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hammerlab / cycledash

Variant Caller Analysis Dashboard and Data Management System
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Varcode annotator fails when there is an intragenic variant #855

Closed armish closed 9 years ago

armish commented 9 years ago 
Traceback (most recent call last):
  File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/celery/app/trace.py", line 437, in __protected_call__
    return self.run(*args, **kwargs)
  File "/home/cycledash/cycledash/workers/varcode_annotator.py", line 39, in annotate
    return _annotate(vcf_id)
  File "/home/cycledash/cycledash/workers/varcode_annotator.py", line 60, in _annotate
    annotations = get_varcode_annotations(genotypes, vcf_id, release)
  File "/home/cycledash/cycledash/workers/varcode_annotator.py", line 135, in get_varcode_annotations
    notation = best_effect.short_description
  File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/varcode/effects.py", line 45, in short_description
    self.__class__.__name__,))
ValueError: Property short_description not implemented for Intragenic