parameters: (self)
return_statement: return cleanLocals(locals())
docstring: Set option defaults.
  
          Every local variable in this method becomes part of the default hash
docstring_summary: Set option defaults.
docstring_tokens: Set option defaults .
function: def getOptionDefaults(self) :
          """
          Set option defaults.
  
          Every local variable in this method becomes part of the default hash
          """
  
          configCommandLine=sys.argv
  
          libexecDir=os.path.abspath(os.path.join(scriptDir,"@THIS_RELATIVE_LIBEXECDIR@"))
          assert os.path.isdir(libexecDir)
  
          bgzipBin=joinFile(libexecDir,exeFile("bgzip"))
          htsfileBin=joinFile(libexecDir,exeFile("htsfile"))
          tabixBin=joinFile(libexecDir,exeFile("tabix"))
          samtoolsBin=joinFile(libexecDir,exeFile("samtools"))
  
          mantaStatsBin=joinFile(libexecDir,exeFile("GetAlignmentStats"))
          mantaMergeStatsBin=joinFile(libexecDir,exeFile("MergeAlignmentStats"))
          getChromDepthBin=joinFile(libexecDir,exeFile("GetChromDepth"))
          mantaGraphBin=joinFile(libexecDir,exeFile("EstimateSVLoci"))
          mantaGraphMergeBin=joinFile(libexecDir,exeFile("MergeSVLoci"))
          mantaGraphCheckBin=joinFile(libexecDir,exeFile("CheckSVLoci"))
          mantaHyGenBin=joinFile(libexecDir,exeFile("GenerateSVCandidates"))
          mantaGraphStatsBin=joinFile(libexecDir,exeFile("SummarizeSVLoci"))
          mantaStatsSummaryBin=joinFile(libexecDir,exeFile("SummarizeAlignmentStats"))
  
          mergeChromDepth=joinFile(libexecDir,"mergeChromDepth.py")
          mantaSortVcf=joinFile(libexecDir,"sortVcf.py")
          mantaExtraSmallVcf=joinFile(libexecDir,"extractSmallIndelCandidates.py")
          mantaPloidyFilter=joinFile(libexecDir,"ploidyFilter.py")
          mantaSortEdgeLogs=joinFile(libexecDir,"sortEdgeLogs.py")
          catScript=joinFile(libexecDir,"cat.py")
          vcfCmdlineSwapper=joinFile(libexecDir,"vcfCmdlineSwapper.py")
          mantaSortBam=joinFile(libexecDir,"sortBam.py")
          mantaMergeBam=joinFile(libexecDir,"mergeBam.py")
  
          workflowScriptName = "runWorkflow.py"
  
          # default memory request per process-type
          #
          # where different values are provided for SGE and local runs note:
          #  1. for SGE the memory limits must be greater than the highest memory use ever
          #      expected in a production run. The consequence of exceeding this limit is a failed
          #      run.
          #   2. for localhost the memory usage should be at least above the highest mean memory
          #       use ever expected in a production run. The consequence of exceeding the mean is
          #       a slow run due to swapping.
          #
          estimateMemMb=1.5*1024
          mergeMemMb=4*1024
          hyGenSGEMemMb=4*1024
          hyGenLocalMemMb=1.5*1024
  
          # extended options
          scanSizeMb = 12
          callRegionsBed = None
          regionStrList = None
          callMemMbOverride = None
  
          return cleanLocals(locals())
function_tokens: def getOptionDefaults ( self ) : configCommandLine = sys . argv libexecDir = os . path . abspath ( os . path . join ( scriptDir , "@THIS_RELATIVE_LIBEXECDIR@" ) ) assert os . path . isdir ( libexecDir ) bgzipBin = joinFile ( libexecDir , exeFile ( "bgzip" ) ) htsfileBin = joinFile ( libexecDir , exeFile ( "htsfile" ) ) tabixBin = joinFile ( libexecDir , exeFile ( "tabix" ) ) samtoolsBin = joinFile ( libexecDir , exeFile ( "samtools" ) ) mantaStatsBin = joinFile ( libexecDir , exeFile ( "GetAlignmentStats" ) ) mantaMergeStatsBin = joinFile ( libexecDir , exeFile ( "MergeAlignmentStats" ) ) getChromDepthBin = joinFile ( libexecDir , exeFile ( "GetChromDepth" ) ) mantaGraphBin = joinFile ( libexecDir , exeFile ( "EstimateSVLoci" ) ) mantaGraphMergeBin = joinFile ( libexecDir , exeFile ( "MergeSVLoci" ) ) mantaGraphCheckBin = joinFile ( libexecDir , exeFile ( "CheckSVLoci" ) ) mantaHyGenBin = joinFile ( libexecDir , exeFile ( "GenerateSVCandidates" ) ) mantaGraphStatsBin = joinFile ( libexecDir , exeFile ( "SummarizeSVLoci" ) ) mantaStatsSummaryBin = joinFile ( libexecDir , exeFile ( "SummarizeAlignmentStats" ) ) mergeChromDepth = joinFile ( libexecDir , "mergeChromDepth.py" ) mantaSortVcf = joinFile ( libexecDir , "sortVcf.py" ) mantaExtraSmallVcf = joinFile ( libexecDir , "extractSmallIndelCandidates.py" ) mantaPloidyFilter = joinFile ( libexecDir , "ploidyFilter.py" ) mantaSortEdgeLogs = joinFile ( libexecDir , "sortEdgeLogs.py" ) catScript = joinFile ( libexecDir , "cat.py" ) vcfCmdlineSwapper = joinFile ( libexecDir , "vcfCmdlineSwapper.py" ) mantaSortBam = joinFile ( libexecDir , "sortBam.py" ) mantaMergeBam = joinFile ( libexecDir , "mergeBam.py" ) workflowScriptName = "runWorkflow.py" # default memory request per process-type # # where different values are provided for SGE and local runs note: #  1. for SGE the memory limits must be greater than the highest memory use ever #      expected in a production run. The consequence of exceeding this limit is a failed #      run. #   2. for localhost the memory usage should be at least above the highest mean memory #       use ever expected in a production run. The consequence of exceeding the mean is #       a slow run due to swapping. # estimateMemMb = 1.5 * 1024 mergeMemMb = 4 * 1024 hyGenSGEMemMb = 4 * 1024 hyGenLocalMemMb = 1.5 * 1024 # extended options scanSizeMb = 12 callRegionsBed = None regionStrList = None callMemMbOverride = None return cleanLocals ( locals ( ) )