def validateAndSanitizeExistingOptions(self, options):
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
groomBamList(options.probandBamList, "proband sample")
groomBamList(options.parentBamList, "parent sample")
groomBamList(options.siblingBamList, "sibling sample")
def validateAndSanitizeExistingOptions(self, options):
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
groomBamList(options.normalBamList, "normal sample")
groomBamList(options.tumorBamList, "tumor sample")
checkFixTabixListOption(options.noiseVcfList, "noise vcf")
options.somaticSnvScoringModelFile = validateFixExistingFileArg(
options.somaticSnvScoringModelFile,
"Somatic SNV empirical scoring file")
options.somaticIndelScoringModelFile = validateFixExistingFileArg(
options.somaticIndelScoringModelFile,
"Somatic indel empirical scoring file")
def validateAndSanitizeExistingOptions(self, options):
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
groomBamList(options.bamList, "input")
def checkFixTabixIndexedFileOption(tabixFile, label):
checkOptionalTabixIndexedFile(tabixFile, label)
if tabixFile is None: return None
return os.path.abspath(tabixFile)
if options.excludedRegions is not None:
for excludeIndex in range(len(options.excludedRegions)):
options.excludedRegions[excludeIndex] = \
checkFixTabixIndexedFileOption(options.excludedRegions[excludeIndex],"excluded-regions bed")
if options.knownVariants is not None:
options.knownVariants = \
checkFixTabixIndexedFileOption(options.knownVariants,"known-variants vcf")
def validateAndSanitizeExistingOptions(self, options):
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
groomBamList(options.bamList, "input")