Bug:

[bbimber]

This is a very minor issue but I thought I would report it. One can provide --hmm-type on the command line. I was surprised when I did this, that the tool still reported the default message. If you look at this line:

https://github.com/macs3-project/MACS/blob/8a833cf29e7357311ae6dc34d69175be5702b0ba/MACS3/Utilities/OptValidator.py#L797

I believe that is going to cause the tool to always output the same message, no matter what the user provides:

# Use --hmm-type to select a Gaussian ('gaussian') or Poisson ('poisson') model for the hidden markov model in HMMRATAC. Default: 'gaussian'. 

For example, I ran this with --hmm-type poisson and got the same default message. It seems like you want to separate the situation where no value is provided (in which case it defaults to gaussian, from one where the user provides a value.