Global algorithm performance improvements

OndrejSladky / kmercamel

KmerCamel🐫 provides implementations of several algorithms for efficiently representing a set of k-mers as a masked superstring.

MIT License

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Closed OndrejSladky closed 1 year ago

OndrejSladky commented 1 year ago

Changes:

Using khash hash table instead of the one in std
Not storing k-mer and its complement, but computing it on the fly
Prefixes hash table and next values are not stored all at once but divided into batches
Computing first and last for reverse complements on the fly

Performance improvements:	Algorithm	Running time	Memory
Global	73 %	33 %