def make_call(self,seq): if self.pct_cov < 1.0: return "Incomplete" if self.mean_cov < 5.0: return "Low coverage" if not self.variants and not self.dips: return "Pass" result = runGD(inputGD(self.name, self.variants+self.dips, seq)) if not result['score'] == '-1': return "Fixable:%s,%s" % (result['primer1'],result['primer2']) if self.variants: return 'Errors' return 'Dips'
def make_call(self, seq):
if self.pct_cov < 1.0: return "Incomplete"
if self.mean_cov < 5.0: return "Low coverage"
if not self.variants and not self.dips: return "Pass"
result = runGD(inputGD(self.name, self.variants + self.dips, seq))
if not result['score'] == '-1':
return "Fixable:%s,%s" % (result['primer1'], result['primer2'])
if self.variants: return 'Errors'
return 'Dips'
def make_call(self,seq):
if self.pct_cov < 1.0: return "Incomplete"
## changed from 5.0 to 100.0
## CHANGE: 08/25/15 -- Ernst Oberortner
## changed threshold from 5.0 to 100.0
## old:
## if self.mean_cov < 5.0: return "Low coverage"
## new:
if self.mean_cov < 100.0: return "Low coverage"
if not self.variants and not self.dips: return "Pass"
result = runGD(inputGD(self.name, self.variants+self.dips, seq))
if not result['score'] == '-1': return "Fixable:%s,%s" % (result['primer1'],result['primer2'])
if self.variants: return 'Errors'
return 'Dips'
def make_call(self, seq):
if self.pct_cov < 1.0: return "Incomplete"
## changed from 5.0 to 100.0
## CHANGE: 08/25/15 -- Ernst Oberortner
## changed threshold from 5.0 to 100.0
## old:
## if self.mean_cov < 5.0: return "Low coverage"
## new:
if self.mean_cov < 100.0: return "Low coverage"
if not self.variants and not self.dips: return "Pass"
result = runGD(inputGD(self.name, self.variants + self.dips, seq))
if not result['score'] == '-1':
return "Fixable:%s,%s" % (result['primer1'], result['primer2'])
if self.variants: return 'Errors'
return 'Dips'