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fix: consider masked sites for dN and dS calculation
Test Sm v9 Apptainer
#47:
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fix: consider masked sites for dN and dS calculation
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refactor: update logging
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fix: consider masked sites for dN and dS calculation
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fix: consider masked sites for dN and dS calculation
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fix: consider masked sites for dN and dS calculation
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refactor: update af-time correlation data logging
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fix: handle variants with fewer than necessary time points
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fix: init missing columns
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