def addExtendedGroupOptions(self, group):
group.add_option(
"--scanSizeMb",
type="int",
metavar="INT",
help=
"Maximum sequence region size (in megabases) scanned by each task during "
"SV Locus graph generation. (default: %default)")
group.add_option(
"--callRegions",
dest="callRegionsBed",
help=
"Optionally provide a bgzip-compressed/tabix-indexed BED file containing the set of regions to call. "
"No VCF output will be provided outside of these regions. The full genome will still be used "
"to estimate statistics from the input (such as expected fragment size distribution). "
"Only one BED file may be specified. (default: call the entire genome)"
)
group.add_option(
"--region",
type="string",
dest="regionStrList",
metavar="REGION",
action="append",
help=
"Limit the 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 regions)'")
ConfigureWorkflowOptions.addExtendedGroupOptions(self, group)
def addExtendedGroupOptions(self,group) :
group.add_option("--scanSizeMb", type="int", metavar="INT",
help="Maximum sequence region size (in megabases) scanned by each task during "
"SV Locus graph generation. (default: %default)")
group.add_option("--region", type="string",dest="regionStrList",metavar="REGION", action="append",
help="Limit the 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 regions)'")
ConfigureWorkflowOptions.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(
"--scanSizeMb",
type="int",
dest="scanSizeMb",
metavar="INT",
help=
"Maximum sequence region size (in megabases) scanned by each task during "
"genome variant calling. (default: %default)")
group.add_option(
"--region",
type="string",
dest="regionStrList",
metavar="REGION",
action="append",
help=
"Limit the 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 regions)'")
group.add_option(
"--callMemMb",
dest="callMemMbOverride",
type="int",
metavar="INT",
help=
"Set variant calling task memory limit (in megabytes). It is not "
"recommended to change the default in most cases, but this might be required "
"for a sample of unusual depth.")
group.add_option(
"--retainTempFiles",
dest="isRetainTempFiles",
action="store_true",
help="Keep all temporary files (for workflow debugging)")
group.add_option("--disableEVS",
dest="isEVS",
action="store_false",
help="Disable empirical variant scoring.")
group.add_option(
"--reportEVSFeatures",
dest="isReportEVSFeatures",
action="store_true",
help=
"Report all Empirical Variant Scoring (EVS) features in VCF output."
)
ConfigureWorkflowOptions.addExtendedGroupOptions(self, group)
def addExtendedGroupOptions(self, group):
group.add_option(
"--scanSizeMb",
dest="scanSizeMb",
type="int",
metavar="INT",
help=
"Maximum sequence region size (in megabases) scanned by each task during "
"SV Locus graph generation. (default: %default)")
group.add_option(
"--callRegions",
dest="callRegionsBed",
metavar="FILE",
help=
"Optionally provide a bgzip-compressed/tabix-indexed BED file containing the set of regions to call. "
"No VCF output will be provided outside of these regions. The full genome will still be used "
"to estimate statistics from the input (such as expected fragment size distribution). "
"Only one BED file may be specified. (default: call the entire genome)"
)
group.add_option(
"--region",
type="string",
dest="regionStrList",
metavar="REGION",
action="append",
help=
"Limit the 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 regions)'. If this "
"option is specified (one or more times) together with the --callRegions BED file, then "
"all region arguments will be intersected with the callRegions BED track."
)
group.add_option(
"--callMemMb",
dest="callMemMbOverride",
type="int",
metavar="INT",
help=
"Set default task memory requirement (in megabytes) for common tasks. This may benefit "
"an analysis of unusual depth, chimera rate, etc.. 'Common' tasks refers to most "
"compute intensive scatter-phase tasks of graph creation and candidate generation."
)
ConfigureWorkflowOptions.addExtendedGroupOptions(self, group)
def addExtendedGroupOptions(self,group) :
group.add_option("--scanSizeMb", dest="scanSizeMb", type="int", metavar="INT",
help="Maximum sequence region size (in megabases) scanned by each task during "
"SV Locus graph generation. (default: %default)")
group.add_option("--region", type="string",dest="regionStrList",metavar="REGION", action="append",
help="Limit the 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 regions)'. If this "
"option is specified (one or more times) together with the --callRegions BED file, then "
"all region arguments will be intersected with the callRegions BED track.")
group.add_option("--callMemMb",dest="callMemMbOverride",type="int",metavar="INT",
help="Set default task memory requirement (in megabytes) for common tasks. This may benefit "
"an analysis of unusual depth, chimera rate, etc.. 'Common' tasks refers to most "
"compute intensive scatter-phase tasks of graph creation and candidate generation.")
ConfigureWorkflowOptions.addExtendedGroupOptions(self,group)
def addExtendedGroupOptions(self, group):
group.add_option(
"--scanSizeMb",
type="int",
metavar="INT",
help=
"Maximum sequence region size (in megabases) scanned by each task during "
"SV Locus graph generation. (default: %default)")
group.add_option(
"--region",
type="string",
dest="regionStrList",
metavar="REGION",
action="append",
help=
"Limit the 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 regions)'")
ConfigureWorkflowOptions.addExtendedGroupOptions(self, group)
def main():
workflowOptions = ConfigureWorkflowOptions().get_run_options()
CNVect = DetectByCNVect(workflowOptions)
CNVect.runWorkflow()