Madc2vcf strawberry fix

[Cristianetaniguti]

• When marker ID has more than one "_", last one is considered to extract the position and the remaining are collapsed as chromosome ID
• If more than one base pair polymorphism is found between Ref_0001 and Alt_0002, tag is discarded because it is not possible to identify which is the target and its position

[Copilot]

Pull Request Overview

This PR refines marker ID parsing for strawberry, preserving multi-part chromosome IDs and ensuring only single-base polymorphisms are processed.

• Add check.names = FALSE to CSV reads and data frame creation to retain original column names
• Collapse all but the last underscore-separated segment of CloneID into the chromosome ID
• Modify comparison logic to only accept single-base polymorphisms and discard tags with multiple mismatches

[Copilot]

The condition uses length(chr > 1), which computes the length of a logical comparison vector. It should be length(chr) > 1 to correctly check for multiple segments before collapsing.

Suggested change

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

[Copilot]

Use && instead of & for scalar logical operations in if conditions to avoid unintended vectorized behavior.

Suggested change

	if(all(alt_base %in% c("A", "T", "C", "G")) & length(align@pattern@mismatch@unlistData) == 1) {
	if(all(alt_base %in% c("A", "T", "C", "G")) && length(align@pattern@mismatch@unlistData) == 1) {

[Copilot]

The clusterExport call is commented out, so hap_seq, nsamples, and add_ref_alt won't be available on the workers. Uncomment or add the export call before parLapply to ensure these objects are passed to the cluster.

Suggested change

	#clusterExport(clust, c("hap_seq","add_ref_alt", "nsamples"))
	clusterExport(clust, c("hap_seq", "add_ref_alt", "nsamples"))

[codecov]

Codecov Report

Attention: Patch coverage is 75.00000% with 1 line in your changes missing coverage. Please review.

Project coverage is 84.14%. Comparing base (297f058) to head (18ad68d).
Report is 3 commits behind head on development.

Files with missing lines	Patch %	Lines
R/madc2vcf_all.R	75.00%	1 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development      #37      +/-   ##
===============================================
+ Coverage        84.13%   84.14%   +0.01%     
===============================================
  Files               16       16              
  Lines             1147     1148       +1     
===============================================
+ Hits               965      966       +1     
  Misses             182      182              

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