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VarAnnote v1.0.0

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@ataumutozsoy ataumutozsoy released this 07 Jun 15:41
· 16 commits to main since this release
v1.0.0
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VarAnnote v1.0.0 - Production Release

VarAnnote has officially reached production status! This major release transforms the toolkit from a beta version into a comprehensive, enterprise-ready solution for genomic variant annotation and clinical interpretation.

What's New in v1.0.0

Major Features

Advanced Configuration Management

  • Complete YAML-based configuration system with environment variable support
  • User preference management and configuration validation
  • Flexible database priority settings and performance tuning options

Sophisticated Filtering System

  • Multiple filter operators (equals, greater than, contains, regex, range)
  • Predefined filter collections for common use cases
  • Custom filter expressions with quality, clinical, and consequence-based filtering
  • Advanced filter validation and optimization

Comprehensive Documentation

  • Complete Sphinx documentation with RTD theme
  • Detailed API documentation with examples
  • User guides for installation, configuration, and advanced usage
  • CLI reference with all commands and options

Enhanced Test Coverage

  • Test coverage increased from 16% to 82%
  • 394 comprehensive tests covering all major functionality
  • Robust error handling and edge case coverage
  • Performance and integration testing

Technical Improvements

Code Quality

  • Production-ready codebase with comprehensive error handling
  • Type hints and documentation throughout
  • Modular architecture with clear separation of concerns
  • Performance optimizations for large-scale analysis

Database Integration

  • Enhanced support for ClinVar, gnomAD, COSMIC, dbSNP, and more
  • Improved API handling with rate limiting and caching
  • Better error recovery and fallback mechanisms

Output Formats

  • Enhanced VCF, JSON, CSV, TSV, Excel, XML, and Parquet support
  • Customizable output formatting and field selection
  • Performance optimizations for large datasets

Breaking Changes

  • Configuration file format changed to YAML (migration guide available)
  • Some CLI argument names updated for consistency
  • Database module names standardized (clinvar_db → clinvar)

Installation

From PyPI

pip install varannote==1.0.0

From Source

git clone https://github.com/AtaUmutOZSOY/VarAnnote.git
cd VarAnnote
pip install -e .

Quick Start

# Basic annotation
varannote annotate variants.vcf --output annotated.vcf

# With custom configuration
varannote annotate variants.vcf --config custom_config.yaml

# Advanced filtering
varannote annotate variants.vcf --filter "quality.score > 30" --filter "clinical.significance != 'benign'"

Documentation

Citation

If you use VarAnnote in your research, please cite:

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