def validateAndSanitizeOptions(self,options) :
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeOptions(self,options)
checkFixTabixListOption(options.noiseVcfList,"noise vcf")
groomBamList(options.normalBamList,"normal sample")
groomBamList(options.tumorBamList, "tumor sample")
def checkRequired(bamList,label):
if (bamList is None) or (len(bamList) == 0) :
raise OptParseException("No %s sample BAM/CRAM files specified" % (label))
checkRequired(options.tumorBamList,"tumor")
bamSetChecker = BamSetChecker()
def singleAppender(bamList,label):
if bamList is None : return
if len(bamList) > 1 :
raise OptParseException("More than one %s sample BAM/CRAM files specified" % (label))
bamSetChecker.appendBams(bamList,label)
singleAppender(options.normalBamList,"normal")
singleAppender(options.tumorBamList,"tumor")
bamSetChecker.check(options.htsfileBin,
options.referenceFasta)
def validateAndSanitizeOptions(self, options):
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeOptions(
self, options)
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")
groomBamList(options.bamList, "input")
bamSetChecker = BamSetChecker()
def singleAppender(bamList, label):
if len(bamList) > 1:
raise OptParseException(
"More than one %s sample BAM/CRAM files specified" %
(label))
bamSetChecker.appendBams(bamList, label)
singleAppender(options.bamList, "Input")
bamSetChecker.check(options.htsfileBin, options.referenceFasta)
def validateAndSanitizeOptions(self, options):
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeOptions(
self, options)
groomBamList(options.bamList, "input")
bamSetChecker = BamSetChecker()
bamSetChecker.appendBams(options.bamList, "Input")
bamSetChecker.check(options.samtoolsBin, options.referenceFasta)
def validateAndSanitizeOptions(self, options):
StrelkaSharedWorkflowOptionsBase.validateAndSanitizeOptions(
self, options)
options.ploidyFilename = checkFixTabixIndexedFileOption(
options.ploidyFilename, "ploidy file")
options.noCompressBed = checkFixTabixIndexedFileOption(
options.noCompressBed, "no-compress bed")
if options.snvScoringModelFile is None:
if options.isRNA:
options.snvScoringModelFile = options.rnaSnvScoringModelFile
else:
options.snvScoringModelFile = options.germlineSnvScoringModelFile
if options.indelScoringModelFile is None:
if options.isRNA:
options.indelScoringModelFile = options.rnaIndelScoringModelFile
else:
options.indelScoringModelFile = options.germlineIndelScoringModelFile
# Disable dynamic error estimation for Exome
if options.isExome:
options.isEstimateSequenceError = False
# Disable dynamic error estimation for RNA
if options.isRNA:
options.isEstimateSequenceError = False
groomBamList(options.bamList, "input")
def safeLen(x):
if x is None: return 0
return len(x)
if safeLen(options.bamList) == 0:
raise OptParseException(
"No input sample alignment files specified")
bamSetChecker = BamSetChecker()
bamSetChecker.appendBams(options.bamList, "Input")
bamSetChecker.check(options.htsfileBin, options.referenceFasta)