Deal with multiple contigs and sequence lengths

[hyanwong]

Introduces a contig_id parameter to variant_data, which adds non matching contigs to the site mask, as described in #949. Fixes #949

[codecov]

Codecov Report

Attention: Patch coverage is 92.30769% with 2 lines in your changes missing coverage. Please review.

Project coverage is 93.21%. Comparing base (7f23758) to head (8742ee8).

Files with missing lines	Patch %	Lines
tsinfer/formats.py	92.30%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #964      +/-   ##
==========================================
+ Coverage   93.15%   93.21%   +0.05%     
==========================================
  Files          18       18              
  Lines        6368     6393      +25     
  Branches     1142     1151       +9     
==========================================
+ Hits         5932     5959      +27     
+ Misses        296      293       -3     
- Partials      140      141       +1     

Flag	Coverage Δ
C	93.21% <92.30%> (+0.05%)	⬆️
python	95.56% <92.30%> (+0.06%)	⬆️

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[hyanwong]

Also fixes #763 I think