def pair1():
p = (SimpleMapping(), SimpleMapping())
p[0].set_name("p1:read/1")
p[1].set_name("p1:read/2")
p[0].tid = "chr1"
p[1].tid = "chr1"
p[0].ref_id = 0
p[1].ref_id = 0
p[0].pos = 12345
p[1].pos = p[0].pos + 150
p[0].set_read1(True)
p[1].set_read2(True)
p[0].qual = 50
p[1].qual = 30
return p
def setUp(self):
self.monitor = StandardMonitor(SavingLogger())
self.filter = FilterLink(self.monitor)
self.receiver = self.filter.set_next(type(self).Receiver())
# create two mappings, m1, m2. We put them in self.pair
# m1 has:
# name = first
# tid = tid1
# m2 has:
# name = second
# tid = tid2
self.pair = [ SimpleMapping(), SimpleMapping() ]
self.m1, self.m2 = self.pair
self.m1.set_name("first") ; self.m2.set_name("second")
self.m1.tid = "tid1" ; self.m2.tid = "tid2"
self.m1.qual = 50 ; self.m2.qual = 30
def pair2():
# reversed reads such that r2 is at a lower position than r1
p = (SimpleMapping(), SimpleMapping())
p[0].set_name("p1:read/1")
p[1].set_name("p1:read/2")
p[0].tid = "chr1"
p[1].tid = "chr1"
p[0].ref_id = 0
p[1].ref_id = 0
p[0].pos = 12345 + 150
p[1].pos = p[0].pos - 150
p[0].set_read1(True)
p[1].set_read2(True)
p[0].qual = 50
p[1].qual = 30
return p
def setUp(self):
self.pair = (SimpleMapping(), SimpleMapping())
self.pair[0].set_read1(True)
self.pair[1].set_read2(True)
for m in self.pair:
m.set_paired(True)
m.set_name("CRESSIA_129:1:1:10605:12550#0")
m.tid = "chr21"
m.ref_id = 20
m.qual = 60
m.set_cigar([(100, "M")])
m.mtid = "chr21"
m.m_ref_id = 20
m1, m2 = self.pair
m1.pos = m2.mpos = 25839277
m2.pos = m1.mpos = 25839109
m1.isize = -268
m2.isize = 268
def setUp(self): self.mapping = SimpleMapping() self.f = SamFormatter()
def setUp(self):
self.mapping = SimpleMapping()
