On Thursday, 16 May 2013 at 10:35:12 UTC, Dicebot wrote:
One open question remains though - can D/Phobos do better here? Can some changes be done to Phobos functions in question to improve performance or creating bioinformatics-specialized library is only practical solution?
Of course things can be improved. For a start, pattern could be a template parameter so that most of the checks are inlined and const-folded.
Using count!(c => c=='G' || c=='C')(line) from std.algorithm would probably perform better as well.
Simply put, countchars is just the obvious naive implementation of the algorithm. It hasn't been tuned at all, and isn't suitable for use in a small kernel like this.
