CRAN Updates

[alex-sandercock]

Function updates and bug fixes in preparation for submission to CRAN

[Copilot]

Pull Request Overview

This PR focuses on function updates, documentation improvements, and bug fixes in preparation for the CRAN submission. Key changes include improved messaging in functions (using message() in place of cat()), enhanced error handling (especially in functions recovering reference/alternative alleles), and updates to documentation and examples.

• Updated function documentation and examples across several R scripts.
• Replaced cat() calls with message() for consistency in user feedback.
• Refactored error handling in functions such as add_ref_alt and check_ped.

Reviewed Changes

Copilot reviewed 57 out of 57 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
R/relationship_qc.R	Updated documentation and messaging style in trio relationship QC functions.
R/merge_MADCs.R	Enhanced function documentation with added return details.
R/madc2vcf_targets.R	Renamed function and added necessary parameter validation for botloci file.
R/madc2vcf_all.R	Extended examples, added alignment_score_thr parameter, and updated warnings.
R/imputation_concordance.R	Replaced cat() with message() for improved console output.
R/get_countsMADC.R	Updated messaging for missing data ratio while enhancing code clarity.
R/filterVCF.R	Replaced cat() with message() and standardized filtering feedback.
R/dosage_ratios.R	Added a basic check to ensure expected column names for dosage percentage data.
R/dosage2vcf.R	Updated messaging and file handling in VCF creation function.
R/check_ped.R	Added optional seed and verbose option; updated error reporting in pedigree check.
NAMESPACE, DESCRIPTION, NEWS.md, .Rbuildignore, CRAN-SUBMISSION	Updated version details and CRAN submission metadata.

[Copilot]

Warning messages in the add_ref_alt function are currently constructed by passing multiple arguments to warning(). To ensure the warning output is a single string, consider using paste() or paste0() to concatenate the message and the tag identifier.

Suggested change

	warning("Ref_0001 sequence not found in hap_seq and not present in one_tag. Removing tag:", cloneID)
	warning(paste0("Ref_0001 sequence not found in hap_seq and not present in one_tag. Removing tag:", cloneID))

[Copilot]

[nitpick] Ensure that the variable 'errors' is always defined and consistently converted to a data.frame before using nrow() for dependency checks. This will improve clarity and avoid potential type mismatches in future modifications.

Suggested change

	if (nrow(errors) >0) {
	if (nrow(as.data.frame(errors))>0) {# Ensure errors is treated as a data.frame

[codecov]

Codecov Report

Attention: Patch coverage is 63.52201% with 58 lines in your changes missing coverage. Please review.

Project coverage is 84.13%. Comparing base (e0fe2b8) to head (297f058).

Files with missing lines	Patch %	Lines
R/check_ped.R	36.00%	16 Missing ⚠️
R/madc2vcf_all.R	72.72%	15 Missing ⚠️
R/utils.R	11.76%	15 Missing ⚠️
R/filterVCF.R	69.23%	4 Missing ⚠️
R/updog2vcf.R	75.00%	4 Missing ⚠️
R/madc2vcf_targets.R	85.00%	3 Missing ⚠️
R/imputation_concordance.R	0.00%	1 Missing ⚠️

Additional details and impacted files

@@ Coverage Diff @@## main #35 +/- ##
==========================================
+ Coverage 83.36% 84.13% +0.77% 
==========================================
Files 17 16 -1 Lines 1148 1147 -1 ==========================================
+ Hits 957 965 +8 + Misses 191 182 -9 

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