def test_gap_compressed_identity(self):
x = [
gap_compressed_identity(699, 5, 28, 13),
gap_compressed_identity(337, 2, 3, 12)
]
_compare_identity(x, self.GC_IDENTITY)
nM = np.array([699, 337])
nMM = np.array([5, 2])
nInsOps = np.array([28, 3])
nDelOps = np.array([13, 12])
ids = gap_compressed_identity(nM, nMM, nInsOps, nDelOps)
np.testing.assert_almost_equal(ids, self.GC_IDENTITY, decimal=4)
def bam_gc_identity():
x = self.transcript()
nM = x.count("M")
nMM = x.count("R")
nInsOps = self.peer.cigarstring.count("I")
nDelOps = self.peer.cigarstring.count("D")
return statistics.gap_compressed_identity(nM, nMM, nInsOps,
nDelOps)
def pbi_gc_identity():
if self.bam.pbi.hasMappingEventInfo:
return statistics.gap_compressed_identity(
self.nM, self.nMM, self.nInsOps, self.nDelOps)
else: # fallback for pre-v4 .pbi files
return bam_gc_identity()
def gap_compressed_identity(self):
assert self.hasMappingEventInfo
return gap_compressed_identity(self.nM, self.nMM, self.nInsOps,
self.nDelOps)