def addExtendedGroupOptions(self, group): group.add_option( "--somaticSnvScoringModelFile", type="string", dest="somaticSnvScoringModelFile", metavar="FILE", help= "Provide a custom EVS model file for somatic SNVs (default: %default)" ) group.add_option( "--somaticIndelScoringModelFile", type="string", dest="somaticIndelScoringModelFile", metavar="FILE", help= "Provide a custom EVS model file for somatic Indels (default: %default)" ) group.add_option( "--noiseVcf", type="string", dest="noiseVcfList", metavar="FILE", action="append", help= "Noise vcf file (submit argument multiple times for more than one file)" ) StrelkaSharedWorkflowOptionsBase.addExtendedGroupOptions(self, group)
def addExtendedGroupOptions(self,group) : # note undocumented library behavior: "dest" is optional, but not including it here will # cause the hidden option to always print group.add_option("--disableSequenceErrorEstimation", dest="isEstimateSequenceError", action="store_false", help="Disable estimation of sequence error rates from data.") group.add_option("--useAllDataForSequenceErrorEstimation", dest="isErrorEstimationFromAllData", action="store_true", help="Instead of sampling a subset of data for error estimation, use all data from sufficiently large chromosomes." " This could greatly increase the workflow's runtime.") StrelkaSharedWorkflowOptionsBase.addExtendedGroupOptions(self,group)
def addExtendedGroupOptions(self, group): group.add_option( "--noiseVcf", type="string", dest="noiseVcfList", metavar="FILE", action="append", help= "Noise vcf file (submit argument multiple times for more than one file)" ) StrelkaSharedWorkflowOptionsBase.addExtendedGroupOptions(self, group)