in #5041
• Fix missing track round3 by @northwestwitch in #5050
• Merge Qual and Callers cell on cancer SNVs page by @northwestwitch in #5045
• Fix missing repeat locus info on STRs export by @northwestwitch in #5052
• Minor release 4.91 by @northwestwitch in #5024

Full Changelog: v4.90.1...v4.91