API Reference

Auto-generated documentation from source code docstrings.

Pipeline orchestration

• Pipeline - Top-level orchestrator connecting all stages
• CohortPipeline - Multi-sample cohort analysis orchestrator

Processing stages

• VCFParser - VCF file streaming
• QualityFilter - Quality-based variant exclusion
• AnnotationEngine - Functional consequence and population data
• PrioritizationEngine - Frequency filtering and scoring
• ACMGClassifier - Evidence tag assignment and classification
• ReportGenerator - Output serialization (JSON, CSV, PDF)

Cohort analysis

• CohortPipeline - Multi-sample orchestrator
• CohortAggregator - Cross-sample variant merging
• CohortStatistics - Per-gene burden and recurrence stats
• CohortReportGenerator - Cohort report generation

Data types

• Data Models - Variant, AnnotatedVariant, ScoredVariant, ClassifiedVariant, enums
• Cohort Models - CohortConfig, CohortVariant, GeneBurden, CohortSummary
• Configuration Classes - All config dataclasses
• Exceptions - Error hierarchy