NetCDF metadata and selected data variables

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Hi All,
I posted the same question last Friday, but I didn't get any response so I
am going to rephrase it now that I have explored the problem myself a little
more.

My program is applying subset and reduction criteria to a netcdf file and
outputting another netcdf file.  I am also allowing the user to choose which
data variables they get in the output.  The problem I am having is that when
I write out the metadata I have conflicting requirements for how that
metadata will look.  How do I reconcile differences in the subset and
reduction criteria which has ben applied to the data variables.  This does
not seem to be posible given the structure of the netcdf file.

When looking closely at the metadata which is written to the output netcdf
file I can see that the length of each coordinate variable is set.   This
doesn't make sense when I am subsequently gong to write out data variables
which either don't use one of the coordinate dimensions at all, or have
different lengths for the coordinate variables.

I suspect I am trying to do something that the netCDF file format does not
support.

Thanks
Brian

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