feat: Add SNP feature matrix helper function for ML workflows (Issue #1185)

[janhavitupe]

Summary

• Implement snp_feature_matrix method in AnophelesSnpFrequencyAnalysis class
• Generate ML-ready feature matrix with total SNP count, nonsynonymous SNP count, and mean allele frequency
• Support both cohort mode (aggregated by cohorts) and sample mode (per-sample)
• Accept either transcript or genomic region as input
• Include comprehensive test suite covering all functionality

Implementation Details

• Main function: snp_feature_matrix() with full parameter support
• Helper functions: _snp_feature_matrix_cohort_mode() and _snp_feature_matrix_sample_mode()
• Input validation: Ensures exactly one of transcript or region is provided
• Output: pandas DataFrame with columns total_snp_count, nonsynonymous_snp_count, mean_allele_frequency
• Metadata: Includes descriptive title with transcript/region information

Testing

• Added 5 comprehensive test functions covering:
  • Cohort mode with multiple cohorts
  • Sample mode for individual samples
  • Region-based analysis
  • Input validation error handling
  • Minimal parameter usage
• All tests pass and maintain existing functionality

Code Quality

• Follows project coding standards
• Proper type hints and docstrings
• Linting and formatting checks pass
• No breaking changes to existing API

Fixes #1185