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edawson / gfakluge

A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
http://edawson.github.io/gfakluge/
MIT License
51 stars 20 forks source link

N50 / L50 / N90 / L90 recipes could be faster #16

Closed edawson closed 6 years ago

edawson commented 6 years ago

The Sanger pathogens group has a better assembly stats algo: https://github.com/sanger-pathogens/assembly-stats/blob/master/stats.cpp#L101

Currently gfakluge is faster (FASTA file compared to converted FASTA -> GFA with only S lines) but this is probably just because of differences in automatic vectorization from the compiler the GFA file contains 1/2 as many lines . We can surely cache values to speed things up.

edawson commented 6 years ago

Closing. I think things are fine as they are.