Previously, the dynamic filter operated on the average haplotype count at each marker, rather than the total count (for dumb historical reasons). This PR updates the dynamic filter so it operates correctly. The effective coverage parameter was dropped, and support for marker-specific thresholds was added via a CSV file.
[x] Changes are clearly described above
Any relevant issue threads are referenced in the description
[x] Any new features are tested (see docs/DEVEL.md for details)
Previously, the dynamic filter operated on the average haplotype count at each marker, rather than the total count (for dumb historical reasons). This PR updates the dynamic filter so it operates correctly. The effective coverage parameter was dropped, and support for marker-specific thresholds was added via a CSV file.
Any relevant issue threads are referenced in the description