clipper algorithms classic, gaussian not supported?

[Sol Katzman]

clipper version 0.2.0

In debugging another problem, I decided to see if the problem was somehow related to the clipper algorithm.

1) The clipper --help does not indicate the default (apparently spline) for the "algorithm" option:

  --algorithm=ALGORITHM  Defines algorithm to run, currently spline, classic, gaussian

2) Tried "gaussian" and got this error:

ERROR:root:peak finding failed:, ENSMUSG00000023795, 'GaussMix' object has no attribute 'hasBeenFit'

3a) Tried "classic" and got this error:

ERROR:root:peak finding failed:, ENSMUSG00000023795, peaks() takes exactly 2 arguments (1 given)

Investigated the code in call_peak.py

Corrected the argument list in this function:

was:    def peaks(self, threshold, plotit):
 is:    def peaks(self, threshold, plotit=False):

3b) Tried "classic" again and got this error:

ERROR:root:peak finding failed:, ENSMUSG00000023795, 'Classic' object has no attribute 'smoothingFactor'

These look like structural errors in the Python code.

If these algorithms are not supported, they should be removed as an option or should cause an immediate exit with a message to indicate that they are not supported.

/Sol.