Notebook continuous integration 01/24/22: simplify genotype simulation notebooks

[williambrandler]

Signed-off-by: William Brandler william.brandler@databricks.com

What changes are proposed in this pull request?

Split the genotype simulation notebook up into three:

1. download 1000G data (before just two chromosomes, now all autosomes)
2. define functions for hardy weinberg etc to simulate genotypes
3. perform data simulation on downloaded VCFs

This avoids having to always download 1000G data, which is the bottleneck for testing the code. Functions are split out into their own notebook, eventually this notebook can be deleted when the simulation is done by a library such as sim1000G

Added a tip that phenotypes and covariates should be sorted in same order as genotypes

How is this patch tested?

• [ ] Integration tests

(Details)

[codecov[bot]]

Codecov Report

Merging #477 (4846dc0) into master (f9eda3e) will not change coverage. The diff coverage is n/a.

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##           master     #477   +/-   ##
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  Coverage   93.66%   93.66%           
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  Files          95       95           
  Lines        4875     4875           
  Branches      457      457           
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  Hits         4566     4566           
  Misses        309      309           

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