MutationFinder

Running in a Windows command (DOS) session, the output file is not showing
up in . as the help statement says it will. Instead it shows up in the same
directory as the input file.

I think the following code is at the root of the problem:

def filename_from_filepath(filepath):
""" Strip the path off a filepath to get a filename"""
try:
return filepath[filepath.rindex('/')+1:]
except ValueError:
return filepath


Windows uses backslashes, so the basename above is the full path.