Changelog

This is the changelog for Rastair 2.

Version 2.2.0 (unreleased)

Highlights:

• The reported beta values might change when updating to rastair 2.2. Methylation beta is now calculated by taking into account both positions of a CpG, meaning only reads containing TG/CA are counted as methylated.
• Reporting insertion and deletion calls. This is not enabled by default, while we're refining the model. Enable with --experimental-indels.
• Support guessing the read orientation using --guess-read-orientation

Further changes:

• Filtering reads by multiple tags now means a read needs to have all of the specified tags.
• Support CRAM input for rastair bam legacy rewrites.

Version 2.1.1 (2026-04-15)

Fixes for mbias plots.

Version 2.1 (2026-03-19)

Highlights:

• Running Rastair's calling model on GPU. Using --gpu gives a significant speedup and works cross-platform (tested with Vulkan on Linux and Metal on macOS). (Other optimizations also improve CPU-only performance.)
• A new subcommand, rastair bam to add methylation annotations to exiting BAM files.

Further changes:

• Support single-stranded reads
• Support filtering reads by tags
• Fix BED output sometimes reporting misleading beta values

Version 2.0 (2026-02-05)

This is a complete rewrite of Rastair. While supporting the same methylation calling output, the main new addition is variant calling (outputting VCF/BCF). Rastair now uses a bundles ML model to produce accurate calls while still being very performant.