0.9.1: first real python commit, duplicate checking is now fully in python
0.9.1: minor cleanups
0.9.1: more cleanups
0.9.1: Updates to convert_external_genome.py, other updates
0.9.1: fixed big bug in convert_external_genome.py
0.9.1: oops small detail
0.9.1: import name misspelling
0.9.1: more mistakes
0.9.1: Added prompt for custom NUCmer arguments
0.9.1: Added logging of NUCmer args
0.9.1: Watch the curlies!
0.9.1: Test twice, commit once.
0.9.1: release
0.9.2: Fixed jar path search code to be more intuitive and less broken on aspen
All methods need to have 'self' as first argument
0.9.2: Reference regions that did not align to an external fasta are now called X instead of N
Merge branch 'python' of https://github.com/TGenNorth/nasp into python

I don't understand what this nano screen that just popped up is.

-- David
0.9.2: Reference regions that did not align to an external fasta are now called X instead of N
Revert "All methods need to have 'self' as first argument"

This reverts commit 022fb1b7e199f77900ce2150546e54a84f35bfb3.

Broke the code:
Traceback (most recent call last):
  File "/media/lumberyard/bin/convert_external_genome.py", line 95, in <module>
    if __name__ == "__main__": main()
  File "/media/lumberyard/bin/convert_external_genome.py", line 86, in main
    external_nickname = Genome.generate_nickname_from_fasta_filename( commandline_args.external )
TypeError: generate_nickname_from_fasta_filename() missing 1 required positional argument: 'fasta_filename'

I think static methods must not have 'self' as the first argument.

-- David
0.9.2: Reference regions that did not align to an external fasta are now called X instead of N