def refineConsensus(ai, arrowConfig, polishDiploid=False):
"""
Given a MultiReadMutationScorer, identify and apply favorable
template mutations. Return (consensus, didConverge) :: (str, bool)
"""
cfg = cc.PolishConfig(arrowConfig.maxIterations,
arrowConfig.mutationSeparation,
arrowConfig.mutationNeighborhood, polishDiploid)
if arrowConfig.maskRadius:
_ = cc.Polish(ai, cfg)
ai.MaskIntervals(arrowConfig.maskRadius, arrowConfig.maskErrorRate)
polishResult = cc.Polish(ai, cfg)
return str(ai), polishResult.hasConverged
def refineConsensus(ai, arrowConfig):
"""
Given a MultiReadMutationScorer, identify and apply favorable
template mutations. Return (consensus, didConverge) :: (str, bool)
"""
cfg = cc.PolishConfig(arrowConfig.maxIterations,
arrowConfig.mutationSeparation,
arrowConfig.mutationNeighborhood)
isConverged, nTested, nApplied = cc.Polish(ai, cfg)
return str(ai), isConverged