Changelog

All notable changes to VariantCentrifuge will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • Comprehensive Sphinx documentation with modern Furo theme

  • GitHub Actions workflow for automated documentation deployment

  • API reference documentation with autodoc

  • User guides for installation, usage, and configuration

  • Development and contributing guides

  • Annotation strategy guides for VCF preprocessing

  • Unified annotation system supporting BED files, gene lists, and JSON gene data

  • JSON gene annotation feature with flexible field mapping (--annotate-json-genes and --json-gene-mapping)

  • Custom annotation integration in the pipeline workflow

  • bcftools pre-filtering (--bcftools-prefilter) for early variant filtering during extraction, significantly improving performance on large VCFs

  • Final filtering (--final-filter) using pandas query syntax, allowing filtering on any column including computed scores and inheritance patterns

  • Comprehensive test suite for new filtering features

  • Sample pseudonymization for privacy-preserving data sharing (Issue #34):

    • Multiple naming schemas: sequential, categorical, anonymous, and custom patterns

    • Consistent pseudonym mapping across all output formats (TSV, Excel, HTML)

    • Automatic handling of genotype and inheritance columns

    • PED file pseudonymization support (--pseudonymize-ped)

    • Secure mapping table storage in parent directory

    • Comprehensive test suite and documentation

  • Checkpoint and resume system for robust pipeline execution:

    • Automatic pipeline state tracking with .variantcentrifuge_state.json

    • Resume capability after interruptions (--enable-checkpoint and --resume)

    • Full support for parallel processing (--threads)

    • Optional file checksum validation (--checkpoint-checksum)

    • Status inspection without resuming (--show-checkpoint-status)

    • Thread-safe state updates for parallel chunk processing

    • Comprehensive tracking of all major pipeline steps

Changed

  • Documentation migrated from README to structured Sphinx documentation

  • Improved configuration documentation with preset examples

  • Enhanced filtering capabilities with three-stage filtering approach (bcftools pre-filter, SnpSift filter, final filter)

Fixed

  • Documentation structure and navigation

  • Numeric type conversion in final filtering to handle mixed data types correctly

  • Gene burden analysis edge cases (Issue #31): Improved handling of infinite and zero odds ratios by:

    • Detecting structural zeros (e.g., entire row/column zero) and returning NaN appropriately

    • Applying continuity correction (default 0.5) to zero cells to calculate meaningful confidence intervals

    • Using score method as primary CI calculation (more robust for sparse data)

    • Removing arbitrary fallback bounds in favor of statistically sound methods

[0.5.0] - 2024-XX-XX

Added

  • Interactive HTML report generation with sortable tables

  • IGV.js integration for genomic visualization

  • Cohort analysis and reporting functionality

  • Gene burden analysis with Fisher’s exact test

  • Phenotype data integration and filtering

  • Preset filter system for common analysis workflows

  • Excel output format support

  • External database links (SpliceAI, Franklin, Varsome, gnomAD, ClinVar)

Changed

  • Improved command-line interface with better argument organization

  • Enhanced configuration system with JSON-based presets

  • Optimized variant filtering pipeline

  • Better error handling and user feedback

Fixed

  • VCF header normalization for indexed fields

  • Sample identification in cohort reports

  • IGV report generation with proper FASTA handling

[0.4.0] - 2024-XX-XX

Added

  • Comprehensive test suite with pytest

  • Pre-commit hooks for code quality

  • Gene list annotation functionality

  • Variant statistics and metadata generation

Changed

  • Modular code architecture with clear separation of concerns

  • Improved logging and debugging capabilities

  • Enhanced VCF processing pipeline

Fixed

  • Gene BED file generation edge cases

  • Genotype replacement functionality

[0.3.0] - 2024-XX-XX

Added

  • Gene-centric variant filtering

  • SnpSift integration for field extraction

  • Basic HTML report generation

  • Phenotype integration capabilities

Changed

  • Migrated from Bash/R to Python-based pipeline

  • Improved error handling and validation

[0.2.0] - 2024-XX-XX

Added

  • Initial Python CLI implementation

  • VCF processing with bcftools integration

  • Basic filtering capabilities

  • Configuration file support

Changed

  • Complete rewrite from shell scripts to Python

[0.1.0] - 2024-XX-XX

Added

  • Initial release

  • Basic variant filtering functionality

  • Shell script-based pipeline

  • Simple output generation

Legend

  • Added for new features

  • Changed for changes in existing functionality

  • Deprecated for soon-to-be removed features

  • Removed for now removed features

  • Fixed for any bug fixes

  • Security for vulnerability fixes