Add Garuds G gwss statistics

[sanjaynagi]

In this PR, I add the Garuds G statistics (G1, G12, G123, G2/G1) to scikit-allel.

We use the same hashing function as the Garuds H functions, as opposed to the optimised (DJB33XA) hash function used in malariagen_data. Currently I cant actually install scikit-allel, not sure whats going on, have asked @alimanfoo for help.

We also add a function diplotype_frequencies() which computes distinct_frequencies of diplotypes. This is not quite analogous to the garuds_h function, as the garuds_h function takes an allel.HaplotypeArray which has the method distinct_frequencies(). garuds_g expects an array of alternate counts (biallelic, from GenotypeArray.to_n_alt() ), which is not a scikit-allel class (just a np array), therefore we cannot add its own methods to it.

As far as I can see, H12 does not have tests, so I haven't added any yet, but will do.

[pep8speaks]

Hello @sanjaynagi! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file allel/stats/selection.py:

Line 842:1: E302 expected 2 blank lines, found 1
Line 863:1: E302 expected 2 blank lines, found 1
Line 893:1: W293 blank line contains whitespace
Line 909:1: E302 expected 2 blank lines, found 1

Comment last updated at 2024-10-10 17:02:09 UTC

[sanjaynagi]

Working nicely!

Havent written any tests yet, otherwise id say this is ready to merge. FWIW, i cant see any tests for H12, otherwise I would've copied them.