Commit b9f21456 by Eric Coissac

Fixes #12

parent 04e099fc
......@@ -310,6 +310,11 @@ def run(config):
# reestimate coverage
if len(asm) == 0:
logger.error('The assembling is empty - Stop the assembling process')
sys.exit(1)
score,length,ecoverage = coverageEstimate(asm,x,r) # @UnusedVariable
if not coverageset:
......@@ -357,6 +362,9 @@ def run(config):
# Run the fill gap procedure
while delta > 0 or delta < -100 :
# intermediate graph are saved before each gap filling step
dumpGraph(output+'.intermediate.oax',asm)
delta = fillGaps(asm,back=back,
minread=minread,
maxjump=0,
......@@ -414,6 +422,12 @@ def run(config):
asm.cleanDeadBranches(maxlength=smallbranches)
cg = asm.compactAssembling(verbose=False)
if len(asm) == 0:
logger.error('The assembling is empty - Stop the assembling process')
sys.exit(1)
score,length,ecoverage = coverageEstimate(asm,x,r) # @UnusedVariable
if not coverageset:
coverage=ecoverage
......
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