Commit 03cd4a59 by Eric Coissac

Add the logger to the scaffold call and modify for this the

`compactGraph2lastgraph` function
parent c80a94ef
......@@ -57,7 +57,7 @@ def addOptions(parser):
def compactGraph2lastgraph(asm,paths=[],minlink=5,back=250):
def compactGraph2lastgraph(asm,paths=[],minlink=5,back=250,logger=None):
#FASTG:begin;
#FASTG:version=1.0:assembly_name=”tiny example”;
cg = asm.compactAssembling(verbose=False)
......@@ -67,7 +67,8 @@ def compactGraph2lastgraph(asm,paths=[],minlink=5,back=250):
cg,
minlink=minlink,
back=int(back),
addConnectedLink=False)
addConnectedLink=False,
logger=logger)
edges = list(cg.stemIterator())
nodes = [e for e in edges if "stemid" in e]
......@@ -231,5 +232,5 @@ def run(config):
back=500
else:
back = 300
compactGraph2lastgraph(asm)
compactGraph2lastgraph(asm,logger=logger)
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