Commit 04e099fc by Eric Coissac

Fixes #11

parent cab8be0c
......@@ -87,7 +87,7 @@ def addOptions(parser):
parser.add_argument('--snp', dest='buildgraph:snp',
action='store_true',
default=False,
help='desactivate the SNP clearing mode')
help='activates the SNP clearing mode')
parser.add_argument('--adapt5', dest ='orgasm:adapt5',
metavar='adapt5',
......@@ -157,6 +157,10 @@ def run(config):
# Clean small unsuccessful extensions
asm.cleanDeadBranches(maxlength=10)
if len(asm) == 0:
logger.error('The assembling is empty - Stop the assembling process')
sys.exit(1)
# reestimate coverage
score,length,ecoverage = coverageEstimate(asm,x,r) # @UnusedVariable
print(score,length,ecoverage)
......@@ -183,7 +187,9 @@ def run(config):
asm.cleanDeadBranches(maxlength=smallbranches)
print(len(asm))
if len(asm) == 0:
logger.error('The assembling is empty - Stop the assembling process')
sys.exit(1)
# reestimate coverage
score,length,ecoverage = coverageEstimate(asm,x,r) # @UnusedVariable
......@@ -299,6 +305,11 @@ 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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