Add LD-pruned biallelic SNP access method

[adilraza99]

Summary

Add support for generating LD-pruned SNP datasets from the existing biallelic SNP call pipeline.

Changes

• introduce AnophelesLdAnalysis mixin
• add biallelic_snp_calls_ld_pruned() method
• add ld_params.py for LD pruning parameters
• integrate the mixin into AnophelesDataResource
• add tests for LD pruning behaviour

Implementation

The method builds on top of biallelic_snp_calls():

1. load SNP dataset using the existing pipeline
2. compute genotype reference counts
3. apply LD pruning using allel.locate_unlinked
4. filter variants using _dask_compress_dataset
5. return an LD-pruned xarray.Dataset

Notes

• implementation follows the repository's cooperative mixin architecture
• returned dataset remains compatible with downstream processing (including PLINK export)
• LD pruning operates on datasets optionally thinned using the existing n_snps parameter

Tests

Added tests to verify:

• variant count is reduced after pruning
• dataset structure remains valid
• compatibility with downstream workflows
• threshold sensitivity (stricter threshold retains fewer variants)

closes #1049

[adilraza99]

Hey Jon,
I was thinking it might be helpful to include a small example notebook demonstrating how to use the LD-pruned SNP access method introduced in this PR.

Would you be okay with me adding one?
@jonbrenas

[adilraza99]

@jonbrenas just checking back on this - would be great to hear your thoughts when you get a chance.

Also linking Tristan’s earlier (#1049 (comment)) here for context.

[adilraza99]

Hi @jonbrenas, could you please review this PR? I’ve also added a small example notebook demonstrating the LD-pruned SNP workflow.