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cerebis / meta-sweeper

Parametric sweep of simulated microbial communities and metagenomic sequencing.
GNU General Public License v3.0
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Read creation rate of ART could be improved. #44

Closed cerebis closed 7 years ago

cerebis commented 7 years ago

The rate at which reads are created with sequencing error is lower than desirable. Approximately 10x slower than simple error-free reads.

Although some profiling has been done, I suspect that occasions where numpy.argwhere() or numpy.where() is called could be replaced with numpy.searchsorted(). This method if faster when the aim is to recall a single index, whereas the "where" methods return all indices meeting a criteria.

cerebis commented 7 years ago

The latest changes to Art.py has improved generation rate by a factor >4.