Introduce low quality clonal mutations

[priesgo]

Changes the classification of mutations from filter to VAF.
The new thresholds are:

• 0.02 for low frequency mutations
• 0.5 for subclonal (intrahost) mutations
• 0.8 for low quality clonal

Related to #56 and TRON-Bioinformatics/covigator-ngs-pipeline#42

[codecov]

Codecov Report

Base: 82.28% // Head: 83.00% // Increases project coverage by +0.72% 🎉

Coverage data is based on head (11a4c71) compared to base (9a939de).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #77      +/-   ##
===========================================
+ Coverage    82.28%   83.00%   +0.72%     
===========================================
  Files           46       46              
  Lines         4024     4173     +149     
===========================================
+ Hits          3311     3464     +153     
+ Misses         713      709       -4     

Impacted Files	Coverage Δ
covigator/pipeline/ena_pipeline.py	47.82% <ø> (ø)
covigator/configuration.py	85.83% <100.00%> (+0.36%)	⬆️
covigator/database/model.py	98.76% <100.00%> (+0.28%)	⬆️
covigator/pipeline/vcf_loader.py	94.82% <100.00%> (+2.86%)	⬆️
covigator/tests/unit_tests/abstract_test.py	94.73% <100.00%> (+0.50%)	⬆️
covigator/tests/unit_tests/test_vcf_loader.py	100.00% <100.00%> (ø)

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[priesgo]

resolves #56