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[bot]]

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 :warning:

Additional details and impacted files

```diff @@ 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](https://app.codecov.io/gh/tskit-dev/tsinfer/pull/964/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | Coverage Δ | | |---|---|---| | [C](https://app.codecov.io/gh/tskit-dev/tsinfer/pull/964/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `93.21% <92.30%> (+0.05%)` | :arrow_up: | | [python](https://app.codecov.io/gh/tskit-dev/tsinfer/pull/964/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev) | `95.56% <92.30%> (+0.06%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=tskit-dev#carryforward-flags-in-the-pull-request-comment) to find out more.

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

[hyanwong]

Also fixes #763 I think