Python sandbox Markov source files as at creation of Git repository.
Use word_len instead of omega as a parameter to build_frequency_array.
Commit bioarray.py before making changes to build_frequency_array.
Prototype faster SAFT using SciPy sparse matrix multiplication (first draft).
First working version of pysaftn to run faster than saft.
Try changing alpha_dict to use char rather than Python str.
Track previously untracked files: optimized parsing of SAFT files and population of sparse frequency matrices.
Make sequence parsing sparser; make printing faster; make p-value calculation more correct but much slower.
Call scipy.stats.gamma.sf with three NumPy arrays of the same shape. This is much faster.
Sort p-values in increasing order. Add --showmax option.
Trying CythonGSL; In var, define m and n as double: definition as int caused m*n to be negative in one case.
Remove debug print statements.
Ensure that certain variables are double, do for mean what was just done for var: make ech of m and n double.
Add args.wordsize-1 to m and to n in calls to mean and var to match sizes used by SAFT in calculating mean and var.
Adjust sorted p-values using Benjamini and Hochberg method, to fully compare output with SAFTN.
Make timing optional; Include defaults in help message.
Move contents of pysaftn.py to new Cython file saftmain.pyx. Execution is marginally faster.
Move repository from markov to pysaft directory.
The file bioarray.py is no longer needed.
Merge branch 'master' of https://github.com/penguian/pysaft