Fix various indexing bugs

[tomwhite]

This fixes #506, and a couple of other related bugs that occur when an index is set and were found when working on #463:

• var_name in ds fails if the data variable var_name has been "moved" to be an index field of ds
• PCA doesn't work properly if there is an index set

Both of these cases are triggered by setting an index like this:

ds = ds.set_index({"variants": ("variant_contig", "variant_position")})

See also #473

[codecov-io]

Codecov Report

Merging #516 (a0e031c) into master (2c9a8e0) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##            master      #516   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           34        34           
  Lines         2642      2646    +4     
=========================================
+ Hits          2642      2646    +4     

Impacted Files	Coverage Δ
sgkit/stats/pca.py	100.00% <100.00%> (ø)
sgkit/variables.py	100.00% <100.00%> (ø)

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