new fixMADC function

[alex-sandercock]

This pull request introduces BIGr version 0.7.0, with the primary change being the addition of a new function, fixMADC, to process and standardize raw MADC files using user-supplied chromosome and position information. The update also includes relevant documentation, namespace, and metadata changes to support this new feature.

New Functionality:

• Added a new function fixMADC to format raw MADC files by updating allele and clone IDs to a standardized Chr_Pos format using a user-provided marker file. This function supports downstream compatibility with madc2vcf and BIGapp functions. (R/fixMADC.R, NAMESPACE, man/fixMADC.Rd, NEWS.md) [1] [2] [3] [4]

Documentation and Metadata Updates:

• Updated the package version to 0.7.0 and added a news entry describing the new fixMADC function. (DESCRIPTION, NEWS.md) [1] [2]
• Updated documentation for the new function, including examples and parameter descriptions. (man/fixMADC.Rd)
• Updated the RoxygenNote version to 7.3.3 in DESCRIPTION.
• Added .suffix_type to the list of global variables to avoid R CMD check warnings. (R/utils.R)

Imports and Namespace:

• Added fixMADC to the list of exported functions and imported replace_na from tidyr for use in the new function. (NAMESPACE) [1] [2]

Other:

• Cleaned up cran-comments.md by removing outdated update notes.

[Copilot]

Pull request overview

Adds a new fixMADC() feature to the BIGr R package to convert raw DArT MADC files to the fixed allele-ID format (standardizing CloneID to Chr_Pos and appending numbered allele suffixes), along with package metadata/docs updates.

Changes:

• Introduces R/fixMADC.R (new exported function) and corresponding Rd documentation.
• Adds a comprehensive testthat suite for fixMADC() and supporting fixture builders.
• Updates package metadata (version bump to 0.7.0, NEWS entry, NAMESPACE imports/exports) and adds an example marker file to inst/.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
R/fixMADC.R	Implements the new fixMADC() function for remapping/standardizing MADC IDs.
tests/testthat/test-fixMADC.R	Adds extensive tests covering mapping, validation, warnings/errors, and file output behavior.
man/fixMADC.Rd	New generated documentation for fixMADC().
NAMESPACE	Exports fixMADC and imports tidyr::replace_na.
DESCRIPTION	Bumps version to 0.7.0 and updates RoxygenNote.
NEWS.md	Adds a 0.7.0 entry describing fixMADC.
R/utils.R	Adds .suffix_type to globalVariables to avoid R CMD check notes.
inst/iris_MADC_marker_file.csv	Adds a packaged example marker file for fixMADC usage.
cran-comments.md	Removes outdated update notes.

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[codecov]

Codecov Report

❌ Patch coverage is 98.78049% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 83.94%. Comparing base (4f30e52) to head (98933f7).

Files with missing lines	Patch %	Lines
R/fixMADC.R	98.78%	1 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development      #51      +/-   ##
===============================================
+ Coverage        83.05%   83.94%   +0.88%     
===============================================
  Files               19       20       +1     
  Lines             1369     1451      +82     
===============================================
+ Hits              1137     1218      +81     
- Misses             232      233       +1     

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