def __init__(self,params) :
cleanPyEnv()
self.params=params
# normalize boolean option input:
safeSetBool(self.params,"enableRemoteReadRetrievalForInsertionsInGermlineCallingModes")
safeSetBool(self.params,"enableRemoteReadRetrievalForInsertionsInCancerCallingModes")
safeSetBool(self.params,"useOverlapPairEvidence")
# Use RNA option for minCandidate size
if self.params.isRNA:
self.params.minCandidateVariantSize = self.params.rnaMinCandidateVariantSize
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
self.params.evidenceDir=os.path.join(self.params.resultsDir,"evidence")
ensureDir(self.params.evidenceDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# determine subset of chroms where we can skip calling entirely
(self.params.callRegionList, self.params.chromIsSkipped) = getCallRegions(self.params)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
# always use overlapping pairs for RNA calling
if (self.params.isRNA) :
self.params.useOverlapPairEvidence = True
def __init__(self, params, iniSections):
cleanPyEnv()
self.params = params
self.iniSections = iniSections
# Use RNA option for minCandidate size
if self.params.isRNA:
self.params.minCandidateVariantSize = self.params.rnaMinCandidateVariantSize
# format bam lists:
if self.params.normalBamList is None: self.params.normalBamList = []
if self.params.tumorBamList is None: self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir = os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir = os.path.join(self.params.runDir, "workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir = os.path.join(self.params.runDir, "results")
ensureDir(self.params.resultsDir)
self.params.statsDir = os.path.join(self.params.resultsDir, "stats")
ensureDir(self.params.statsDir)
self.params.variantsDir = os.path.join(self.params.resultsDir,
"variants")
ensureDir(self.params.variantsDir)
self.params.evidenceDir = os.path.join(self.params.resultsDir,
"evidence")
ensureDir(self.params.evidenceDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta = self.params.referenceFasta + ".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta, "reference fasta")
checkFile(indexRefFasta, "reference fasta index")
# read fasta index
(self.params.chromOrder,
self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
# determine subset of chroms where we can skip calling entirely
(self.params.callRegionList,
self.params.chromIsSkipped) = getCallRegions(self.params)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome
or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
def __init__(self,params,iniSections) :
cleanPyEnv()
self.params=params
self.iniSections=iniSections
# format bam lists:
if self.params.normalBamList is None : self.params.normalBamList = []
if self.params.tumorBamList is None : self.params.tumorBamList = []
# make sure run directory is setup:
self.params.runDir=os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir=os.path.join(self.params.runDir,"workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transfered to resultsDir
self.params.resultsDir=os.path.join(self.params.runDir,"results")
ensureDir(self.params.resultsDir)
self.params.statsDir=os.path.join(self.params.resultsDir,"stats")
ensureDir(self.params.statsDir)
self.params.variantsDir=os.path.join(self.params.resultsDir,"variants")
ensureDir(self.params.variantsDir)
# self.params.reportsDir=os.path.join(self.params.resultsDir,"reports")
# ensureDir(self.params.reportsDir)
indexRefFasta=self.params.referenceFasta+".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta,"reference fasta")
checkFile(indexRefFasta,"reference fasta index")
# read fasta index
(self.params.chromOrder,self.params.chromSizes) = getFastaChromOrderSize(indexRefFasta)
self.paths = PathInfo(self.params)
self.params.isHighDepthFilter = (not (self.params.isExome or self.params.isRNA))
self.params.isIgnoreAnomProperPair = (self.params.isRNA)
def __init__(self, params, PathInfoType):
cleanPyEnv()
self.params = params
# make sure run directory is setup:
self.params.runDir = os.path.abspath(self.params.runDir)
ensureDir(self.params.runDir)
# everything that's not intended to be a final result should dump directories/files in workDir
self.params.workDir = os.path.join(self.params.runDir, "workspace")
ensureDir(self.params.workDir)
# all finalized pretty results get transferred to resultsDir
self.params.resultsDir = os.path.join(self.params.runDir, "results")
ensureDir(self.params.resultsDir)
self.params.variantsDir = os.path.join(self.params.resultsDir,
"variants")
ensureDir(self.params.variantsDir)
# timings and other stats go into statsDir
self.params.statsDir = os.path.join(self.params.resultsDir, "stats")
ensureDir(self.params.statsDir)
self.paths = PathInfoType(self.params)
referenceFastaIndex = self.params.referenceFasta + ".fai"
if self.params.referenceFasta is None:
raise Exception("No reference fasta defined.")
else:
checkFile(self.params.referenceFasta, "reference fasta")
checkFile(referenceFastaIndex, "reference fasta index")
# read fasta index
(self.params.chromOrder,
self.params.chromSizes) = getFastaChromOrderSize(referenceFastaIndex)
# determine subset of chroms where we can skip calling entirely
self.params.chromIsSkipped = getChromIsSkipped(self)
self.params.isHighDepthFilter = (not (self.params.isExome
or self.params.isRNA))