Structural variantS header fix and IGV.js v3.1.0

Fixed

• Update IGV.js to v3.1.0
• Columns/headings on SV variantS shifted

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

Fixed parsing of Matchmaker Exchange's matches dates causing matchings page to crash

[4.90.1]

Fixed

• Parsing Matchmaker Exchange's matches dates

ACMG classification improvements, gene panels import/export fixes and more

[4.90]

Added

• Link to chanjo2 MANE coverage overview on case page and panel page
• More SVI recommendation links on the ACMG page
• IGV buttons for SMN CN page
• Warnings on ACMG classifications for potentially conflicting classification pairs
• ACMG Bayesian foundation point scale after Tavtigian for variant heat profile

Changed

• Variants query backend allows rank_score filtering
• Added script to tabulate causatives clinical filter rank
• Do not display inheritance models associated to ORPHA terms on variant page
• Moved edit and delete buttons close to gene names on gene panel page and other aesthetical fixes
• SNV VariantS page functional annotation and region annotation columns merged
• VariantS pages (not cancer) gene cells show OMIM inheritance pattern badges also without hover
• STR variantS page to show STR inheritance model without hover (fallback to OMIM for non-Stranger annotation)
• VariantS page local observation badges have counts visible also without hover
• On Matchmaker page, show number of matches together with matching attempt date
• Display all custom inheritance models, both standard and non-standard, as gathered from the gene panel information on the variant page

Fixed

• Make BA1 fully stand-alone to Benign prediction
• Modifying Benign terms to "Moderate" has no effect under Richards. Ignored completely before, will retain unmodified significance now
• Extract all fields correctly when exporting a panel to file from gene panel page
• Custom updates to a gene in a panel
• Gene panel PDF export, including gene links
• Cancer SV, Fusion, MEI and Outlier filters are shown on the Institute Filters overview
• CaseS advanced search limit
• Visibility of Matchmaker Exchange matches on dark mode
• When creating a new gene panel from file, all gene fields are saved, including comments and manual inheritance models
• Downloading on gene names from EBI
• Links to gene panels on variant page, summary panel
• Exporting gene variants when one or more variants' genes are missing HGNC symbol

OMIM-AUTO gene panel gene symbols alias fallback

Patch release due to a current issue with in particular one gene symbol alias (POPDC1 aka BVES) on OMIM-AUTO.

[4.89.2]

Fixed

• If OMIM gene panel gene symbols are not mapping to hgnc_id, allow fallback use of a unique gene alias

Patch general case report

[4.89.1]

Fixed

• General case report crash when encountering STR variants without source tags
• Coloring and SV inheritance patterns on general case report

Minor version 4.89 - advanced search, more OMICS load options, chanjo2 for MT report and user level request log

[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

Patch update igv.js to 3.0.5

[4.88.1]

Fixed

• Patch update igv.js to 3.0.5

Fixed broken database setup command, new -omics variants keys

[4.88]

Added

• Added CoLoRSdb frequency to Pop Freq column on variantS page
• Hovertip to gene panel names with associated genes in SV variant view, when variant covers more than one gene
• RNA sample ID can be provided in case load config if different from sample_id

Fixed

• Broken scout setup database command
• Update demo VCF header, adding missing keys found on variants
• Broken upload to Codecov step in Tests & Coverage GitHub action
• Tomte DROP column names have been updated (backwards compatibility preserved for main fields)
• WTS outlierS view to display correct individual IDs for cases with multiple individuals
• WTS outlierS not displayed on WTS outlierS view

Positioning and alignment of genes cell on variantS page

Quick patch release.

[4.87.1]

Fixed

• Positioning and alignment of genes cell on variantS page