ged-lab/khmer — pull request #218 by cswelcher (2013-11-15 14:07:46+00:00)
Title: Sparse median

Open pull req for sparse median diginorm.

Thus far there is a new c++ function, and a new python script making use of it.

Algorithm is essentially the same; pseudocode:

'''
if sparse_median_count(read) < COV_CUTOFF:
consume(read)
else:
continue
'''

TODO:
* [ ] performance testing ipython notebook
* [ ] implement version of normal median without std dev and avg calcs
* [ ] tests!

Other thoughts, @ctb @mr-c?