def test_len_h5(self):
# HdfSubreadSet
# len means something else in bax/bas land. These numbers may actually
# be correct...
sset = HdfSubreadSet(data.getXml(17), strict=True)
self.assertEqual(len(sset), 9)
self.assertEqual(sset._length, (9, 128093))
self.assertEqual(sset.totalLength, 128093)
self.assertEqual(sset.numRecords, 9)
sset.totalLength = -1
sset.numRecords = -1
self.assertEqual(sset.totalLength, -1)
self.assertEqual(sset.numRecords, -1)
sset.updateCounts()
self.assertEqual(sset.totalLength, 128093)
self.assertEqual(sset.numRecords, 9)
# AlignmentSet with cmp.h5
aln = AlignmentSet(upstreamData.getBamAndCmpH5()[1], strict=True)
self.assertEqual(len(aln), 112)
self.assertEqual(aln._length, (112, 59970))
self.assertEqual(aln.totalLength, 59970)
self.assertEqual(aln.numRecords, 112)
aln.totalLength = -1
aln.numRecords = -1
self.assertEqual(aln.totalLength, -1)
self.assertEqual(aln.numRecords, -1)
aln.updateCounts()
self.assertEqual(aln.totalLength, 59970)
self.assertEqual(aln.numRecords, 112)
def test_len(self):
# AlignmentSet
aln = AlignmentSet(data.getXml(8), strict=True)
self.assertEqual(len(aln), 92)
self.assertEqual(aln._length, (92, 123588))
self.assertEqual(aln.totalLength, 123588)
self.assertEqual(aln.numRecords, 92)
aln.totalLength = -1
aln.numRecords = -1
self.assertEqual(aln.totalLength, -1)
self.assertEqual(aln.numRecords, -1)
aln.updateCounts()
self.assertEqual(aln.totalLength, 123588)
self.assertEqual(aln.numRecords, 92)
# AlignmentSet with filters
aln = AlignmentSet(data.getXml(15), strict=True)
self.assertEqual(len(aln), 40)
self.assertEqual(aln._length, (40, 52023))
self.assertEqual(aln.totalLength, 52023)
self.assertEqual(aln.numRecords, 40)
aln.totalLength = -1
aln.numRecords = -1
self.assertEqual(aln.totalLength, -1)
self.assertEqual(aln.numRecords, -1)
aln.updateCounts()
self.assertEqual(aln.totalLength, 52023)
self.assertEqual(aln.numRecords, 40)
# NO LONGER SUPPORTED AlignmentSet with cmp.h5
#aln = AlignmentSet(upstreamData.getCmpH5(), strict=True)
#self.assertEqual(len(aln), 84)
#self.assertEqual(aln._length, (84, 26103))
#self.assertEqual(aln.totalLength, 26103)
#self.assertEqual(aln.numRecords, 84)
#aln.totalLength = -1
#aln.numRecords = -1
#self.assertEqual(aln.totalLength, -1)
#self.assertEqual(aln.numRecords, -1)
#aln.updateCounts()
#self.assertEqual(aln.totalLength, 26103)
#self.assertEqual(aln.numRecords, 84)
# SubreadSet
# TODO Turn this back on when pbi's are fixed for subreadsets
#sset = SubreadSet(data.getXml(10), strict=True)
#self.assertEqual(len(sset), 92)
#self.assertEqual(sset._length, (92, 123588))
#self.assertEqual(sset.totalLength, 123588)
#self.assertEqual(sset.numRecords, 92)
#sset.totalLength = -1
#sset.numRecords = -1
#self.assertEqual(sset.totalLength, -1)
#self.assertEqual(sset.numRecords, -1)
#sset.updateCounts()
#self.assertEqual(sset.totalLength, 123588)
#self.assertEqual(sset.numRecords, 92)
# HdfSubreadSet
# len means something else in bax/bas land. These numbers may actually
# be correct...
sset = HdfSubreadSet(data.getXml(17), strict=True)
self.assertEqual(len(sset), 9)
self.assertEqual(sset._length, (9, 128093))
self.assertEqual(sset.totalLength, 128093)
self.assertEqual(sset.numRecords, 9)
sset.totalLength = -1
sset.numRecords = -1
self.assertEqual(sset.totalLength, -1)
self.assertEqual(sset.numRecords, -1)
sset.updateCounts()
self.assertEqual(sset.totalLength, 128093)
self.assertEqual(sset.numRecords, 9)
# ReferenceSet
sset = ReferenceSet(data.getXml(9), strict=True)
self.assertEqual(len(sset), 59)
self.assertEqual(sset.totalLength, 85774)
self.assertEqual(sset.numRecords, 59)
sset.totalLength = -1
sset.numRecords = -1
self.assertEqual(sset.totalLength, -1)
self.assertEqual(sset.numRecords, -1)
sset.updateCounts()
self.assertEqual(sset.totalLength, 85774)
self.assertEqual(sset.numRecords, 59)
