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 _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()])