Feature request: Add Debug Messages for Other Scripts

[berntpopp]

Description Currently, the debug messages are only implemented for the API request scripts (variantRecoder.js and vepRegionsAnnotation.js). To improve the overall debugging capability, we should extend the debug logging to other scripts within the project. This will provide a more comprehensive view of the tool's operation and help in troubleshooting.

Acceptance Criteria

• Add debug messages to the main.js script to log key steps in the variant analysis process.
• Add debug messages to the variantLinkerProcessor.js script to log data processing, filtering, and formatting steps.
• Ensure that the debug messages provide clear and useful information about the flow and state of the application.
• Update tests to verify that the debug messages are correctly logged.
• Update the documentation to mention the enhanced debugging capabilities.

Relevant Scripts

• main.js
• variantLinkerProcessor.js

Example Debug Messages to Add

• In main.js:

  • Log when the CLI arguments are parsed.
  • Log the detected input format (VCF or HGVS).
  • Log the start and end of the main variant analysis process.

• In variantLinkerProcessor.js:

  • Log when variant linking starts and ends.
  • Log the filtering and formatting steps.
  • Log any errors encountered during processing.