Improve the algorithm of the main peeling function

[XingerTang]

@gregorgorjanc @AprilYUZhang

The following are the steps we can take for the algorithm improvements:

• [ ] Improvements regarding the errors of the main peeling function
  • [ ] Make a list of errors, which contains the following information:
    • [ ] specify the usage of the errors
    • [ ] create new names
    • [ ] suggest new default values or other modifications
  • [ ] Test with new default values, make modifications based on the test
• [ ] Improvements regarding posterior update
  • [ ] understand and organize the posterior update process (why separate update and the calculation)
  • [ ] modify posterior update
• [ ] Baum-Welch parameter updates