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)
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 validateOptionExistence(self, options):
StrelkaSharedWorkflowOptionsBase.validateOptionExistence(self, options)
bcheck = BamSetChecker()
def singleAppender(bamList, label):
if len(bamList) > 1:
raise OptParseException(
"More than one %s sample BAM/CRAM files specified" %
(label))
bcheck.appendBams(bamList, label)
singleAppender(options.bamList, "Input")
bcheck.check(options.htsfileBin, options.referenceFasta)
def validateOptionExistence(self, options):
StrelkaSharedWorkflowOptionsBase.validateOptionExistence(self, options)
if len(options.probandBamList) != 1:
raise OptParseException(
"Must specify one proband sample BAM/CRAM file")
if len(options.parentBamList) != 2:
raise OptParseException(
"Must specify two parent sample BAM/CRAM files")
bcheck = BamSetChecker()
bcheck.appendBams(options.probandBamList, "proband")
bcheck.appendBams(options.parentBamList, "parent")
bcheck.appendBams(options.siblingBamList, "sibling", isAllowEmpty=True)
bcheck.check(options.htsfileBin, options.referenceFasta)
def validateOptionExistence(self,options) :
if (((options.normalBamList is None) or (len(options.normalBamList) == 0)) and
((options.tumorBamList is None) or (len(options.tumorBamList) == 0))) :
raise OptParseException("No normal & tumor sample BAM files specified")
bcheck = BamSetChecker()
bcheck.appendBams(options.normalBamList,"Normal")
bcheck.appendBams(options.tumorBamList,"Tumor")
bcheck.check(options.samtoolsBin,
options.referenceFasta)
MantaWorkflowOptionsBase.validateOptionExistence(self,options)
def validateOptionExistence(self, options):
StrelkaSharedWorkflowOptionsBase.validateOptionExistence(self, options)
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")
bcheck = 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))
bcheck.appendBams(bamList, label)
singleAppender(options.normalBamList, "normal")
singleAppender(options.tumorBamList, "tumor")
bcheck.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):
MantaWorkflowOptionsBase.validateAndSanitizeOptions(self, options)
def safeLen(x):
if x is None: return 0
return len(x)
if ((safeLen(options.normalBamList) == 0)
and (safeLen(options.tumorBamList) == 0)):
raise OptParseException(
"No normal or tumor sample alignment files specified")
if (safeLen(options.tumorBamList) > 1):
raise OptParseException("Can't accept more then one tumor sample")
if ((safeLen(options.tumorBamList) > 0)
and (safeLen(options.normalBamList) > 1)):
raise OptParseException(
"Can't accept multiple normal samples for tumor subtraction")
if options.isRNA:
if ((safeLen(options.normalBamList) != 1)
or (safeLen(options.tumorBamList) != 0)):
raise OptParseException(
"RNA mode currently requires exactly one normal sample")
else:
if options.isUnstrandedRNA:
raise OptParseException(
"Unstranded only applied for RNA inputs")
if options.existingAlignStatsFile is not None:
options.existingAlignStatsFile = validateFixExistingFileArg(
options.existingAlignStatsFile, "existing align stats")
groomBamList(options.normalBamList, "normal sample")
groomBamList(options.tumorBamList, "tumor sample")
bamSetChecker = BamSetChecker()
if safeLen(options.normalBamList) > 0:
bamSetChecker.appendBams(options.normalBamList, "Normal")
if safeLen(options.tumorBamList) > 0:
bamSetChecker.appendBams(options.tumorBamList, "Tumor")
bamSetChecker.check(options.htsfileBin, options.referenceFasta)
def validateOptionExistence(self, options):
def safeLen(x):
if x is None: return 0
return len(x)
if ((safeLen(options.normalBamList) == 0)
and (safeLen(options.tumorBamList) == 0)):
raise OptParseException(
"No normal or tumor sample alignment files specified")
if (safeLen(options.tumorBamList) > 1):
raise OptParseException("Can't accept more then one tumor sample")
if ((safeLen(options.tumorBamList) > 0)
and (safeLen(options.normalBamList) > 1)):
raise OptParseException(
"Can't accept multiple normal samples for tumor subtraction")
bcheck = BamSetChecker()
bcheck.appendBams(options.normalBamList, "Normal")
bcheck.appendBams(options.tumorBamList, "Tumor")
bcheck.check(options.htsfileBin, options.referenceFasta)
MantaWorkflowOptionsBase.validateOptionExistence(self, options)
def validateAndSanitizeOptions(self,options) :
MantaWorkflowOptionsBase.validateAndSanitizeOptions(self,options)
def safeLen(x) :
if x is None : return 0
return len(x)
if ((safeLen(options.normalBamList) == 0) and
(safeLen(options.tumorBamList) == 0)) :
raise OptParseException("No normal or tumor sample alignment files specified")
if (safeLen(options.tumorBamList) > 1) :
raise OptParseException("Can't accept more then one tumor sample")
if ((safeLen(options.tumorBamList) > 0) and (safeLen(options.normalBamList) > 1)) :
raise OptParseException("Can't accept multiple normal samples for tumor subtraction")
if options.isRNA :
if ((safeLen(options.normalBamList) != 1) or
(safeLen(options.tumorBamList) != 0)) :
raise OptParseException("RNA mode currently requires exactly one normal sample")
else :
if options.isUnstrandedRNA :
raise OptParseException("Unstranded only applied for RNA inputs")
if options.existingAlignStatsFile is not None :
options.existingAlignStatsFile=validateFixExistingFileArg(options.existingAlignStatsFile,"existing align stats")
groomBamList(options.normalBamList,"normal sample")
groomBamList(options.tumorBamList, "tumor sample")
bamSetChecker = BamSetChecker()
if safeLen(options.normalBamList) > 0 :
bamSetChecker.appendBams(options.normalBamList,"Normal")
if safeLen(options.tumorBamList) > 0 :
bamSetChecker.appendBams(options.tumorBamList,"Tumor")
bamSetChecker.check(options.htsfileBin,
options.referenceFasta)
def validateOptionExistence(self,options) :
def safeLen(x) :
if x is None : return 0
return len(x)
if ((safeLen(options.normalBamList) == 0) and
(safeLen(options.tumorBamList) == 0)) :
raise OptParseException("No normal or tumor sample alignment files specified")
if (safeLen(options.tumorBamList) > 1) :
raise OptParseException("Can't accept more then one tumor sample")
if ((safeLen(options.tumorBamList) > 0) and (safeLen(options.normalBamList) > 1)) :
raise OptParseException("Can't accept multiple normal samples for tumor subtraction")
bcheck = BamSetChecker()
bcheck.appendBams(options.normalBamList,"Normal")
bcheck.appendBams(options.tumorBamList,"Tumor")
bcheck.check(options.htsfileBin,
options.referenceFasta)
MantaWorkflowOptionsBase.validateOptionExistence(self,options)
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)
def validateOptionExistence(self, options):
StrelkaSharedWorkflowOptionsBase.validateOptionExistence(self, options)
bcheck = BamSetChecker()
bcheck.appendBams(options.bamList, "Input")
bcheck.check(options.samtoolsBin, options.referenceFasta)
