Expanded annotations on report, improved case status and loading support, more ACMG warnings, fixes and updates

[4.96]

Added

• Support case status assignment upon loading (by providing case status in the case config file)
• Severity predictions on general case report for SNVs and cancer SNVs
• Variant functional annotation on general case report for SNVs and cancer SNVs
• Version of Scout used when the case was loaded is displayed on case page and general report

Removed

• Discontinue ClinVar submissions via CSV files and support only submission via API: removed buttons for downloading ClinVar submission objects as CSV files

Changed

• Display STR variant filter status on corresponding variantS page
• Warning and reference to Biesecker et al when using PP1/BS4 and PP4 together in ACMG classifications
• Warning to not use PP4 criterion together with PS2/PM6 in ACMG classifications with reference to the SVI Recommendation for de novo Criteria (PS2 & PM6)
• Button to directly remove accepted submissions from ClinVar
• Upgraded libs in uv.lock file

Fixed

• Release docs to include instructions for upgrading dependencies
• Truncated long HGVS descriptions on cancer SNV and SNVs pages
• Avoid recurrent error by removing variant ranking settings in unranked demo case
• Actually re-raise exception after load aborts and has rolled back variant insertion