Release Switch from pyd4 library to d4tools calls and fixes · Clinical-Genomics/chanjo2

[1.5]

coverage.d4_intervals_coverage responses contain also interval name as provided in bed file
coverage.d4_interval_coverage responses now returns also the genomic region used to compute the stats on
Test for modified function collecting coverage report data

Speed up response by coverage.d4_intervals_coverage by replacing pyd4 lib with direct calls d4tools and multiprocessing
Removed 2 redundant functions in meta.handle.bed.py
coverage.d4_interval_coverage is using direct calls to d4tools to retrieve stats over an entire chromosome or a genomic interval
Reformat report sample' sex rows and coverage.get_samples_predicted_sex endpoint to use d4tools and not pyd4 for evaluating sample sex
Refactored code to create coverage report and genes overview report to be faster by using d4tools calls and multiprocessing
Renamed handle_tasks.py to handle_completeness_tasks.py
Refactored coverage endpoints samples_genes_coverage, samples_transcripts_coverage and samples_exons_coverage to use calls to d4tools instead of the pyd4 library
Speed up coverage report creation by collecting SQL intervals before looping through samples stats
Refactored gene overview to use d4tools instead of pyd4 lib to compute gene-level intervals stats
Removed pyd4 lib and all remaining code which was still using it

coverage.d4_interval_coverage endpoint crashing trying to computer coverage completeness over an entire chromosome
Samples mean coverage values a hundredfold higher on coverage reports
Install software packages using poetry v<1.8 to avoid problems installing pyd4 (pyd4 not supporting PEP 517 builds)
Typo in report template with unclosed span/div causing cramped genes not found message
Mariadb container not passing healthcheck when runned from demo docker-compose file
Fixed an error on gene overview that made the coverage seem 100-folds higher
Return error when genes are not provided in the request form to create a coverage report