Refactor handling of virtual contigs

[alimanfoo]

Towards #366, refactor handling of virtual contigs.

The main benefit here is that it allows testing using simulated data.

Also configuration of virtual contigs is more flexible, a virtual contig can be made of any number and combination of reference genome contigs.

Also here a haplotype_sites() function is surfaced in the public API - it's required internally within G123 but moving to public API as could be generally useful.

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (b38b34b) 98.42% compared to head (8db789d) 98.49%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #489 +/- ## ========================================== + Coverage 98.42% 98.49% +0.07% ========================================== Files 30 30 Lines 2408 2520 +112 ========================================== + Hits 2370 2482 +112 Misses 38 38 ```

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