pywombat 0.5.0__tar.gz → 1.0.0__tar.gz

pywombat-1.0.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to PyWombat will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [1.0.0] - 2026-01-23
+
+First stable release of PyWombat! 🎉
+
+### Added
+
+#### Core Features
+
+- **Fast TSV Processing**: Efficient processing of bcftools tabulated TSV files using Polars
+- **Flexible Output Formats**: Support for TSV, compressed TSV (`.gz`), and Parquet formats
+- **Streaming Mode**: Memory-efficient processing for large files
+- **Pedigree Support**: Trio and family analysis with automatic parent genotype joining
+- **Multiple Sample Formats**: Handles various genotype formats (GT:DP:GQ:AD and variants)
+
+#### Filtering Capabilities
+
+- **Quality Filters**: Configurable thresholds for depth (DP), genotype quality (GQ), and variant allele frequency (VAF)
+- **Genotype-Specific VAF Filters**: Separate thresholds for heterozygous, homozygous alternate, and homozygous reference calls
+- **Expression-Based Filtering**: Complex logical expressions with comparison operators (`=`, `!=`, `<`, `>`, `<=`, `>=`) and logical operators (`&`, `|`)
+- **Parent Quality Filtering**: Optional quality filter application to parent genotypes
+
+#### De Novo Mutation Detection
+
+- **Sex-Chromosome Aware Logic**: Proper handling of X and Y chromosomes in males
+- **PAR Region Support**: Configurable pseudo-autosomal region (PAR) coordinates for GRCh37 and GRCh38
+- **Hemizygous Variant Detection**: Specialized VAF thresholds for X chromosome in males (non-PAR) and Y chromosome
+- **Homozygous VAF Thresholds**: Higher VAF requirements (≥85%) for homozygous variants
+- **Parent Genotype Validation**: Ensures parents are homozygous reference with low VAF (<2%)
+- **Missing Genotype Filtering**: Removes variants with partial/missing genotypes (`./.`, `0/.`, etc.)
+- **Population Frequency Filtering**: Maximum allele frequency thresholds (gnomAD fafmax_faf95_max_genomes)
+- **Quality Filter Support**: gnomAD genomes_filters PASS-only option
+
+#### User Experience
+
+- **Debug Mode**: Inspect specific variants by chromosome:position for troubleshooting
+- **Verbose Mode**: Detailed filtering step information with variant counts
+- **Automatic Output Naming**: Intelligent output file naming based on input and filter config
+- **Configuration Examples**: Two comprehensive example configurations with extensive documentation
+  - `rare_variants_high_impact.yml`: Ultra-rare, high-impact variant filtering
+  - `de_novo_mutations.yml`: De novo mutation detection with full documentation
+
+#### Documentation
+
+- **Comprehensive README**: Complete usage guide with examples for all features
+- **Example Workflows**: Real-world usage scenarios (rare disease, autism trios, etc.)
+- **Input Requirements**: Detailed bcftools command examples for generating input files
+- **VEP Annotation Guide**: Complete workflow from VEP annotation to PyWombat processing
+- **Examples Directory**: Dedicated directory with configuration files and detailed README
+- **Troubleshooting Section**: Common issues and solutions
+
+#### Installation Methods
+
+- **uvx Support**: One-line execution without installation (`uvx pywombat`)
+- **uv Development Mode**: Local installation for repeated use (`uv sync`, `uv run wombat`)
+
+### Changed
+
+- Improved performance with streaming lazy operations
+- Optimized parent genotype lookup (excludes 0/0 genotypes from storage)
+- Enhanced error messages for better user experience
+- Normalized chromosome names for PAR region matching (handles both 'X' and 'chrX')
+
+### Fixed
+
+- Sex column reading from pedigree file
+- Parent genotype column naming consistency (father_id/mother_id)
+- Genotype filtering to catch all partial genotypes (`./.`, `0/.`, `1/.`)
+- PAR region matching for different chromosome naming conventions
+- Empty chunk handling in output to avoid blank lines
+
+### Performance Optimizations
+
+- Delayed annotation expansion (filter before expanding `(null)` field)
+- Vectorized filtering operations (no Python loops)
+- Early genotype filtering (skip 0/0 before parent lookup)
+- Optimized parent lookup (stores only non-reference genotypes)
+- Streaming mode by default for memory efficiency
+
+### Removed
+
+- **Progress bar options**: Removed `--progress`/`--no-progress` and `--chunk-size` options for simplicity
+- **Chunked processing mode**: Simplified to use only efficient streaming mode
+
+## [0.5.0] - 2026-01-20
+
+### Added
+
+- Initial de novo mutation detection implementation
+- Pedigree file support
+- Basic quality filtering
+- Expression-based filtering
+
+### Known Issues
+
+- Progress bar had reliability issues (removed in 1.0.0)
+- Chunked processing was complex (simplified in 1.0.0)
+
+---
+
+## Release Notes
+
+### v1.0.0 - Production Ready
+
+This release marks PyWombat as production-ready for:
+
+- Rare disease gene discovery
+- De novo mutation detection in autism and developmental disorders
+- Trio and family-based variant analysis
+- High-throughput variant filtering workflows
+
+**Recommended for**: Research groups working with rare variants, de novo mutations, and family-based genomic studies.
+
+**Breaking Changes**: None from 0.5.0, but removed progress bar options for cleaner interface.
+
+---
+
+[1.0.0]: https://github.com/bourgeron-lab/pywombat/releases/tag/v1.0.0
+[0.5.0]: https://github.com/bourgeron-lab/pywombat/releases/tag/v0.5.0