Consistent method for dealing with ref bias in ska map

[johnlees]

Code now writes all mapped middle bases at the end

This ensures consistency with the ska nk output, but is not necessarily 'more correct'

[codecov-commenter]

Codecov Report

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

Project coverage is 92.43%. Comparing base (b99a298) to head (8b33279).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #70 +/- ## ======================================= Coverage 92.42% 92.43% ======================================= Files 16 16 Lines 2272 2273 +1 ======================================= + Hits 2100 2101 +1 Misses 172 172 ```

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