Numpy deprecation warnings

[jeromekelleher]

Getting these in CI:

tests/test_cli.py: 8 warnings
36
tests/test_vcf.py: 38 warnings
37
tests/test_vcf_examples.py: 1365 warnings
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  /home/runner/work/bio2zarr/bio2zarr/bio2zarr/vcf.py:386: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
39
    buff[j] = x

Should be an easy fix