The codons belonging to the classes are not present in the output.

The default behaviour has been changed to be of more general use.
The previous default was to fill the NaNs not belonging to
all NaN columns with 0, which was suitable for standardized usage
biases (which are expected to be centered on 0), but we might prefer
to keep NaNs if we want to later replace those values with something
else when dealing with other usage metrics than biases. If a single
filling value is desired, it can be set using argument fill_other_nas.

Implementation detail: The fillna still happens, but with a default
value of np.nan, which hopefully should be OK.

Hopefully, this can be used to fill NaNs for PCA.

This consists in dividing counts by the maximum across synonymous codons
for a given amino-acid, and is supposed to avoid certain biases in PCA.

The main loading code is now in the function with more general name
*load_table_with_info_index*, which is also useful to load pre-filtered
counts tables with many info columns to be included in the index, and
not just bias tables.

Not tested.