v0.5.5

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.
• Updated the madc2vcf() function to madc2vcf_targets, and changed get_OffTargets() to madc2vcf_all()