v2.2.0-rc.1

What's Changed

• indels: improve genotyping + some other tweaks by @killercup in #7

Full Changelog: v2.0.0...v2.2.0-rc.1

v2.2.0

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.

v2.1.1

Fixes for mbias plots.

v2.1.0

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.

v2.0.0

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 bundled ML model to produce accurate calls while still being very performant.