almlab/SmileTrain — pull request #76 by elsherbini (2014-12-01 22:31:47+00:00)
Title: add support for pre-demultiplexed files separated by sample

This should allow users with a collection of files each corresponding to a different sample to enter the pipeline. I tested with both demultiplexed data and with data formatted the old way.

Not an optimal solution: it concatenates all the files so it doubles up on the data. Also it assumes that each of these files only contain reads in one direction, and makes the resulting concatenated file the `self.forward` parameter in the OTUCaller instance.

These issues could be solved in the future without too much grief since the new feature was put in new files.