igphyml wrapper crashes when given custom V library

[ressy]

I get this exception when trying to use the --lib option to sonar igphyml:

Traceback (most recent call last):
  File "/SONAR/phylogeny/3.2-run_IgPhyML.py", line 358, in <module>
    if not os.path.isfile(arguments['-lib']):
KeyError: '-lib'

I think there's a missing second dash in a few places for the lib argument:

if arguments['--lib'] is not None:
    if not os.path.isfile(arguments['-lib']):
        sys.exit("Can't find germline file %s" % argument['-lib'])

It works if I replace that with:

if arguments['--lib'] is not None:
    if not os.path.isfile(arguments['--lib']):
        sys.exit("Can't find germline file %s" % argument['--lib'])

(This is in https://github.com/scharch/SONAR/blob/master/phylogeny/3.2-run_IgPhyML.py#L365)

[scharch]

Yeah, sorry about that. Fixed in commit 4625c29

[ressy]

Thanks!