feat(qannotate): allow the homCutoff option to be used in IndelConfidenceMode

[holmeso]

This pull request enhances the configurability and test coverage of the IndelConfidenceMode class, improves code clarity, and fixes minor typos. The most significant change is the introduction of a configurable homopolymer cutoff, which is now tested in the unit tests. Additionally, the code and comments have been improved for readability and maintainability.

Configurability and Logic Improvements:

• Added a configurable homopolymerCutoff parameter to IndelConfidenceMode, allowing users to specify the cutoff via options or command line (--homCutoff). The logic for determining high-confidence indels now uses this parameter instead of a hardcoded value. [1] [2] [3]
• Updated log output to reflect the configurable homopolymer cutoff and improved log message clarity.

Documentation and Code Quality:

• Improved and expanded JavaDoc comments for methods, especially for loadMask and isRepeat, to clarify their purpose and usage. [1] [2]
• Fixed typos in variable names and comments, such as DESCRITPION_INFO_CONFIDENCE to DESCRIPTION_INFO_CONFIDENCE, and improved code formatting and consistency. [1] [2] [3]

Testing Enhancements:

• Added a comprehensive test (homopolymerOptionTest) to verify that the configurable homopolymer cutoff is correctly applied, including new helper methods to generate appropriate test VCF files. [1] [2]
• Refactored existing tests for improved clarity and consistency, using assertSame and assertEquals for better assertion semantics, and updated test method names to follow Java conventions. [1] [2]

General Code Cleanup:

• Removed unnecessary imports and improved import organization in test files. [1] [2]
• Made minor improvements to code style, such as using diamond operators and consistent variable naming. [1] [2]