Updated to Bootstrap 4

[4.8.0]

Added

• Updated Scout to use Bootstrap 4.3
• New looks for Scout
• Improved dashboard using Chart.js
• Ask before inactivating a case where last assigned user leaves it
• Genes can be manually added to the dynamic gene list directly on the case page
• Dynamic gene panels can optionally be used with clinical filter, instead of default gene panel
• Dynamic gene panels get link out to chanjo-report for coverage report
• Load all clinvar variants with clinvar Pathogenic, Likely Pathogenic and Conflicting pathogenic
• Show transcripts with exon numbers for structural variants
• Case sort order can now be toggled between ascending and descending.
• Variants can be marked as partial causative if phenotype is available for case.
• Show a frequency tooltip hover for SV-variants.
• Added support for LDAP login system
• Search snv and structural variants by chromosomal coordinates
• Structural variants can be marked as partial causative if phenotype is available for case.
• Show normal and pathologic limits for STRs in the STR variants view.
• Institute level persistent variant filter settings that can be retrieved and used.
• export causative variants to Excel
• Add support for ROH, WIG and chromosome PNGs in case-view

Fixed

• Fixed missing import for variants with comments
• Instructions on how to build docs
• Keep sanger order + verification when updating/reloading variants
• Fixed and moved broken filter actions (HPO gene panel and reset filter)
• Fixed string conversion to number
• UCSC links for structural variants are now separated per breakpoint (and whole variant where applicable)
• Reintroduced missing coverage report
• Fixed a bug preventing loading samples using the command line
• Better inheritance models customization for genes in gene panels
• STR variant page back to list button now does its one job.
• Allows to setup scout without a omim api key
• Fixed error causing "favicon not found" flash messages
• Removed flask --version from base cli
• Request rerun no longer changes case status. Active or archived cases inactivate on upload.
• Fixed missing tooltip on the cancer variants page
• Fixed weird Rank cell in variants page
• Next and first buttons order swap
• Added pagination (and POST capability) to cancer variants.
• Improves loading speed for variant page
• Problem with updating variant rank when no variants
• Improved Clinvar submission form
• General report crashing when dismissed variant has no valid dismiss code
• Also show collaborative case variants on the All variants view.
• Improved phenotype search using dataTables.js on phenotypes page
• Search and delete users with email instead of _id
• Fixed css styles so that multiselect options will all fit one column