Dosage2vcf update

[alex-sandercock]

This pull request improves the documentation and testing of the dosage2vcf function, clarifying its support for different DArT genotype report formats and ensuring correct handling of SNP/INDEL reports. It also adds comprehensive tests to verify the function's behavior with various input formats and edge cases.

Documentation updates:

• Clarified in the .Rd documentation that dosage2vcf supports both Allele Dose Reports and SNP/INDEL genotype reports, and described how these formats are interpreted and mapped to VCF genotype codes. [1] [2]

Testing improvements:

• Added helper functions in test-dosage2vcf.R to generate synthetic DArT report and count fixtures for different scenarios, enabling robust and reusable test setups.
• Added tests to verify that SNP/INDEL 1-row and 2-row reports are handled as diploid genotype reports, that sample names are aligned between reports and counts, and that the output VCF matches expectations.
• Added a test to ensure that an error is raised if a non-diploid ploidy is specified for SNP/INDEL reports, enforcing correct usage.

Namespace update:

• Exported the validate_pedigree function in the NAMESPACE file.

[Copilot]

Pull request overview

This PR expands dosage2vcf to support additional DArT genotype report formats while updating documentation and tests around SNP/INDEL handling.

Changes:

• Refactors dosage2vcf parsing/validation for Allele Dose, SNP/INDEL 1-row, and SNP/INDEL 2-row reports.
• Adds synthetic test fixtures and tests for SNP/INDEL conversion behavior.
• Updates documentation and exports validate_pedigree.

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 2 comments.

File	Description
R/dosage2vcf.R	Adds report/count parsing helpers, SNP/INDEL genotype conversion, validation, and VCF formatting updates.
tests/testthat/test-dosage2vcf.R	Adds fixture writers and tests for SNP/INDEL report conversion and ploidy validation.
man/dosage2vcf.Rd	Updates generated documentation for supported report formats.
NAMESPACE	Exports validate_pedigree.

Files not reviewed (1)

• man/dosage2vcf.Rd: Language not supported

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[codecov]

Codecov Report

❌ Patch coverage is 85.18519% with 56 lines in your changes missing coverage. Please review.
✅ Project coverage is 81.87%. Comparing base (ccc0952) to head (7ae6e3d).

Files with missing lines	Patch %	Lines
R/dosage2vcf.R	85.18%	56 Missing ⚠️

Additional details and impacted files

@@               Coverage Diff               @@
##           development      #60      +/-   ##
===============================================
+ Coverage        81.53%   81.87%   +0.34%     
===============================================
  Files               23       23              
  Lines             2616     2886     +270     
===============================================
+ Hits              2133     2363     +230     
- Misses             483      523      +40     

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