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)