Decouple CLI and lib #32
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nh13
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Sep 12, 2023
| @@ -93,7 +94,7 @@ impl AlignmentOperation { | |||
| /// | |||
| /// The default alignment mode is Global. | |||
| #[cfg_attr(feature = "serde", derive(Serialize, Deserialize))] | |||
| #[derive(Default, Debug, PartialEq, Eq, Copy, Clone, ValueEnum)] | |||
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was ValueEnum removed so we could have multiple strings per enum value?
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ValueEnum comes from clap. We don't want to have any CLI dependencies in lib. And Rust doesn't allow you to implement an external trait on an external struct, so there's really no easy way around it.
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Decouple CLI from lib and split them into separate crates. Create a `Builder` struct for creating `Aligners`. The CLI then calls the builder and copies over most of the CLI argument values. Add a `SamRecordFormatter` struct to encapsulate details of formatting alignments for SAM output (the builder also creates this).
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First, I split the lib and CLI into separate crates within a single workspace. This allows for managing common config, dependencies, etc. across related crates.
Second, I created a
aligners::Optionsobject to encapsulate all the options. It derivesderive_builder::Builderto auto-generate a builder struct. I then extend the builder to add methods for building theAlignersstruct, and the newSamRecordFormatterstruct I created to encapsulate details related to formatting of alignments.There's still some work to be done to get the right visibility for the other structs/traits so you're not exposing more than necessary as part of the public API. This may involve splitting off some additional crates, e.g.
util. But that's work for another PR.