def test_reads_in_range(self):
ds = DataSet(data.getBam())
refNames = ds.refNames
rn = refNames[15]
reads = ds.readsInRange(rn, 10, 100)
self.assertEqual(len(list(reads)), 10)
ds2 = DataSet(data.getBam(0))
reads = ds2.readsInRange("E.faecalis.1", 0, 1400)
self.assertEqual(len(list(reads)), 20)
lengths = ds.refLengths
for rname, rId in ds.refInfo('ID'):
rn = ds._idToRname(rId)
self.assertEqual(rname, rn)
rlen = lengths[rn]
self.assertEqual(len(list(ds.readsInReference(rn))),
len(list(ds.readsInReference(rId))))
self.assertEqual(len(list(ds.readsInRange(rn, 0, rlen))),
len(list(ds.readsInRange(rId, 0, rlen))))
def test_reads_in_range(self):
ds = DataSet(data.getBam())
refNames = ds.refNames
rn = refNames[15]
reads = ds.readsInRange(rn, 10, 100)
self.assertEqual(len(list(reads)), 10)
ds2 = DataSet(data.getBam(0))
reads = ds2.readsInRange("E.faecalis.1", 0, 1400)
self.assertEqual(len(list(reads)), 20)
lengths = ds.refLengths
for rname, rId in ds.refInfo('ID'):
rn = ds._idToRname(rId)
self.assertEqual(rname, rn)
rlen = lengths[rn]
self.assertEqual(len(list(ds.readsInReference(rn))),
len(list(ds.readsInReference(rId))))
self.assertEqual(len(list(ds.readsInRange(rn, 0, rlen))),
len(list(ds.readsInRange(rId, 0, rlen))))
