def _parseTagValue(cls, tag, value): if tag[0] in cls._tagReservedFieldPrefixes: # user reserved fields... not really sure what to do here return protocol.getValueFromValue(value.values[0]) \ .encode(cls._encoding) elif tag in cls._tagIntegerFields: return int(protocol.getValueFromValue(value.values[0])) elif tag in cls._tagStringFields: return protocol.getValueFromValue(value.values[0]) \ .encode(cls._encoding) elif tag in cls._tagIntegerArrayFields: return [int(integerString) for integerString in value] else: raise SamException("unrecognized tag '{}'".format(tag))
def _assertEquivalentGaVCFValues(gaValue, pyvcfValue): compareValue = protocol.getValueFromValue(gaValue) if isinstance(pyvcfValue, str): self.assertEqual(compareValue, pyvcfValue) elif isinstance(pyvcfValue, (int, bool)): self.assertEqual(compareValue, str(pyvcfValue)) elif isinstance(pyvcfValue, float): self.assertAlmostEqual(float(compareValue), float(pyvcfValue)) elif pyvcfValue is None: self.assertEqual(compareValue, ".") else: raise Exception(key, (" values are inconsistent", "between ga4ghObject and pyvcf!"))
def _assertEquivalentGaVCFValues(gaValue, pyvcfValue): compareValue = protocol.getValueFromValue(gaValue) if isinstance(pyvcfValue, str): self.assertEqual(compareValue, pyvcfValue) elif isinstance(pyvcfValue, (int, bool)): self.assertEqual(compareValue, str(pyvcfValue)) elif isinstance(pyvcfValue, float): self.assertAlmostEqual(float(compareValue), float(pyvcfValue)) elif pyvcfValue is None: self.assertEqual(compareValue, ".") else: raise Exception(key, ( " values are inconsistent", "between ga4ghObject and pyvcf!"))
def getDictFromMessageMap(self, messageMap): return dict([ (k, [protocol.getValueFromValue(x) for x in v.values]) for (k, v) in messageMap._values.items()])
def getDictFromMessageMap(self, messageMap): return dict([(k, [protocol.getValueFromValue(x) for x in v.values]) for (k, v) in messageMap._values.items()])