Performance improvements - Githubissues

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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Performance improvements #38

Closed GordonHoklinder closed 1 year ago

GordonHoklinder commented 1 year ago

Performance related changes:

All: output string is printed directly
Local(AC), GlobalAC: reading input using kseq.h
GlobalAC: removed unnecessary merges
Local(AC): handling strings correctly

Other changes:

Added support for outputting to files.

Performance compared to the previous version (with spneumoniae and k=12):

Algorithm	Running time	Memory
Global	85 %	72 %
Local	64 %	100 %
GlobalAC	92 %	100 %
LocalAC	49 %	97 %