def test_isBarcoded(self):
empty = upstreamdata.getEmptyBam()
nonempty = ('/pbi/dept/secondary/siv/testdata/'
'pblaa-unittest/Sequel/Phi29/m54008_160219_003234'
'.tiny.subreadset.xml')
# One empty one non empty
sset = SubreadSet(nonempty, empty, skipMissing=True)
self.assertTrue(sset.isBarcoded)
# Just nonempty
sset = SubreadSet(nonempty, skipMissing=True)
self.assertEqual(len(sset), 15133)
self.assertTrue(sset.isBarcoded)
# Just empty
# This is crazy, the pbi must be out of date:
sset = SubreadSet(empty)
self.assertEqual(len(sset), 0)
self.assertTrue(sset.isBarcoded)
# To confirm current behavior, I will regenerate the pbi with a
# current pbindex:
efn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
log.info("Copying to {}".format(efn))
sset.copyTo(efn)
sset.induceIndices(force=True)
self.assertFalse(sset.isBarcoded)
def test_empty_bam(self):
fn = data.getEmptyBam()
bam = IndexedBamReader(fn)
EQ(len(bam), 0)
def test_empty_bam(self):
fn = data.getEmptyBam()
bam = IndexedBamReader(fn)
assert len(bam) == 0
def test_empty_bam(self):
fn = data.getEmptyBam()
bam = IndexedBamReader(fn)
EQ(len(bam), 0)