Major release 2.0

[2.0]

Added

• Improve report explanation to better interpret average coverage and coverage completeness stats shown on the coverage report
• Check that provided d4 files when running queries using /coverage/d4/genes/summary endpoint are valid, with test
• General report with coverage over the entire genome when no genes or genes panels are provided
• A MANE coverage report, showing coverage and coverage completeness only on MANE transcripts for the provided list of genes
• Link out from MANE overview to gene overview
• Save ensembl_transcript_id and exon rank info on exons database records
• Display MANE badges on gene overview report
• Create PDF button on MANE overview and gene overview pages
• Documentation on how to create MANE overview reports

Changed

• Do not use stored cases/samples any more and run stats exclusively on d4 files paths provided by the user in real time
• How parameters are passed to starlette.templating since it was raising a deprecation warning.
• Replaced deprecated Pydantic parse_obj method with model_validate
• Report and genes overview endpoints accept only POST requests with form data now (application/x-www-form-urlencoded) - no json
• Sort alphabetically the list genes that are incompletely covered on report page
• d4_genes_condensed_summary coverage endpoint will not convert nan or inf coverage values to None, but to str(value)
• Updated the Dockerfile base image so it contains the latest d4tools (master branch)
• Updated tests workflow to cargo install the latest d4tools from git (master branch)
• Computing coverage completeness stats using d4tools perc_cov stat function (much quicker reports)
• Moved functions computing the coverage stats to a separate meta/handle_coverage_stats.py module
• Refactored code collecting stats shown on gene overview report
• Gene report to contain both transcripts and exons stats

Fixed

• Updated dependencies including certifi to address dependabot alert
• Update pytest to v.7.4.4 to address a ReDoS vulnerability
• Colored logs
• Link for switching between coverage thresholds on overview report
• Gene links in genes overview page open into new tabs