Commit c3bb1bc2 by Eric Coissac

With the missing function definition

parent 7e50ffc1
......@@ -345,7 +345,22 @@ def PELengthEstimate(PEiterator, double threshold=0.9,int minlength=81):
def PELengthCut(PEiterator, int length):
cdef tuple forward
cdef tuple reverse
cdef int fb,rb
for forward,reverse in PEiterator:
fb = bestWindow(forward[2],length)
rb = bestWindow(reverse[2],length)
yield ((forward[0],
forward[1][fb:(fb+length)],
forward[2][fb:(fb+length)]),
(reverse[0],
reverse[1][rb:(rb+length)],
reverse[2][rb:(rb+length)]))
def PESkipFirstReads(PEI,int skip=0):
cdef int n = 0
......@@ -463,7 +478,7 @@ def readPairedEnd(filenames,
PEI = PEPhiXCleaner(PEI)
if length>0 :
PEI =
PEI = PELengthCut(PEI,length)
elif lengthestimate > 0:
PEI = PELengthEstimate(PEI,lengthestimate,minlength)
......
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