Refactor report/overview code so coverage completeness is obtained directly from d4tools

[northwestwitch]

OBS: this PR can be merged only after d4tools contains the new "perc_cov" option in the stats command line, so I'm marking it as a draft

Description

Added/Changed/Fixed

• Fixes partially Improve performance of get_coverage_completeness.py #316 - This PR will be fixing the report and genes overview enpoints

How to test

• Deploy on stage and compare the coverage report from a scout case with coverage report obtained using main branch
• Compare also the genes overview using the same scout case

Expected outcome

• Numbers should be comparable (not exactly the same, because the new function calculates the mean completeness as the mean of all coverage completeness over all intervals. These numbers are collected from the d4tools output

Review

• Tests executed by
• "Merge and deploy" approved by

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 7.69231% with 36 lines in your changes missing coverage. Please review.

Project coverage is 89.66%. Comparing base (719f1b8) to head (153df0a).
Report is 11 commits behind head on main.

Files	Patch %	Lines
src/chanjo2/meta/handle_d4.py	7.89%	35 Missing ⚠️
src/chanjo2/meta/handle_report_contents.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #340      +/-   ##
==========================================
- Coverage   90.18%   89.66%   -0.52%     
==========================================
  Files          30       30              
  Lines        1457     1481      +24     
==========================================
+ Hits         1314     1328      +14     
- Misses        143      153      +10     

Flag	Coverage Δ
unittests	89.66% <7.69%> (-0.52%)	⬇️

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[northwestwitch]

To avoid errors I'm going to simplify and change the code of the completeness multitasker to code that uses the new perc_cov d4tools function. Closing this PR