def __init__(self, localId, dataPath):
self._backend = backend.AbstractBackend()
self._referenceSet = None
self._dataset = datasets.AbstractDataset("ds")
self._readGroupInfos = {}
self._readGroupSetInfo = None
self._samFile = pysam.AlignmentFile(dataPath)
self._readReferences()
super(ReadGroupSetTest, self).__init__(localId, dataPath)
self._readAlignmentInfo()
def setUp(self):
class FakeRequest(object):
pass
class FakeTopLevelObject(object):
def toProtocolElement(self):
return self
self.request = FakeRequest()
self.request.pageToken = None
self.numObjects = 3
self.objects = [FakeTopLevelObject() for j in range(self.numObjects)]
self.backend = backend.AbstractBackend()
def setUp(self):
class FakeRequest(object):
pass
class FakeTopLevelObject(object):
def toProtocolElement(self):
return self
self.request = FakeRequest()
self.request.pageToken = None
self.idMap = {
"a": FakeTopLevelObject(),
"b": FakeTopLevelObject(),
"c": FakeTopLevelObject(),
}
self.idList = sorted(self.idMap.keys())
self.backend = backend.AbstractBackend()
def setUp(self):
self._backend = backend.AbstractBackend()
def setUp(self):
self._variantSetName = "testVariantSet"
self._backend = backend.AbstractBackend()
self._dataset = datasets.AbstractDataset(self._backend)
self._variantSet = variants.AbstractVariantSet(self._dataset,
self._variantSetName)
def setUp(self):
self._backend = backend.AbstractBackend()
self._referenceSet = references.AbstractReferenceSet(self._backend)
self._reference = references.AbstractReference(self._referenceSet,
"ref")