Commit 5640db43 by Eric Coissac

Add a missing colon

parent 7097ef3b
......@@ -327,7 +327,7 @@ def PEQualityTrimmer(PEiterator, int quality, int shift=33):
#cython: initializedcheck=False
def PELengthEstimate(PEiterator, double threshold=0.9,int minlength=81):
def PELengthEstimate(PEiterator, double threshold=0.9,int minlength=81, bint zip=False):
cdef tuple pair
cdef tuple forward
cdef tuple reverse
......@@ -338,6 +338,7 @@ def PELengthEstimate(PEiterator, double threshold=0.9,int minlength=81):
cdef int fb,rb
cdef int readcount
cdef int cumsum=0
cdef int lpair=0
cdef int lcut=1001
cdef int counter=0
cdef ProgressCounter pc = ProgressCounter(8,
......@@ -357,7 +358,10 @@ def PELengthEstimate(PEiterator, double threshold=0.9,int minlength=81):
l = lf if lf < lr else lr
chisto[l]+=1
store.append((l,compress(dumps(pair,protocol=3),9)))
if zip:
store.append((l,compress(dumps(pair,protocol=3),9)))
else:
store.append((l,pair))
readcount= sum(histo) * threshold
......@@ -376,8 +380,10 @@ def PELengthEstimate(PEiterator, double threshold=0.9,int minlength=81):
for lpair,cpair in store:
if lpair >= lcut:
forward,reverse = loads(decompress(cpair))
if zip:
forward,reverse = loads(decompress(cpair))
else:
forward,reverse = cpair
fb = bestWindow(forward[2],lcut)
rb = bestWindow(reverse[2],lcut)
......
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