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 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)
