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)