DefineClones fails to execute with "bygroup --model aa"

[Jason Vander Heiden]

Traceback (most recent call last):
  File "/usr/lib64/python2.7/multiprocessing/process.py", line 258, in _bootstrap
PID 30107:  Error in sibling process detected. Cleaning up.
PID 30108:  Error in sibling process detected. Cleaning up.
    self.run()
  File "/usr/lib64/python2.7/multiprocessing/process.py", line 114, in run
    self._target(*self._args, **self._kwargs)
  File "/home/jason/workspace/igpipeline/changeo_v0.4/DefineClones.py", line 496, in processQueue
    clones = clone_func(records, **clone_args) if data else None
  File "/home/jason/workspace/igpipeline/changeo_v0.4/DefineClones.py", line 241, in distanceClones
    dists = squareform(dists)
  File "/usr/lib64/python2.7/site-packages/scipy/spatial/distance.py", line 1481, in squareform
    is_valid_dm(X, throw=True, name='X')
  File "/usr/lib64/python2.7/site-packages/scipy/spatial/distance.py", line 1570, in is_valid_dm
    'be zero.') % name)
ValueError: Distance matrix 'X' diagonal must be zero.

[Namita Gupta]

X scoring was mistakenly 0, is now 1 so all amino acids are considered matches

[Ang Cui]

Still experiencing the issue in the 3/13/15 version

Command used: DefineClones.py bygroup -d <file> --model aa --dist 10

[Namita Gupta]

Issue was that score of X with itself was non-zero. Fixed by not calculating distance between junction and itself anymore, so diagonal of distance matrix asserted to be zero.