Move seeding-related code into a new "seeding" module#570
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This reflects better that the parameters are used both when processing the reference and the query sequences.
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IndexParameterstoSeedingParameters: This reflects better that the parameters are used both when processing the reference and the query sequences.seedingmodule and move this code into it:hash.rs)SeedingParameters(and the seeding parameter profiles, i.e. things related to canonical read length). This makesindex.rsa bit shorter and with the rename fromIndexParameterstoSeedingParameters, it makes it even clearer than before that this code shouldn’t be in that file.randstrobes_query. This reduces the size ofmapper.rsa little bit.I am usually in favor of flat hierarchies, but just having everything be a top module is a bit unwieldy. I think this "seeding" subcategory is a nice, well-contained part the project.
There is now only one project-internal
usestatement within theseedingmodule that refers to something outside the module, which isREF_RANDSTROBE_HASH_MASK. I think this is fine because it shows that there is a dependency between the index and how we choose to compute the hash for the randstrobes.