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

Configure RNA build, add igv.js genome aliases

[4.87]

Added

• Option to configure RNA build on case load (default '38')

Changed

• Tooltip on RNA alignments now shows RNA genome build version
• Updated igv.js to v3.0.4

Fixed

• Style of "SNVs" and "SVs" buttons on WTS Outliers page
• Chromosome alias files for igv.js
• Genes track displayed also when RNA alignments are present without splice junctions track on igv browser
• Genes track displayed again when splice junction tracks are present

Fix loading and updating of PanelApp panels

[4.86.1]

Fixed

• Loading and updating PanelApp panels, including PanelApp green