2015-02-07 13:14:59,399 ERROR [oncotator.output.VcfOutputRenderer:214] Traceback (most recent call last):
File "/Users/aramos/repos/oncotator/venv/lib/python2.7/site-packages/Oncotator-1.5.0.0-py2.7.egg/oncotator/output/VcfOutputRenderer.py", line 206, in _renderSortedTsv
recordBuilder = self._parseRecordBuilder(m, recordBuilder, dataManager, inferGenotypes)
File "/Users/aramos/repos/oncotator/venv/lib/python2.7/site-packages/Oncotator-1.5.0.0-py2.7.egg/oncotator/output/VcfOutputRenderer.py", line 268, in _parseRecordBuilder
recordBuilder.addInfo(sampleName, ID, num, dataType, val, isSplit)
File "/Users/aramos/repos/oncotator/venv/lib/python2.7/site-packages/Oncotator-1.5.0.0-py2.7.egg/oncotator/output/RecordBuilder.py", line 292, in addInfo
val = self._map(MutUtils.str2bool, self._fixVal(val, isSplit)) # convert the value to boolean
File "/Users/aramos/repos/oncotator/venv/lib/python2.7/site-packages/Oncotator-1.5.0.0-py2.7.egg/oncotator/output/RecordBuilder.py", line 98, in _map
return [func(v) if v not in bad else None for v in iterable]
File "/Users/aramos/repos/oncotator/venv/lib/python2.7/site-packages/Oncotator-1.5.0.0-py2.7.egg/oncotator/utils/MutUtils.py", line 195, in str2bool
return v.lower() in ("yes", "true", "t", "1", "y")
AttributeError: 'NoneType' object has no attribute 'lower'
This is happening because the new 1000g phase3 datasource has a new INFO field "IMPRECISE" that is of type 'Flag'. It seems that the vcf flag type is not handled properly by RecordBuilder.py