def testHashVariantAnnotation(self):
annotation = protocol.VariantAnnotation()
variant = protocol.Variant()
expected = 'bec63dc7c876bb3c7b71422203b101d1'
hashed = self._variantAnnotationSet.hashVariantAnnotation(
variant, annotation)
self.assertEqual(hashed, expected)
def testHashVariantAnnotation(self):
annotation = protocol.VariantAnnotation()
variant = protocol.Variant()
expected = hashlib.md5('\t()\t[]\t').hexdigest()
hashed = self._variantAnnotationSet.hashVariantAnnotation(
variant, annotation)
self.assertEqual(hashed, expected)
def _createGaVariant(self):
"""
Convenience method to set the common fields in a GA Variant
object from this variant set.
"""
ret = protocol.Variant()
ret.created = self._creationTime
ret.updated = self._updatedTime
ret.variantSetId = self.getId()
return ret
def testMaxBufferSizeOverridesPageSize(self):
responseClass = protocol.SearchVariantsResponse
typicalValue = protocol.Variant()
# We have to put some values in here or it will have zero length.
typicalValue.start = 1
typicalValue.end = 2
typicalValue.reference_bases = "AAAAAAAA"
typicalValueLength = typicalValue.ByteSize()
for numValues in range(1, 10):
maxBufferSize = numValues * typicalValueLength
builder = protocol.SearchResponseBuilder(responseClass, 1000,
maxBufferSize)
self.assertEqual(maxBufferSize, builder.getMaxBufferSize())
while not builder.isFull():
builder.addValue(typicalValue)
instance = protocol.fromJson(builder.getSerializedResponse(),
responseClass)
valueList = getattr(instance, getValueListName(responseClass))
self.assertEqual(len(valueList), numValues)
def setUp(self):
self.variant = protocol.Variant()
self.variant.start = 4
self.variant.end = 6
self.intervalIterator = backend.VariantsIntervalIterator
def generateVariant():
variant = protocol.Variant()
return variant