Summary
The variant effect annotation system returns a literal "TODO" string for in-frame complex variants (SNP+indel combinations), which propagates to user-facing DataFrames and corrupts downstream analysis.
Problem
In-frame complex variants are classified with placeholder code that returns:
- A "TODO" string as the effect annotation
impact="UNKNOWN" instead of scientifically justified values
This breaks data quality, filtering, and analysis pipelines.
Impact
- User-facing DataFrames contain incomplete TODO strings
- Impact levels cannot be reliably determined or filtered
- Downstream code fails to process or analyze these variants correctly
- Indicates unfinished implementation in the codebase
Context
In-frame complex variants are rare but scientifically important. Complete amino acid sequences are available for these variants, enabling proper classification through amino acid comparison logic.
Summary
The variant effect annotation system returns a literal "TODO" string for in-frame complex variants (SNP+indel combinations), which propagates to user-facing DataFrames and corrupts downstream analysis.
Problem
In-frame complex variants are classified with placeholder code that returns:
impact="UNKNOWN"instead of scientifically justified valuesThis breaks data quality, filtering, and analysis pipelines.
Impact
Context
In-frame complex variants are rare but scientifically important. Complete amino acid sequences are available for these variants, enabling proper classification through amino acid comparison logic.