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bias_test try except: Exception is AttributeError not KeyError when i…

…nput is GATK
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commit 119f19df23dafcad56e6168b3adb14e1dcbd7917 1 parent 6e91990
@ian1roberts ian1roberts authored
Showing with 2 additions and 1 deletion.
  1. +2 −1  vcf/filters.py
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3  vcf/filters.py
@@ -138,11 +138,12 @@ def __call__(self, record):
def bias_test(self, calls):
calls = [x for x in calls if x.called]
#TODO: single genotype assumption
+ print calls
try:
# freebayes
ra = robjects.IntVector([x['RO'][0] for x in calls])
aa = robjects.IntVector([x['AO'][0] for x in calls])
- except KeyError:
+ except AttributeError:
# GATK
ra = robjects.IntVector([x['AD'][0] for x in calls])
aa = robjects.IntVector([x['AD'][1] for x in calls])
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