def addExtendedGroupOptions(self, group):
group.add_option("--useExistingAlignStats",
dest="useExistingAlignStats",
action="store_true",
help="Use pre-calculated alignment statistics.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths",
action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option(
"--candidateBins",
type="int",
dest="nonlocalWorkBins",
metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
group.add_option(
"--retainTempFiles",
dest="isRetainTempFiles",
action="store_true",
help="Keep all temporary files (for workflow debugging)")
group.add_option("--generateEvidenceBam",
dest="isGenerateSupportBam",
action="store_true",
help="Generate a bam of supporting reads for all SVs")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self, group)
def addExtendedGroupOptions(self, group):
group.add_option(
"--defaultAlignStatsFile",
"--existingAlignStatsFile",
dest="defaultAlignStatsFile",
metavar="FILE",
help=
"Default alignment statistics to use when direct estimation from the sample fails"
)
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths",
action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option(
"--retainTempFiles",
dest="isRetainTempFiles",
action="store_true",
help="Keep all temporary files (for workflow debugging)")
group.add_option("--generateEvidenceBam",
dest="isGenerateSupportBam",
action="store_true",
help="Generate a bam of supporting reads for all SVs")
group.add_option("--outputContig",
dest="isOutputContig",
action="store_true",
help="Output assembled contig sequences in VCF file")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self, group)
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):
groomBamList(options.normalBamList, "normal sample")
groomBamList(options.tumorBamList, "tumor sample")
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(
self, options)
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 addExtendedGroupOptions(self,group) :
group.add_option("--useExistingAlignStats",
dest="useExistingAlignStats", action="store_true",
help="Use pre-calculated alignment statistics.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths", action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option("--candidateBins",type="int",dest="nonlocalWorkBins",metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self,group)
def addWorkflowGroupOptions(self,group) :
group.add_option("--bam","--normalBam", type="string",dest="normalBamList",metavar="FILE", action="append",
help="Normal sample BAM or CRAM file. May be specified more than once, multiple inputs will be treated as each BAM file representing a different sample. [optional] (no default)")
group.add_option("--tumorBam","--tumourBam", type="string",dest="tumorBamList",metavar="FILE", action="append",
help="Tumor sample BAM or CRAM file. Only up to one tumor bam file accepted. [optional] (no default)")
group.add_option("--exome", dest="isExome", action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option("--rna", dest="isRNA", action="store_true",
help="Set options for RNA-Seq input. Must specify exactly one bam input file")
group.add_option("--unstrandedRNA", dest="isUnstrandedRNA", action="store_true",
help="Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand")
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
def addWorkflowGroupOptions(self,group) :
group.add_option("--normalBam", type="string",dest="normalBam",metavar="FILE",
help="Normal sample BAM file. [required] (no default)")
group.add_option("--tumorBam", type="string",dest="tumorBam",metavar="FILE",
help="Tumor sample BAM file. [optional] (no default)")
# group.add_option("--aligner", type="string",dest="alignerMode",metavar="ALIGNER",
# help="Aligner type. Accepted option are {%s} [required] (no default)" % (",".join(['%s' % (x) for x in self.validAlignerModes])))
group.add_option("--exome", dest="isExome", action="store_true",
help="Turn off depth filters which don't make sense for exome or other targeted output.")
# TODO:
# need argument to set the workflow to either ISAAC or bwa mode
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
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 addWorkflowGroupOptions(self,group) :
group.add_option("--normalBam", type="string",dest="normalBamList",metavar="FILE", action="append",
help="Normal sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)")
group.add_option("--tumorBam","--tumourBam", type="string",dest="tumorBamList",metavar="FILE", action="append",
help="Tumor sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)")
group.add_option("--exome", dest="isExome", action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option("--rna", dest="isRNA", action="store_true",
help="Set options for RNA-Seq input: turn off depth filters and don't treat "
"anomalous reads as SV evidence when the proper-pair bit is set.")
group.add_option("--unstrandedRNA", dest="isUnstrandedRNA", action="store_true",
help="Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand")
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
def addWorkflowGroupOptions(self,group) :
group.add_option("--normalBam", type="string",dest="normalBamList",metavar="FILE", action="append",
help="Normal sample BAM file. May be specified more than once, multiple inputs will be merged. [at least one required] (no default)")
group.add_option("--tumorBam","--tumourBam", type="string",dest="tumorBamList",metavar="FILE", action="append",
help="Tumor sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)")
# group.add_option("--aligner", type="string",dest="alignerMode",metavar="ALIGNER",
# help="Aligner type. Accepted option are {%s} [required] (no default)" % (",".join(['%s' % (x) for x in self.validAlignerModes])))
group.add_option("--exome", dest="isExome", action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option("--rna", dest="isRNA", action="store_true",
help="Set options for RNA-Seq input: turn off depth filters and don't treat "
"anomalous reads as SV evidence when the proper-pair bit is set.")
group.add_option("--referenceFasta",type="string",dest="referenceFasta",metavar="FILE",
help="samtools-indexed reference fasta file [required] (default: %default)")
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
def addWorkflowGroupOptions(self, group):
group.add_option(
"--bam",
"--normalBam",
type="string",
dest="normalBamList",
metavar="FILE",
action="append",
help=
"Normal sample BAM or CRAM file. May be specified more than once, multiple inputs will be treated as each BAM file representing a different sample. [optional] (no default)"
)
group.add_option(
"--tumorBam",
"--tumourBam",
type="string",
dest="tumorBamList",
metavar="FILE",
action="append",
help=
"Tumor sample BAM or CRAM file. Only up to one tumor bam file accepted. [optional] (no default)"
)
group.add_option(
"--exome",
dest="isExome",
action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option(
"--rna",
dest="isRNA",
action="store_true",
help=
"Set options for RNA-Seq input. Must specify exactly one bam input file"
)
group.add_option(
"--unstrandedRNA",
dest="isUnstrandedRNA",
action="store_true",
help=
"Set if RNA-Seq input is unstranded: Allows splice-junctions on either strand"
)
group.add_option("--outputContig",
dest="isOutputContig",
action="store_true",
help="Output assembled contig sequences in VCF file")
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self, group)
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 addWorkflowGroupOptions(self, group):
group.add_option(
"--normalBam",
type="string",
dest="normalBamList",
metavar="FILE",
action="append",
help=
"Normal sample BAM file. May be specified more than once, multiple inputs will be merged. [at least one required] (no default)"
)
group.add_option(
"--tumorBam",
"--tumourBam",
type="string",
dest="tumorBamList",
metavar="FILE",
action="append",
help=
"Tumor sample BAM file. May be specified more than once, multiple inputs will be merged. [optional] (no default)"
)
# group.add_option("--aligner", type="string",dest="alignerMode",metavar="ALIGNER",
# help="Aligner type. Accepted option are {%s} [required] (no default)" % (",".join(['%s' % (x) for x in self.validAlignerModes])))
group.add_option(
"--exome",
dest="isExome",
action="store_true",
help="Set options for WES input: turn off depth filters")
group.add_option(
"--rna",
dest="isRNA",
action="store_true",
help=
"Set options for RNA-Seq input: turn off depth filters and don't treat "
"anomalous reads as SV evidence when the proper-pair bit is set.")
group.add_option(
"--referenceFasta",
type="string",
dest="referenceFasta",
metavar="FILE",
help=
"samtools-indexed reference fasta file [required] (default: %default)"
)
MantaWorkflowOptionsBase.addWorkflowGroupOptions(self, group)
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 getOptionDefaults(self) :
self.configScriptDir=scriptDir
defaults=MantaWorkflowOptionsBase.getOptionDefaults(self)
defaults.update({
'alignerMode' : "isaac",
'runDir' : 'MantaWorkflow',
'isExome' : False,
'binSize' : 25000000,
'nonlocalWorkBins' : 128
})
return defaults
def addExtendedGroupOptions(self,group) :
group.add_option("--useExistingAlignStats",
dest="useExistingAlignStats", action="store_true",
help="Use pre-calculated alignment statistics.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths", action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option("--scanSizeMb",type="int",dest="scanSizeMb",metavar="scanSizeMb",
help="Maximum sequence region size (in Mb) scanned by each task during "
"SV locus graph generation. (default: %default)")
group.add_option("--candidateBins",type="int",dest="nonlocalWorkBins",metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
group.add_option("--region",type="string",dest="regionStrList",metavar="samtoolsRegion", action="append",
help="Limit the SV analysis to a region of the genome for debugging purposes. "
"If this argument is provided multiple times all specified regions will "
"be analyzed together. All regions must be non-overlapping to get a "
"meaningful result. Examples: '--region chr20' (whole chromosome), "
"'--region chr2:100-2000 --region chr3:2500-3000' (two translocation regions)'")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self,group)
def addExtendedGroupOptions(self,group) :
group.add_option("--existingAlignStatsFile",
dest="existingAlignStatsFile", metavar="FILE",
help="Pre-calculated alignment statistics file. Skips alignment stats calculation.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths", action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option("--candidateBins",type="int",
dest="nonlocalWorkBins", metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
group.add_option("--retainTempFiles",
dest="isRetainTempFiles", action="store_true",
help="Keep all temporary files (for workflow debugging)")
group.add_option("--generateEvidenceBam",
dest="isGenerateSupportBam", action="store_true",
help="Generate a bam of supporting reads for all SVs")
group.add_option("--outputContig", dest="isOutputContig", action="store_true",
help="Output assembled contig sequences in VCF file")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self,group)
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):
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 addExtendedGroupOptions(self, group):
group.add_option("--useExistingAlignStats",
dest="useExistingAlignStats",
action="store_true",
help="Use pre-calculated alignment statistics.")
group.add_option("--useExistingChromDepths",
dest="useExistingChromDepths",
action="store_true",
help="Use pre-calculated chromosome depths.")
group.add_option(
"--scanSizeMb",
type="int",
dest="scanSizeMb",
metavar="scanSizeMb",
help=
"Maximum sequence region size (in Mb) scanned by each task during "
"SV locus graph generation. (default: %default)")
group.add_option(
"--candidateBins",
type="int",
dest="nonlocalWorkBins",
metavar="candidateBins",
help="Provide the total number of tasks which candidate generation "
" will be sub-divided into. (default: %default)")
group.add_option(
"--region",
type="string",
dest="regionStrList",
metavar="samtoolsRegion",
action="append",
help=
"Limit the SV analysis to a region of the genome for debugging purposes. "
"If this argument is provided multiple times all specified regions will "
"be analyzed together. All regions must be non-overlapping to get a "
"meaningful result. Examples: '--region chr20' (whole chromosome), "
"'--region chr2:100-2000 --region chr3:2500-3000' (two translocation regions)'"
)
MantaWorkflowOptionsBase.addExtendedGroupOptions(self, group)
def getOptionDefaults(self) :
self.configScriptDir=scriptDir
defaults=MantaWorkflowOptionsBase.getOptionDefaults(self)
defaults.update({
'runDir' : 'MantaWorkflow',
'isExome' : False,
'isRNA' : False,
'isUnstrandedRNA' : False,
'useExistingAlignStats' : False,
'useExistingChromDepths' : False,
'nonlocalWorkBins' : 256
})
return defaults
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 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 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 getOptionDefaults(self) :
self.configScriptDir=scriptDir
defaults=MantaWorkflowOptionsBase.getOptionDefaults(self)
defaults.update({
'alignerMode' : "isaac",
'runDir' : 'MantaWorkflow',
'isExome' : False,
'isRNA' : False,
'useExistingAlignStats' : False,
'useExistingChromDepths' : False,
'scanSizeMb' : 12,
'nonlocalWorkBins' : 256
})
return defaults
def getOptionDefaults(self):
self.configScriptDir = scriptDir
defaults = MantaWorkflowOptionsBase.getOptionDefaults(self)
defaults.update({
'alignerMode': "isaac",
'runDir': 'MantaWorkflow',
'isExome': False,
'isRNA': False,
'useExistingAlignStats': False,
'useExistingChromDepths': False,
'scanSizeMb': 12,
'nonlocalWorkBins': 256
})
return defaults
def getOptionDefaults(self):
self.configScriptDir = scriptDir
defaults = MantaWorkflowOptionsBase.getOptionDefaults(self)
defaults.update({
'runDir': 'MantaWorkflow',
'isExome': False,
'isRNA': False,
'isOutputContig': False,
'isUnstrandedRNA': False,
'useExistingChromDepths': False,
'isRetainTempFiles': False,
'isGenerateSupportBam': False,
'nonlocalWorkBins': 256
})
return defaults
def getOptionDefaults(self) :
self.configScriptDir=scriptDir
defaults=MantaWorkflowOptionsBase.getOptionDefaults(self)
defaults.update({
'runDir' : 'MantaWorkflow',
'isExome' : False,
'isRNA' : False,
'isOutputContig' : False,
'isUnstrandedRNA' : False,
'existingAlignStatsFile' : None,
'useExistingChromDepths' : False,
'isRetainTempFiles' : False,
'isGenerateSupportBam' : False,
'nonlocalWorkBins' : 256
})
return defaults
def validateAndSanitizeExistingOptions(self,options) :
groomBamList(options.normalBamList,"normal sample")
groomBamList(options.tumorBamList, "tumor sample")
MantaWorkflowOptionsBase.validateAndSanitizeExistingOptions(self,options)
def addExtendedGroupOptions(self,group) :
group.add_option("--referenceFasta",type="string",dest="referenceFasta",metavar="FILE",
help="samtools-indexed reference fasta file [required] (default: %default)")
MantaWorkflowOptionsBase.addExtendedGroupOptions(self,group)