def validateOptionExistence(self,options) :
assertOptionExists(options.normalBam,"normal sample BAM file")
assertOptionExists(options.alignerMode,"aligner mode")
assertOptionExists(options.referenceFasta,"reference fasta file")
MantaWorkflowOptionsBase.validateOptionExistence(self,options)
# check that the reference and the two bams are using the same set of chromosomes:
bamList=[]
bamLabels=[]
if options.normalBam is not None :
bamList.append(options.normalBam)
bamLabels.append("Normal")
if options.tumorBam is not None :
bamList.append(options.tumorBam)
bamLabels.append("Tumor")
checkChromSet(options.samtoolsBin,
options.referenceFasta,
bamList,
bamLabels,
isReferenceLocked=True)
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):
if (options.normalBamList is None) or (len(options.normalBamList)
== 0):
raise OptParseException("No normal sample BAM files specified")
assertOptionExists(options.alignerMode, "aligner mode")
assertOptionExists(options.referenceFasta, "reference fasta file")
MantaWorkflowOptionsBase.validateOptionExistence(self, options)
# check that the reference and all bams are using the same
# set of chromosomes:
bamList = []
bamLabels = []
def appendBams(inputBamList, inputLabel):
if inputBamList is None: return
for inputBamFile in inputBamList:
bamList.append(inputBamFile)
bamLabels.append(inputLabel)
appendBams(options.normalBamList, "Normal")
appendBams(options.tumorBamList, "Tumor")
checkChromSet(options.samtoolsBin,
options.referenceFasta,
bamList,
bamLabels,
isReferenceLocked=True)
# check for repeated bam entries:
#
bamSet = set()
for bamFile in bamList:
if bamFile in bamSet:
raise OptParseException("Repeated input BAM file: %s" %
(bamFile))
bamSet.add(bamFile)
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 validateOptionExistence(self,options) :
if (options.normalBamList is None) or (len(options.normalBamList) == 0) :
raise OptParseException("No normal sample BAM files specified")
assertOptionExists(options.alignerMode,"aligner mode")
assertOptionExists(options.referenceFasta,"reference fasta file")
MantaWorkflowOptionsBase.validateOptionExistence(self,options)
# check that the reference and all bams are using the same
# set of chromosomes:
bamList=[]
bamLabels=[]
def appendBams(inputBamList,inputLabel) :
if inputBamList is None : return
for inputBamFile in inputBamList :
bamList.append(inputBamFile)
bamLabels.append(inputLabel)
appendBams(options.normalBamList,"Normal")
appendBams(options.tumorBamList,"Tumor")
checkChromSet(options.samtoolsBin,
options.referenceFasta,
bamList,
bamLabels,
isReferenceLocked=True)
# check for repeated bam entries:
#
bamSet=set()
for bamFile in bamList :
if bamFile in bamSet :
raise OptParseException("Repeated input BAM file: %s" % (bamFile))
bamSet.add(bamFile)
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)
