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