0.2.1

Nanalogue 0.2.1 is a security and correctness patch release.

Security and upgrade guidance

This release includes certificate-distrust updates following the eMudhra intermediate-CA compromise, alongside other dependency security fixes.

• Docker builds now require a patched CA certificate bundle and include it in the runtime image.
• Update your operating system’s CA certificate package or custom bundle as well as nanalogue. Updating nanalogue alone does not update the host’s certificates.
• Container users must pull an updated image and recreate existing containers. Updating the Docker host does not update a container’s bundle.
• Check existing certificate environment overrides: a stale custom bundle can bypass the updated default.

These precautions apply to remote HTTPS alignment files and to reference downloads triggered by local CRAM files. See the HTTPS certificate guidance.

Other improvements

• Further MM/ML parsing optimizations and fixes to empty-MM and MN validation.
• Support for internal # characters in read IDs, PanSN contig names, and unambiguous colon-containing contig names.
• Fixes to genomic-region limits, modification-region filtering, density thresholds, and HTSlib record-capacity compatibility.
• Additional alignment-format regression coverage and the public maybe! macro.

See the full changelog.