Some of the functions are duplicated across different scripts in "src". I suggest going through all scripts, deciding which are more useful for users and removing the rest.
An example of duplicated functions is readBamStats in both utils.py and covPUFilter.py. There are also some unused functions like markBadRegionsMQ and findTotalNMatches (more examples mentioned in #85)
Some of the functions are duplicated across different scripts in "src". I suggest going through all scripts, deciding which are more useful for users and removing the rest.
An example of duplicated functions is readBamStats in both utils.py and covPUFilter.py. There are also some unused functions like markBadRegionsMQ and findTotalNMatches (more examples mentioned in #85)