feat: allow passing query name to map #85
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Yeah. My rust skills have gotten better, so having it take in &[u8] would be a definite improvement, and leave it to the end-user to worry about strings. I'll take a look at both PRs soon. I've gotten behind here, but it's time to catch up! |
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Merging this, and the other, then will reconcile and work on #71 and push out a release |
jguhlin
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@rob-p Dunno if you can test it, or added the proper tests? @mbhall88 Query name is passed in as AsRef<[u8]> and there is some not my favorite code in there to prevent a new allocation if the query name is already nul-allocated, and to do an allocation if needed. Also I've updated Mappings to return Arc<String>'s for query name and target name, which should decrease performance for very small jobs but increase for large jobs.... but I need to benchmark
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This PR adds the ability to pass a query name to the map function.
This has been discussed/proposed in #80 but that PR seems to have grown quite large and tries to multiple things.
For the sake of keeping pieces of work smaller, easier to review, and easier to determine where issues may be introduced, I thought I would put in this small one.
It does take a slightly different approach to #80 where Rob creates a new function
map_with_name. My reasoning for altering the existingmapfunction is that it mirrors the minimap2mm_mapfunction, which takes a query name.This will obviously require a minor version bump as it won't be backwards compatible, but as the project is still in the major version 0 phase that is valid semver.
Happy to discuss further.
PS. (as an aside) I think a future alteration to the
MappingAPI might also be to use&[u8](orVec<u8>) for the target and query names. This avoids the heavy conversion to strings for every mapping call. It is also quite conventional with other bioinfo Rust libraries such as noodles and needletail which work in byte space and leave it to the user to convert to Strings if required.