v0.2.0

patformm v0.2.0

Release Notes

First pre-release of patformm, a specialised tool for processing methylation data from Biomodal sequencing.

Key Features

• Efficient extraction of methylation information from MM tags in BAM files
• Parallel processing support with configurable chunk sizes
• Memory-optimised CpG index mapping
• Robust handling of both forward and reverse strand methylation
• Outputs standardised PAT format compatible with downstream methylation analysis

Major Updates

• Implemented chunked processing for large BAM files
• Added support for parallel processing
• Optimised CpG index mapping with preloaded reference
• Improved memory management for large datasets
• Added comprehensive error handling for malformed MM tags

Dependencies

• Python 3.8+
• samtools
• wgbstools

Known Issues

• Currently optimised for hg38 genome build only
• Requires significant memory for very large BAM files (64GB+ recommended)

Next Steps

• Add support for additional genome builds
• Implement memory-efficient streaming for very large files
• Add direct integration with downstream analysis tools