def testNoRename(self):
read = MockRead('foo1')
ngsutils.bam.renamepair.read_renamepair(read, '/')
self.assertEqual(read.qname, 'foo1')
assertNotIn(('ZN', '1'), read.tags)
def testNoRename(self):
read = MockRead("foo1")
ngsutils.bam.renamepair.read_renamepair(read, "/")
self.assertEqual(read.qname, "foo1")
assertNotIn(("ZN", "1"), read.tags)
def testCufflinksXS(self):
read1 = MockRead('foo',
tid=1,
pos=1,
is_reverse=True,
tags=[('ZZ', 1)])
read2 = MockRead('bar', tid=1, pos=1, tags=[('ZZ', 1)])
read3 = MockRead('baz', tags=[('ZZ', 1)])
chain = _TestChain([
read1,
read2,
read3,
])
chain = ngsutils.bam.tag.CufflinksXS(chain)
for r in chain.filter():
assertIn(('ZZ', 1), r.tags)
if r.qname == 'foo':
assertIn(('XS', '-'), r.tags)
elif r.qname == 'bar':
assertIn(('XS', '+'), r.tags)
elif r.qname == 'baz':
assertNotIn(('XS', '+'), r.tags)
assertNotIn(('XS', '-'), r.tags)
