Commit b0006c21 by Eric Coissac

Patch a bug in the gap length estimation

parent 0c0cf629
......@@ -1475,15 +1475,18 @@ def path2fasta(self,assgraph,path,identifier="contig",minlink=10,nlength=20,back
label.append('{connection: %d}' % connected)
else:
if connected >= minlink:
glength = frglen - ml - self.index.getReadSize()
if logger is None:
print("Path is circular but disconnected" ,file=sys.stderr)
print("Linked by %d pair ended links" % connected,file=sys.stderr)
print(" But linked by %d pair ended links (gap length=%f sd=%f)" % (connected,glength,sl),file=sys.stderr)
else:
logger.info("Path is circular but disconnected")
logger.info("Linked by %d pair ended links" % connected)
logger.info("Linked by %d pair ended links (gap length=%f sd=%f)" % (connected,glength,sl))
label.append('{N-connection: %d}' % connected)
seq.append(b'N'*nlength)
seq.append(b'N'*glength)
slength.append(glength)
circular=True
elif forceconnection:
if logger is None:
......
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