Match seed samples without recombination

[jeromekelleher]

Samples listed in include_samples are usually far diverged from the current ARG, so matching them with the standard num_mismatches gives spurious recombinations. Match them in a separate pass with a large num_mismatches so they are inserted on a single non-recombinant path.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 87.50000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 88.13%. Comparing base (465f72d) to head (4f791c1).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
sc2ts/inference.py	87.50%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #624      +/-   ##
==========================================
- Coverage   88.14%   88.13%   -0.02%     
==========================================
  Files          12       12              
  Lines        4159     4163       +4     
  Branches      594      596       +2     
==========================================
+ Hits         3666     3669       +3     
  Misses        363      363              
- Partials      130      131       +1     

Flag	Coverage Δ
python-tests	88.13% <87.50%> (-0.02%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.