def validateAndSanitizeExistingOptions(self, options):
groomBamList(options.normalBamList, "normal sample")
groomBamList(options.tumorBamList, "tumor sample")
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
def validateAndSanitizeExistingOptions(self,options) :
options.normalBam=validateFixExistingFileArg(options.normalBam,"normal sample BAM file")
options.tumorBam=validateFixExistingFileArg(options.tumorBam,"tumor sample BAM file")
# check for bam index files:
for bam in (options.tumorBam,options.normalBam) :
if bam is None : continue
baiFile=bam+".bai"
if not os.path.isfile(baiFile) :
raise OptParseException("Can't find expected BAM index file: '%s'" % (baiFile))
# check alignerMode:
if options.alignerMode is not None :
options.alignerMode = options.alignerMode.lower()
if options.alignerMode not in self.validAlignerModes :
raise OptParseException("Invalid aligner mode: '%s'" % options.alignerMode)
options.referenceFasta=validateFixExistingFileArg(options.referenceFasta,"reference")
# check for reference fasta index file:
if options.referenceFasta is not None :
faiFile=options.referenceFasta + ".fai"
if not os.path.isfile(faiFile) :
raise OptParseException("Can't find expected fasta index file: '%s'" % (faiFile))
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(self,options)
def validateAndSanitizeExistingOptions(self, options):
def checkForBamIndex(bamFile):
baiFile = bamFile + ".bai"
if not os.path.isfile(baiFile):
raise OptParseException(
"Can't find expected BAM index file: '%s'" % (baiFile))
def groomBamList(bamList, sampleLabel):
if bamList is None: return
for (index, bamFile) in enumerate(bamList):
bamList[index] = validateFixExistingFileArg(
bamFile, "%s BAM file" % (sampleLabel))
checkForBamIndex(bamList[index])
groomBamList(options.normalBamList, "normal sample")
groomBamList(options.tumorBamList, "tumor sample")
# check alignerMode:
if options.alignerMode is not None:
options.alignerMode = options.alignerMode.lower()
if options.alignerMode not in self.validAlignerModes:
raise OptParseException("Invalid aligner mode: '%s'" %
options.alignerMode)
options.referenceFasta = validateFixExistingFileArg(
options.referenceFasta, "reference")
# check for reference fasta index file:
if options.referenceFasta is not None:
faiFile = options.referenceFasta + ".fai"
if not os.path.isfile(faiFile):
raise OptParseException(
"Can't find expected fasta index file: '%s'" % (faiFile))
if (options.regionStrList is None) or (len(options.regionStrList)
== 0):
options.genomeRegionList = None
else:
options.genomeRegionList = [
parseGenomeRegion(r) for r in options.regionStrList
]
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
def validateAndSanitizeExistingOptions(self,options) :
def checkForBamIndex(bamFile):
baiFile=bamFile + ".bai"
if not os.path.isfile(baiFile) :
raise OptParseException("Can't find expected BAM index file: '%s'" % (baiFile))
def groomBamList(bamList, sampleLabel):
if bamList is None : return
for (index,bamFile) in enumerate(bamList) :
bamList[index]=validateFixExistingFileArg(bamFile,"%s BAM file" % (sampleLabel))
checkForBamIndex(bamList[index])
groomBamList(options.normalBamList,"normal sample")
groomBamList(options.tumorBamList, "tumor sample")
# check alignerMode:
if options.alignerMode is not None :
options.alignerMode = options.alignerMode.lower()
if options.alignerMode not in self.validAlignerModes :
raise OptParseException("Invalid aligner mode: '%s'" % options.alignerMode)
options.referenceFasta=validateFixExistingFileArg(options.referenceFasta,"reference")
# check for reference fasta index file:
if options.referenceFasta is not None :
faiFile=options.referenceFasta + ".fai"
if not os.path.isfile(faiFile) :
raise OptParseException("Can't find expected fasta index file: '%s'" % (faiFile))
if (options.regionStrList is None) or (len(options.regionStrList) == 0) :
options.genomeRegionList = None
else :
options.genomeRegionList = [parseGenomeRegion(r) for r in options.regionStrList]
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(self,options)
def validateAndSanitizeExistingOptions(self,options) :
groomBamList(options.normalBamList,"normal sample")
groomBamList(options.tumorBamList, "tumor sample")
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(self,options)
