def addExtendedGroupOptions(self, group):
group.add_option(
"--defaultAlignStatsFile",
"--existingAlignStatsFile",
dest="defaultAlignStatsFile",
metavar="FILE",
help=
"Default alignment statistics to use when direct estimation from the sample fails"
)
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths",
action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option(
"--retainTempFiles",
dest="isRetainTempFiles",
action="store_true",
help="Keep all temporary files (for workflow debugging)")
group.add_option("--generateEvidenceBam",
dest="isGenerateSupportBam",
action="store_true",
help="Generate a bam of supporting reads for all SVs")
group.add_option("--outputContig",
dest="isOutputContig",
action="store_true",
help="Output assembled contig sequences in VCF file")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self, group)
def addExtendedGroupOptions(self, group):
group.add_option("--useExistingAlignStats",
dest="useExistingAlignStats",
action="store_true",
help="Use pre-calculated alignment statistics.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths",
action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option(
"--candidateBins",
type="int",
dest="nonlocalWorkBins",
metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
group.add_option(
"--retainTempFiles",
dest="isRetainTempFiles",
action="store_true",
help="Keep all temporary files (for workflow debugging)")
group.add_option("--generateEvidenceBam",
dest="isGenerateSupportBam",
action="store_true",
help="Generate a bam of supporting reads for all SVs")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self, group)
def addExtendedGroupOptions(self,group) :
group.add_option("--useExistingAlignStats",
dest="useExistingAlignStats", action="store_true",
help="Use pre-calculated alignment statistics.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths", action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option("--candidateBins",type="int",dest="nonlocalWorkBins",metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self,group)
def addExtendedGroupOptions(self,group) :
group.add_option("--existingAlignStatsFile",
dest="existingAlignStatsFile", metavar="FILE",
help="Pre-calculated alignment statistics file. Skips alignment stats calculation.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths", action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option("--candidateBins",type="int",
dest="nonlocalWorkBins", metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
group.add_option("--retainTempFiles",
dest="isRetainTempFiles", action="store_true",
help="Keep all temporary files (for workflow debugging)")
group.add_option("--generateEvidenceBam",
dest="isGenerateSupportBam", action="store_true",
help="Generate a bam of supporting reads for all SVs")
group.add_option("--outputContig", dest="isOutputContig", action="store_true",
help="Output assembled contig sequences in VCF file")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self,group)
def addExtendedGroupOptions(self,group) :
group.add_option("--useExistingAlignStats",
dest="useExistingAlignStats", action="store_true",
help="Use pre-calculated alignment statistics.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths", action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option("--scanSizeMb",type="int",dest="scanSizeMb",metavar="scanSizeMb",
help="Maximum sequence region size (in Mb) scanned by each task during "
"SV locus graph generation. (default: %default)")
group.add_option("--candidateBins",type="int",dest="nonlocalWorkBins",metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
group.add_option("--region",type="string",dest="regionStrList",metavar="samtoolsRegion", action="append",
help="Limit the SV analysis to a region of the genome for debugging purposes. "
"If this argument is provided multiple times all specified regions will "
"be analyzed together. All regions must be non-overlapping to get a "
"meaningful result. Examples: '--region chr20' (whole chromosome), "
"'--region chr2:100-2000 --region chr3:2500-3000' (two translocation regions)'")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self,group)
def addExtendedGroupOptions(self, group):
group.add_option("--useExistingAlignStats",
dest="useExistingAlignStats",
action="store_true",
help="Use pre-calculated alignment statistics.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths",
action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option(
"--scanSizeMb",
type="int",
dest="scanSizeMb",
metavar="scanSizeMb",
help=
"Maximum sequence region size (in Mb) scanned by each task during "
"SV locus graph generation. (default: %default)")
group.add_option(
"--candidateBins",
type="int",
dest="nonlocalWorkBins",
metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
group.add_option(
"--region",
type="string",
dest="regionStrList",
metavar="samtoolsRegion",
action="append",
help=
"Limit the SV analysis to a region of the genome for debugging purposes. "
"If this argument is provided multiple times all specified regions will "
"be analyzed together. All regions must be non-overlapping to get a "
"meaningful result. Examples: '--region chr20' (whole chromosome), "
"'--region chr2:100-2000 --region chr3:2500-3000' (two translocation regions)'"
)
MantaWorkflowOptionsBase.addExtendedGroupOptions(self, group)
def addExtendedGroupOptions(self,group) :
group.add_option("--referenceFasta",type="string",dest="referenceFasta",metavar="FILE",
help="samtools-indexed reference fasta file [required] (default: %default)")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self,group)
