This pull request adds support for highlighting variant and region positions using VCF and BED files in the visualization and CLI workflow. It refactors the highlight interval logic to allow multiple named intervals, introduces new modules for handling VCF/BED highlights, and updates the wizard and main CLI interfaces to accept these files. Additionally, it improves the interval data structure and the plot configuration for better clarity.

Highlighting and Data Input Enhancements

• Added support for highlighting variant positions from VCF files and regions from BED files by introducing new CLI options (--vcf and --bed) and extending the wizard interface to prompt for these files. [1] [2] [3]
• Refactored the highlight interval logic to accept multiple intervals (Vec<Interval>) with names, and updated the interval parsing to support named intervals in the format name:start-end. [1] [2]

New Highlight Module

• Added a new highlight module with Highlight trait and implementations for VCF and BED files, extracting intervals relevant to the selected region. Includes unit tests for VCF/BED interval extraction.

CLI and Data Flow Updates

• Updated the main CLI and wizard logic to aggregate highlight intervals from direct input, VCF, and BED files, and apply preprocessing to all intervals for correct plotting. [1] [2] [3]

Plot and Utility Improvements

• Changed the plot configuration to color highlight rectangles by their name (site) and slightly increased their opacity for better visibility.
• Added a utility function ellipsis to truncate long allele names for display, with corresponding tests. [1] [2]

These changes collectively make the visualization tool more flexible and informative by allowing users to highlight specific variants and regions from external files, improving both the user experience and the clarity of the generated plots.