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import pytest
from pbcore import data
from pbcore.io import BamReader
from pbcore.io.align._BamSupport import UnavailableFeature
class TestUnalignedBam:
@classmethod
def setup_class(cls):
cls.bam = BamReader(data.getUnalignedBam())
cls.bamRead0 = next(iter(cls.bam))
def testInvalidOperations(self):
# These kinds of things presently work. Do we want them to
# fail?
# with assert_raises(UnavailableFeature):
# self.bamRead0.isForwardStrand
# with assert_raises(UnavailableFeature):
# self.bamRead0.tStart
# attempts to get read aligned or oriented
with pytest.raises(UnavailableFeature):
self.bamRead0.read(aligned=True, orientation="native")
with pytest.raises(UnavailableFeature):
self.bamRead0.read(aligned=False, orientation="genomic")
with pytest.raises(UnavailableFeature):
self.bamRead0.read()
with pytest.raises(UnavailableFeature):
self.bamRead0.InsertionQV(aligned=True, orientation="native")
with pytest.raises(UnavailableFeature):
self.bamRead0.InsertionQV(aligned=False, orientation="genomic")
with pytest.raises(UnavailableFeature):
self.bamRead0.InsertionQV()
def testIpd(self):
"""Check that 'Ipd' feature is recognized correctly."""
pfa = self.bam.baseFeaturesAvailable()
assert pfa == frozenset(['Ipd', 'DeletionTag', 'MergeQV', 'SubstitutionQV',
'InsertionQV', 'DeletionQV'])
ipd = self.bamRead0.IPD(aligned=False, orientation="native")
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