vcztools view: INFO field computation performance

[Will-Tyler]

Description

When the user specifies a sample selection in vcztools view, vcztools recalculates the AC and AN INFO fields. This is consistent with bcftools' behavior. vcztools calculates these INFO fields using all of the samples in a variant-wise chunk of genotype data. The current implementation in pure Python using NumPy may be slow and create a lot of overhead. This issue is to improve the computation and memory efficiency. The solution may require calculating AC and AN in a C extension module.

The original code was added in #77.

References

• bcftools view

[jeromekelleher]

We already have a C extension module, so it wouldn't be that hard to update it to include computing AC and AN.

[jeromekelleher]

See #77 (comment) for details on slowdown

[jeromekelleher]

Putting this in the initial release milestone for now, can triage out later if it's not critical.

[jeromekelleher]

Removing this from initial release as sample subsetting is temporarily dropped in #120