Commit 0962476c authored by Eric Coissac's avatar Eric Coissac

Remove all the filtering on the aligment in the fillgaps procedure. Each

alignment is now considered as a possible seed.
parent e74f59ac
......@@ -473,7 +473,8 @@ def fillGaps(self,minlink=5,
ali= multiAlignReads(ex,index,kmer,smin,delta)
print('',file=sys.stderr)
goodali = [i for i in ali if len(i) >= nreads/4]
#goodali = [i for i in ali if len(i) >= nreads/4]
goodali=ali
print("--> %d consensus to add" % len(goodali),
file=sys.stderr)
......@@ -519,7 +520,8 @@ def fillGaps(self,minlink=5,
if ex not in __cacheAli:
ali= multiAlignReads(ex,index,kmer,smin,delta)
print('',file=sys.stderr)
goodali = [i for i in ali if len(i) >= nreads/4]
#goodali = [i for i in ali if len(i) >= nreads/4]
goodali=ali
print("--> %d consensus to add" % len(goodali),
file=sys.stderr)
......
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