Fixed parsing of DR key in VCF files created with Tiddit

[4.57.4]

Fixed

• Parsing of variant.FORMAT "DR" key in parse variant file

Validated variants export fixes

[4.57.3]

Fixed

• Export of STR verified variants
• Do not download as verified variants first verified and then reset to not validated
• Avoid duplicated lines in downloaded verified variants reflecting changes in variant validation status

Fixed export of verified variants and ranked cancer variants pages

[4.57.2]

Fixed

• Export of verified variants when variant gene has no transcripts
• HTTP 500 when visiting a the details page for a cancer variant that had been ranked with genmod

Multiple loqusdb instances, dismiss counts and user events timeline

[4.57]

Added

• Display last 50 or 500 events for a user in a timeline
• Show dismiss count from other cases on matching variantS
• Save Beacon-related events in events collection
• Institute settings allow saving multiple loqusdb instances for one institute
• Display stats from multiple instances of loqusdb on variant page
• Display date and frequency of obs derived from count of local archive observations from MIP11 (requires fix in MIP)

Changed

• Prior ACMG classifications view is no longer limited by pathogenicity

Fixed

• Visibility of Sanger ordered badge on case page, light mode
• Some of the DataTables tables (Phenotypes and Diagnoses pages) got a bit dark in dark mode
• Remove all redundancies when displaying timeline events (some events are saved both as case-related and variant-related)
• Missing link in saved MatchMaker-related events
• Genes with mixed case gene symbols missing in PanelApp panels
• Alignment of elements on the Beacon submission modal window
• Locus info links from STR variantS page open in new browser tabs

Fix updating/replacing a gene panel using a malformed file

[4.57.1]

Fixed

• Updating/replacing a gene panel from file with a corrupted or malformed file

v4.56 - CLI database update fix and a PANEL-UMI analysis category

[4.56]

Added

• Test for PanelApp panels loading
• panel-umi tag option when loading cancer analyses

Changed

• Black text to make comments more visible in dark mode
• Loading PanelApp panels replaces pre-existing panels with same version
• Removed sidebar from Causatives page - navigation is available on the top bar for now

Fixed

• Remove a:visited css style from all buttons
• Update of HPO terms via command line
• Background color of MIXED and PANEL-UMI sequencing types on cases page
• Fixed regex error when searching for cases with query ending with \
• Gene symbols on Causatives page lighter in dark mode
• SpliceAI tooltip of multigene variants

v4.55 - force update and fixes

[4.55]

Changed

• Represent different tumor samples as vials in cases page
• Option to force-update the OMIM panel

Fixed

• Low tumor purity badge alignment in cancer samples table on cancer case view
• VariantS comment popovers reactivate on hover
• Updating database genes in build 37
• ACMG classification summary hidden by sticky navbar
• Logo backgrounds fixed to white on welcome page
• Visited links turn purple again
• Style of link buttons and dropdown menus
• Update KUH and GMS logos
• Link color for Managed variants

4.54 - Dark Mode, Bootstrap 5

[4.54]

Added

• Dark mode, using browser/OS media preference
• Allow marking case as solved without defining causative variants
• Admin users can create missing beacon datasets from the institute's settings page
• GenCC links on gene and variant pages
• Deprecation warnings when launching the app using a .yaml config file or loading cases using .ped files

Changed

• Improved HTML syntax in case report template
• Modified message displayed when variant rank stats could not be calculated
• Expanded instructions on how to test on CG development server (cg-vm1)
• Added more somatic variant callers (Balsamic v9 SNV, develop SV)

Fixed

• Remove load demo case command from docker-compose.yml
• Text elements being split across pages in PDF reports
• Made login password field of type password in LDAP login form
• Gene panels HTML select in institute's settings page
• Bootstrap upgraded to version 5
• Fix some Sourcery and SonarCloud suggestions
• Escape special characters in case search on institute and dashboard pages
• Broken case PDF reports when no Madeline pedigree image can be created
• Removed text-white links style that were invisible in new pages style
• Variants pagination after pressing "Filter variants" or "Clinical filter"
• Layout of buttons Matchmaker submission panel (case page)
• Removing cases from Matchmaker (simplified code and fixed functionality)
• Reintroduce check for missing alignment files purged from server

MIP11 compatibility adjustments and vulnerability fixes

[4.53]

Added

Changed

• Point Alamut API key docs link to new API version
• Parse dbSNP id from ID only if it says "rs", else use VEP CSQ fields
• Removed MarkupSafe from the dependencies

Fixed

• Reintroduced loading of SVs for demo case 643595
• Successful parse of FOUND_IN should avoid GATK caller default
• All vulnerabilities flagged by SonarCloud

Security fixes, new features and general maintenance

[4.52]

Added

• Demo cancer case gets loaded together with demo RD case in demo instance
• Parse REVEL_score alongside REVEL_rankscore from csq field and display it on SNV variant page
• Rank score results now show the ranking range
• cDNA and protein changes displayed on institute causatives pages
• Optional SESSION_TIMEOUT_MINUTES configuration in app config files
• Script to convert old OMIM case format (list of integers) to new format (list of dictionaries)
• Additional check for user logged in status before serving alignment files
• Download .cgh files from cancer samples table on cancer case page
• Number of documents and date of last update on genes page

Changed

• Verify user before redirecting to IGV alignments and sashimi plots
• Build case IGV tracks starting from case and variant objects instead of passing all params in a form
• Unfreeze Werkzeug lib since Flask_login v.0.6 with bugfix has been released
• Sort gene panels by name (panelS and variant page)
• Removed unused server.blueprints.alignviewers.unindexed_remote_static endpoint
• User sessions to check files served by server.blueprints.alignviewers.remote_static endpoint
• Moved Beacon-related functions to a dedicated app extension
• Audit Filter now also loads filter displaying the variants for it

Fixed

• Handle attachment_filename parameter renamed to download_name when Flask 2.2 will be released
• Removed cursor timeout param in cases find adapter function to avoid many code warnings
• Removed stream argument deprecation warning in tests
• Handle no intervals found warning in load_region test
• Beacon remove variants
• Protect remote_cors function in alignviewers view from Server-Side Request Forgery (SSRF)
• Check creation date of last document in gene collection to display when genes collection was updated last