-OMICs variants, searchable SV genes, echtvar fields parsing and more

[4.86]

Added

• Display samples' name (tooltip) and affected status directly on caseS page
• Search SVs across all cases, in given genes
• CLINVAR_API_URL param can be specified in app settings to override the URL used to send ClinVar submissions to. Intended for testing.
• Support for loading and storing OMICS data
• Parse DROP Fraser and Outrider TSVs
• Display omics variants - wts outliers (Fraser, Outrider)
• Parse GNOMAD gnomad_af and gnomad_popmax_af keys from variants annotated with echtvar
• Make removed panel optionally visible to non-admin or non maintainers
• Parse CoLoRSdb frequencies annotated in the variant INFO field with the colorsdb_af key
• Download -omics variants using the Filter and export button
• Clickable COSMIC links on IGV tracks
• Possibility to un-audit previously audited filters
• Reverted table style and removed font awesome style from IGV template
• Case status tags displayed on dashboard case overview

Changed

• Updated igv.js to v3.0.1
• Alphabetically sort IGV track available for custom selection
• Updated wokeignore to avoid unfixable warning
• Update Chart.js to v4.4.3
• Use tornado library version >= 6.4.1
• Fewer variants in the MEI demo file
• Switch to FontAwesome v.6 instead of using icons v.5 + kit with icons v.6
• Show time (hours and minutes) additionally to date on comments and activity panel

Fixed

• Only add expected caller keys to variant (FOUND_IN or SVDB_ORIGIN)
• Splice junction merged track height offset in IGV.js
• Splice junction initiation crash with empty variant obj
• Splice junction variant routing for cases with WTS but without outlier data
• Variant links to ExAC, now pointing to gnomAD, since the ExAC browser is no longer available
• Style of HPO terms assigned to a case, now one phenotype per line
• RNA sashimi view rendering should work also if the gene track is user disabled
• Respect IGV tracks chosen by user in variant IGV settings

Load IGH genes and fixes

[4.85]

Added

• Load also genes which are missing Ensembl gene ID (72 in both builds), including immunoglobulins and fragile sites

Changed

• Unfreeze werkzeug again
• Show "(Removed)" after removed panels in dropdown
• The REVEL score is collected as the maximum REVEL score from all of the variant's transcripts
• Parse GNOMAD POPMAX values only if they are numerical when loading variants

Fixed

• Alphabetically sort "select default panels" dropdown menu options on case page
• Show gene panel removed status on case page
• Fixed visibility of the following buttons: remove assignee, remove pinned/causative, remove comment, remove case from group

Fix load order, loqusdbapi connection and chanjo-report extension load warning

[4.84]

Changed

• Clearer error message when a loqusdb query fails for an instance that initially connected
• Do not load chanjo-report module if not needed and more visible message when it fails loading
• Converted the HgncGene class into a Pydantic class
• Swap menu open and collapse indicator chevrons - down is now displayed-open, right hidden-closed
• Linters and actions now all use python 3.11

Fixed

• Safer way to update variant genes and compounds that avoids saving temporary decorators into variants' database documents
• Link to HGNC gene report on gene page
• Case file load priority so that e.g. SNV get loaded before SV, or clinical before research, for consistent variant_id collisions

Load MT VCFs, case-editing events, local IGV tracks & more

[4.83]

Added

• Edit ACMG classifications from variant page (only for classifications with criteria)
• Events for case CLI events (load case, update case, update individual)
• Support for loading and displaying local custom IGV tracks
• MANE IGV track to be used as a local track for igv.js (see scout demo config file)
• Optional separate MT VCFs, for nf-core/raredisease

Changed

• Avoid passing verbs from CaseHandler - functions for case sample and individual in CaseEventHandler
• Hide mtDNA report and coverage report links on case sidebar for cases with WTS data only
• Modified OMIM-AUTO gene panel to include genes in both genome builds
• Moved chanjo code into a dedicated extension
• Optimise the function that collects "match-safe" genes for an institute by avoiding duplicated genes from different panels
• Users must actively select "show matching causatives/managed" on a case page to see matching numbers
• Upgraded python version from 3.8 to 3.11 in Docker images

Fixed

• Fix several tests that relied on number of events after setup to be 0
• Removed unused load case function
• Artwork logo sync sketch with png and export svg
• Clearer exception handling on chanjo-report setup - fail early and visibly
• mtDNA report crashing when one or more samples from a case is not in the chanjo database
• Case page crashing on missing phenotype terms
• ACMG benign modifiers
• Speed up tests by caching python env correctly in Github action and adding two more test groups
• Agile issue templates were added globally to the CG-org. Adding custom issue templates to avoid exposing customers
• PanelApp panel not saving genes with empty EnsembleGeneIds list
• Speed up checking outdated gene panels
• Do not load research variants automatically when loading a case

Show STR size, red warning on sex check

[4.82.2]

Fixed

• Warning icon in case pages for individuals where confirmed_sex is false
• Show allele sizes form ExpansionHunter on STR variantS page again

Revert installation of flask-ldapconn

[4.82.1]

Fixed

• Revert the installation of flask-ldapconn to use the version available on PyPI to be able to push new scout releases to PyPI

ClinVar submission updates, TRGT STR VCFs and other fixes

[4.82]

Added

• Tooltip for combined score in tables for compounds and overlapping variants
• Checkbox to filter variants by excluding genes listed in selected gene panels, files or provided as list
• STR variant information card with database links, replacing empty frequency panel
• Display paging and number of HPO terms available in the database on Phenotypes page
• On case page, typeahead hints when searching for a disease using substrings containing source ("OMIM:", "ORPHA:")
• Button to monitor the status of submissions on ClinVar Submissions page
• Option to filter cancer variants by number of observations in somatic and germline archived database
• Documentation for integrating chanjo2
• More up-to-date VEP CSQ dbNSFP frequency keys
• Parse PacBio TRGT (Tandem repeat genotyping tool) Short Tandem Repeat VCFs

Changed

• In the case_report #panel-tables has a fixed width
• Updated IGV.js to 2.15.11
• Fusion variants in case report now contain same info as on fusion variantS page
• Block submission of somatic variants to ClinVar until we harmonise with their changed API
• Additional control on the format of conditions provided in ClinVar form
• Errors while loading managed variants from file are now displayed on the Managed Variants page
• Chanjo2 coverage button visible only when query will contain a list of HGNC gene IDs
• Use Python-Markdown directly instead of the unmaintained Flask-Markdown
• Use Markupsafe instead of long deprecated, now removed Flask Markup
• Prepare to unfreeze Werkzeug, but don't actually activate until chanjo can deal with the change

Fixed

• Submit requests to Chanjo2 using HTML forms instead of JSON data
• Research somatic variants link name on caseS page
• Broken Install the HTML 2 PDF renderer step in a GitHub action
• Fix ClinVar form parsing to not include ":" in conditionType.id when condition conditionType.db is Orphanet
• Fix condition dropdown and pre-selection on ClinVar form for cases with associated ORPHA diagnoses
• Improved visibility of ClinVar form in dark mode
• End coordinates for indels in ClinVar form
• Diagnoses API search crashing with empty search string
• Variant's overlapping panels should show overlapping of variant genes against the latest version of the panel
• Case page crashing when case has both variants in a ClinVar submission and pinned not loaded variants
• Installation of git in second build stage of Dockerfile, allowing correct installation of libraries

Somatic SV IGH-DUX4 tag, case report improvements and other fixes

[4.81]

Added

• Tag for somatic SV IGH-DUX4 detection samtools script

Changed

• Upgraded Bootstrap version in reports from 4.3.1 to 5.1.3

Fixed

• Buttons layout in HPO genes panel on case page
• Added back old variant rankscore index with different key order to help loading on demo instance
• Cancer case_report panel-table no longer contains inheritance information
• Case report pinned variants card now displays info text if all pinned variants are present in causatives
• Darkmode setting now applies to the comment-box accordion
• Typo in case report causing cancer_rank_options is undefined error

chanjo2 integration, index updates, frontend and Fusion gene fixes

[4.80]

Added

• Support for .d4 files coverage using chanjo2 (Case page sidebar link) with test
• Link to chanjo2 coverage report and coverage gene overview on gene panel page
• Link to chanjo2 coverage report on Case page, HPO dynamic gene list
• Link to genes coverage overview report on Case page, HPO dynamic gene list

Changed

• All links in disease table on diagnosis page now open in a new tab
• Dark mode settings applied to multi-selects on institute settings page
• Comments on case and variant pages can be viewed by expanding an accordion
• On case page information on pinned variants and variants submitted to ClinVar are displayed in the same table
• Demo case file paths are now stored as absolute paths
• Optimised indices to address slow queries
• On case page default panels are now found at the top of the table, and it can be sorted by this trait

Fixed

• On variants page, search for variants in genes present only in build 38 returning no results
• Pin/unpin with API was not able to make event links
• A new field Explanation for multiple conditions is available in ClinVar for submitting variants with more than one associated condition
• Fusion genes with partners lacking gene HGNC id will still be fully loaded
• Fusion variantS export now contains fusion variant specific columns
• When Loqusdb observations count is one the table includes information on if observation was for the current or another case

v4.79.1

[4.79.1]

Fixed

• Exporting variants without rank score causing page to crash
• Display custom annotations also on cancer variant page