update examples

[alex-sandercock]

No description provided.

[Copilot]

Pull Request Overview

This PR updates the examples for the madc2vcf_all function. Key changes include:

• Wrapping the example usage in both Rd and R files with a \donttest block.
• Increasing the n.cores parameter from 1 to 2 in the examples.
• Bumping the package version in DESCRIPTION and updating NEWS.md accordingly.

Reviewed Changes

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

File	Description
man/madc2vcf_all.Rd	Updated example block: wrapped in \donttest and updated n.cores.
R/madc2vcf_all.R	Updated example comments: wrapped in \donttest and updated n.cores.
NEWS.md	Added release notes for the updated madc2vcf_all example.
DESCRIPTION	Updated package version to 0.5.3.

[Copilot]

[nitpick] Consider adding a brief comment explaining why the OMP_THREAD_LIMIT is set to 2 in this example to aid user understanding.

Suggested change

	\donttest{
	\donttest{
	# Set the maximum number of threads for OpenMP to 2 to ensure consistent behavior

[Copilot]

[nitpick] It might be helpful to include a short inline note clarifying the purpose of setting the OMP_THREAD_LIMIT environment variable in the example usage.

Suggested change

	#' Sys.setenv("OMP_THREAD_LIMIT" = 2)
	#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # Limits the number of threads used by OpenMP to match the n.cores parameter

[Copilot]

[nitpick] Consider providing more detail in the release notes about the changes in the madc2vcf_all example for clarity to end users.

Suggested change

	- Updated madc2vcf_all example
	- Updated madc2vcf_all example to include support for additional filtering options and improved error handling. The example now demonstrates how to use the new parameters for specifying target regions and output formats.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.03%. Comparing base (b4830a6) to head (c15f3e0).
Report is 6 commits behind head on development.

Additional details and impacted files

@@ Coverage Diff @@## development #33 +/- ##
============================================
Coverage 85.03% 85.03% ============================================
Files 16 16 Lines 1136 1136 ============================================
Hits 966 966 Misses 170 170 

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