Added MADC Functions

[alex-sandercock]

New functions to filter and convert MADC files

• filterMADC: Filter MADC files to remove low-quality microhaplotypes
• madc2gmat: convert an MADC file to an additive relationship matrix using rrBLUP

[Copilot]

Pull Request Overview

This pull request adds two new functions—madc2gmat and filterMADC—for processing MADC files. The changes include adding comprehensive roxygen2 documentation, implementing the conversion of MADC files into an additive genomic relationship matrix (via madc2gmat), and providing filtering functionality for MADC files (via filterMADC).

Reviewed Changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
man/madc2gmat.Rd	Added documentation for the madc2gmat function.
man/filterMADC.Rd	Added documentation for the filterMADC function.
R/madc2gmat.R	Implemented the madc2gmat function including file parsing, scaling, and matrix conversion.
R/filterMADC.R	Implemented the filterMADC function with configurable filtering on MADC files.
NAMESPACE	Updated exports and imports to support the new functions.

Comments suppressed due to low confidence (2)

R/madc2gmat.R:52

• [nitpick] Consider using a broader regex pattern (e.g., "|Ref_.*") for removing suffixes to ensure consistency and handle potential variations in the allele ID suffix.

filtered_df$AlleleID <- sub("\|Ref_001", "|Ref", filtered_df$AlleleID)

R/madc2gmat.R:53

• The regex "|Alt_002*" may not reliably match the intended pattern; consider using a consistent and precise pattern such as "|Alt_.*" to correctly remove all extra characters.

filtered_df$AlleleID <- sub("\|Alt_002*", "|Alt", filtered_df$AlleleID)

[codecov]

Codecov Report

Attention: Patch coverage is 94.50549% with 5 lines in your changes missing coverage. Please review.

Project coverage is 84.90%. Comparing base (73ec035) to head (0594201).
Report is 14 commits behind head on development.

Files with missing lines	Patch %	Lines
R/filterMADC.R	95.23%	3 Missing ⚠️
R/madc2gmat.R	92.85%	2 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development      #36      +/-   ##
===============================================
+ Coverage        84.14%   84.90%   +0.76%     
===============================================
  Files               16       18       +2     
  Lines             1148     1239      +91     
===============================================
+ Hits               966     1052      +86     
- Misses             182      187       +5     

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