Commit 21285286 authored by Eric Coissac's avatar Eric Coissac

Add a small cython optimisation

parent e2411f13
......@@ -322,10 +322,11 @@ def mergeAlignments(common, ali1,ali2,rsize):
def multiAlignReads(readids,index,kmer=12,smin=10,delta=2):
readids = list(set(readids))
rsize = index.getReadSize()
cdef list scores=alignReads(readids,index,kmer,smin,delta)
cdef int rsize = index.getReadSize()
cdef dict alignment={}
for (score,(r1,ali1),(r2,ali2)) in scores:
partial1 = [x for x in alignment.items() if r1 in x[0]]
partial2 = [x for x in alignment.items() if r2 in x[0]]
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