chainfile-v0.3.0

Update and Rerun Notice

With this release, we've reached ~100% accuracy of lifted over segments using examples/chain_check.rs and demonstrated 100% concordance with CrossMap (https://crossmap.sourceforge.net) over 1,000,000 randomly selected position liftovers. That being said, this release also includes fixes for translations to positions on the negative strand, which is a typically a very small number (~0.1% - 1% of real positions you might want to lift over).

That being said, if you've used chainfile before to liftover variants before, we highly recommend that you rerun previous liftovers with this version of the crate. The vast majority of liftovers are not expected to change, but liftovers to positions on the negative strand should be corrected.

Added

• Added a new bin/kitchen_sink.rs that compares the performance of chainfile with CrossMap (https://crossmap.sourceforge.net).

Revise

• The inner data structures were replaced with facilities provided by the omics family of crates (#4).
• In a subsequent pull request, the omics crates were updated to v0.2.0. This was a much more robust system for representing coordinates (#5).

v0.2.1

0.2.1 — 09-09-2023

Fixes

• Checks strand equality before performing liftover in chainfile::liftover::Machine.

v0.2.0

0.2.0 — 04-24-2023

Added

• Adds liftover capabilities and related examples.

v0.1.0

0.1.0 — 03-30-2023

Added

• Includes first version of the crate, including correct chain file parsing and
  iteration over alignment data sections within the chain file.