Development

[alex-sandercock]

This pull request introduces several new features and improvements to the BIGr package, including new functions for filtering and processing MADC files, generating genomic relationship matrices, and enhancements to existing functions. It also updates package metadata and dependencies. The most important changes are summarized below:

New Functionality

• Added filterMADC function to filter and process MADC files with various quality control options. This function supports filtering based on mean read depth, number of microhaplotypes per locus, and other criteria, and can optionally save filtered results to a file.
• Added madc2gmat function to convert MADC files into additive genomic relationship matrices using the VanRaden (2008) method, supporting both "unique" and "collapsed" processing modes.
• Added thinSNP function (exported), and new exports for allele_freq_poly, solve_composition_poly, and madc2gmat to the package namespace. [1] [2] [3]

Improvements and Bug Fixes

• Updated madc2vcf_all to read MADC files without altering column names, preserving original headers.
• Various bug fixes and improvements to existing functions, as described in the updated NEWS.md.

Package Metadata and Dependency Updates

• Updated package version to 0.6.1, changed maintainer email, and added new dependencies on rlang and stringr. [1] [2] [3]
• Updated NEWS.md with new features, bug fixes, and version history.

[Copilot]

Pull Request Overview

This pull request introduces significant new functionality to the BIGr package including MADC file filtering, genomic relationship matrix generation, and SNP thinning capabilities. It also updates package metadata, dependencies, and includes various bug fixes.

• Added filterMADC function for quality control filtering of MADC files
• Added madc2gmat function to convert MADC files to additive genomic relationship matrices
• Added thinSNP function for SNP pruning based on physical distance

Reviewed Changes

Copilot reviewed 25 out of 26 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
tests/testthat/test-thinSNP.R	Test coverage for new thinSNP function
tests/testthat/test-madc2vcf_targets.R	Enhanced tests with bottom strand marker validation
tests/testthat/test-madc2gmat.R	Test coverage for new madc2gmat function
tests/testthat/test-filterMADC.R	Test coverage for new filterMADC function
R/thinSNP.R	New SNP thinning function implementation
R/madc2gmat.R	New genomic relationship matrix generation function
R/filterMADC.R	New MADC file filtering function
R/breedtools_functions.R	Exported previously internal functions
R/updog2vcf.R	Added RefAlt parameter for reference/alternate allele specification
R/madc2vcf_targets.R	Fixed bottom strand marker REF/ALT handling
R/madc2vcf_all.R	Fixed column name preservation and chromosome parsing
Documentation files	Updated documentation for new and modified functions
Package metadata	Version bump, maintainer email change, dependency updates

Comments suppressed due to low confidence (2)

R/filterMADC.R:1

• The condition checks alt_base but then uses the same condition to filter ref_base and pos_ref_idx. This should filter based on the positions where alt_base contains invalid nucleotides.

#' Filter MADC Files

R/filterMADC.R:1

• The condition checks alt_base but then uses the same condition to filter ref_base and pos_ref_idx. This should filter based on the positions where alt_base contains invalid nucleotides.

#' Filter MADC Files

---

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[Copilot]

The comparison chr > 1 should be length(chr) > 1 to check if the chromosome vector has more than one element.

Suggested change

	if(length(chr > 1)) chr <- paste(chr, collapse = "_")
	if(length(chr) > 1) chr <- paste(chr, collapse = "_")

[Copilot]

The comment uses roxygen2 syntax ##' which is not appropriate in test files. Use regular R comments # instead.

Suggested change

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

[Copilot]

[nitpick] The magic number calculation (1/as.numeric(ploidy)) should be clarified or extracted to a named variable. The comment explains the logic but the implementation could be more explicit.

Suggested change

	denominator <- (1/as.numeric(ploidy))*sum(p * q, na.rm = TRUE)
	ploidy_ratio <- 1 / as.numeric(ploidy) # Scaling factor for allele ratios based on ploidy
	denominator <- ploidy_ratio * sum(p * q, na.rm = TRUE)

[codecov]

Codecov Report

❌ Patch coverage is 79.46429% with 46 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.35%. Comparing base (297f058) to head (a248e93).
⚠️ Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
R/madc2gmat.R	74.41%	22 Missing ⚠️
R/updog2vcf.R	16.66%	15 Missing ⚠️
R/filterMADC.R	95.23%	3 Missing ⚠️
R/madc2vcf_all.R	70.00%	3 Missing ⚠️
R/madc2vcf_targets.R	90.00%	2 Missing ⚠️
R/thinSNP.R	96.29%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #44      +/-   ##
==========================================
- Coverage   84.13%   83.35%   -0.78%     
==========================================
  Files          16       19       +3     
  Lines        1147     1358     +211     
==========================================
+ Hits          965     1132     +167     
- Misses        182      226      +44     

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