ksahlin / strobealign

Aligns short reads using dynamic seed size with strobemers
MIT License
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Get rid of add_to_hits_per_ref() min_diff parameter #330

Closed marcelm closed 10 months ago

marcelm commented 10 months ago

The intention of this parameter is to disallow hits that span too different lengths on the query compared to the reference.

The parameter has a bit of a misleading name because it is actually the maximum allowed difference. (This can come from some of my refactoring. Within the function, it represents the minimum observed difference so far. The value provided as argument is merely its initial value.)

But mainly, the parameter has no effect at all and just initializing it to std::numeric_limits<int>::max() leads to the same decisions being made. (I temporarily added some code tested this.)

ksahlin commented 10 months ago

approved.