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Instead of a single `PackedSeq`, it now stores `Vec<PackedSeq>`. Type of function parameters are adjusted accordingly from `&[RefSequence]` to `&RefSequence`. This lets us have a single data structure that stores the full genome sequence.
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By the way, to avoid getting confused, I’m now trying to consistently use the term reference for the full genome and the term contig for the parts it is made of (a FASTA record, so a single chromosome or contig). |
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Okay, approved! |
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This contains all of the purely refactoring commits of PR #607. That is, we can just merge this without having to wait for the other minor things that need to be done in that PR.
Instead of a single
PackedSeq, the change is to store aVec<PackedSeq>inRefSequence. So this means that what gets passed to a function that needs to know about the reference is no longer a&[RefSequence], but a&RefSequence.This lets us have a single data structure that stores the full genome sequence.
Also, this moves the
RefSequenceto a newrefseqmodule (refseq.rs).