Shade compounds, improved general report SVs

[4.51]

Added

• Config file containing codecov settings for pull requests
• Add an IGV.js direct link button from case page
• Security policy file
• Hide/shade compound variants based on rank score on variantS from filter
• Chromograph legend documentation direct link

Changed

• Updated deprecated Codecov GitHub action to v.2
• Simplified code of scout/adapter/mongo/variant
• Update IGV.js to v2.11.2
• Show summary number of variant gene panels on general report if more than 3

Fixed

• Marrvel link for variants in genome build 38 (using liftover to build 37)
• Remove flags from codecov config file
• Fixed filter bug with high negative SPIDEX scores
• Renamed IARC TP53 button to to TP53 Database, modified also link since IARC has been moved to the US NCI: https://tp53.isb-cgc.org/
• Parsing new format of OMIM case info when exporting patients to Matchmaker
• Remove flask-debugtoolbar lib dependency that is using deprecated code and causes app to crash after new release of Jinja2 (3.1)
• Variant page crashing for cases with old OMIM terms structure (a list of integers instead of dictionary)
• Variant page crashing when creating MARRVEL link for cases with no genome build
• SpliceAI documentation link
• Fix deprecated safe_str_cmp import from werkzeug.security by freezing Werkzeug lib to v2.0 until Flask_login v.0.6 with bugfix is released
• List gene names densely in general report for SVs that contain more than 3 genes
• Show transcript ids on refseq genes on hg19 in IGV.js, using refgene source
• Display correct number of genes in general report for SVs that contain more than 32 genes
• Broken Google login after new major release of lepture/authlib
• Fix frequency and callers display on case general report