Added thinSNP function

[alex-sandercock]

Added a thinSNP() to be able to thin a data.frame of genomic positions using a specified distance

[codecov]

Codecov Report

❌ Patch coverage is 72.66187% with 38 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.35%. Comparing base (1998376) to head (b98602e).
⚠️ Report is 18 commits behind head on development.

Files with missing lines	Patch %	Lines
R/madc2gmat.R	72.97%	20 Missing ⚠️
R/updog2vcf.R	16.66%	15 Missing ⚠️
R/madc2vcf_targets.R	90.00%	2 Missing ⚠️
R/thinSNP.R	96.29%	1 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development      #40      +/-   ##
===============================================
- Coverage        84.87%   83.35%   -1.52%     
===============================================
  Files               18       19       +1     
  Lines             1243     1358     +115     
===============================================
+ Hits              1055     1132      +77     
- Misses             188      226      +38     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[Cristianetaniguti]

@alex-sandercock I think you just need to roxygenise to fix the actions error

[Copilot]

Pull Request Overview

This PR adds a new thinSNP function for genomic data processing and makes several improvements to existing functions. The thinSNP function enables filtering SNPs based on minimum genomic distance between markers within chromosomes, which is useful for reducing linkage disequilibrium in genomic analyses.

• Added thinSNP() function to thin SNP datasets by genomic position and minimum distance
• Enhanced updog2vcf() function to accept optional reference/alternate allele information
• Updated madc2gmat() function to support polyploid genomics with VanRaden method implementation

Reviewed Changes

Copilot reviewed 14 out of 14 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
R/thinSNP.R	New function implementation for SNP thinning based on genomic coordinates
tests/testthat/test-thinSNP.R	Test suite for the new thinSNP function
man/thinSNP.Rd	Documentation for the thinSNP function
R/updog2vcf.R	Enhanced to support optional RefAlt parameter for actual allele information
R/madc2gmat.R	Major refactor to support polyploid analysis and VanRaden method
R/breedtools_functions.R	Exported previously internal functions for breed composition analysis
NAMESPACE	Updated exports and imports for new functionality

---

_{Tip: Customize your code reviews with copilot-instructions.md. Create the file or learn how to get started.}

[Copilot]

The documentation includes parameters p and names that are not present in the actual function signature. The QPsolve function only accepts Y and X parameters.

Suggested change

	\item{p}{numeric indicating number of breeds represented in X}
	\item{names}{character names of breeds}

[Copilot]

The comment uses Roxygen2 syntax (##') instead of regular R comment syntax (#) in a test file. Test files should use standard R comments.

Suggested change

	##' # Create sample SNP data
	# Create sample SNP data