No sure if your repository is still live. I have created the .rmap file from my digest file for mouse data. However, I have no idea about making the .baitmap file, and can not find how to make it in your documentation files. Also same issues here: https://bitbucket.org/chicagoTeam/chicago/issues/15/input-files-and-how-to-get-them
Would you please help me to find the correct way to generate the baitmap file? Thank you very much!