Suggestions for get_data function

[standage]

The get_data function is small enough that it didn't take too long to understand what it's doing. However, there are several changes that should make it much clearer for future review/maintenance.

• a few variable name replacements
  • thefile --> filename to clarify that it's a file name, rather than an already-opened file handle
  • position_reads --> run_index and read_type --> run_acc: the original variable names were unclear at best, and potentially misleading at worst. Made it more difficult to understand the purpose of the code.
  • a few other minor changes
• cut verbosity of code by using a dict of sets instead of a dict of lists; a set automatically handles duplicates, so you don't have to check that it's already there