[riverdweller]

A few years ago I built some tools https://github.com/tf318/tamtools to store alignments against two different reference assemblies in an efficient way (taking advantage of the fact that the majority of each alignment to different assemblies would in fact be the same, just shifted in position).

The intent was to enhance this to store alignments against multiple references as new references are published, and probably to rewrite in Rust or C rather than the initial Python version.

In retrospect I would be interested to know whether this domain-specific compression effort, with zstd to the resulting "hybrid" alignment, would be more efficient than just letting zstd do its own thing with a full set of individual alignments against the different references.