Add variant/sample summary statistic methods

[quansight-bot]

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• url: https://github.com/pystatgen/sgkit/issues/142
• state: closed
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• state: closed
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• url: https://github.com/pystatgen/sgkit/issues/142
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• state: open
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• url: https://github.com/pystatgen/sgkit/issues/142
• state: open
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• url: https://github.com/pystatgen/sgkit/issues/29
• state: open
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• created by: Eric Czech [[[[[[@eric-czech](https://github.com/eric-czech)](https://github.com/eric-czech)](https://github.com/eric-czech)](https://github.com/eric-czech)](https://github.com/eric-czech)](https://github.com/eric-czech)
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  • core operations
• assigned:
  • Tom White [[[[[[@tomwhite](https://github.com/tomwhite)](https://github.com/tomwhite)](https://github.com/tomwhite)](https://github.com/tomwhite)](https://github.com/tomwhite)](https://github.com/tomwhite)

Issue description

At a minimum, we need to be able to calculate these axis-wise aggregations (for GWAS QC):

• Variants (across samples)
  • genotype counts
  • allele counts and frequency
  • call count and rate
  • hwe p value (https://github.com/pystatgen/sgkit/issues/28)
• Samples (across variants)
  • call count and rate
  • genotype counts

I would propose that we start by making methods for each that take a single Dataset and return Dataset instances (it will be easier to define the frequencies/rates when the counts are defined in the same functions).

This should consider whatever the solution to https://github.com/pystatgen/sgkit/issues/3 ends up being.

[tomwhite]

Does anyone know why this PR (and dozens of others!) are being created? They are all duplicates of existing issues.

/cc @ericdatakelly @jerowe @daletovar @jeromekelleher

[goanpeca]

I am so sorry @tomwhite, I was testing something internally and used the wrong repo 🤦 .

I have closed all the redundant issues.

[tomwhite]

Thanks for responding @goanpeca. Looks like it's still running...

[goanpeca]

Looks like it's still running...

Yes I am shutting it down. Really sorry 😞 for this mess.