Differences between optandcalcCCM and makeoptimizationplots

[fermosc]

Hi,

I've been trying to use your library, which I think can be extremely useful. I would like to access the actual results from the calculations (rather than just get the plots using makeoptimizationplots as you describe in the manual), and from your code it seems like this would be done by optandcalcCCM. As I was getting very different results using each function, I went into the source code. There seem to be two differences in how the results are calculated, which makes me suspect one of them can be a bug.

1. The following code in optandcalcCCM:

libsizemin_12 = max(res12["E"] + b_offset + 1, libsizemin)
libsizemin_21 = max(res21["E"] + b_offset + 1, libsizemin)

corresponds, in makeoptimizationplots, to:

libsizemin_12 = max(res12["E"] + b_offset + 1, 10)
libsizemin_21 = max(res21["E"] + b_offset + 1, 10)

which I suspect might not be desired.

1. When calling calcCCM in makeoptimizationplots, you set a parameter lib_start=1, which is not done in the corresponding calls in optandcalcCCM.