Everything
  All Classes
    core.AnalyseMapping.CustomRead
    core.AnalyseMapping.ReadID
    core.AnalyseMapping.TPRead
  All Functions
    core.AnalyseMapping.CheckForSameAlignments
    core.AnalyseMapping.CompareAlignments
    core.AnalyseMapping.ComputeRQScore
    core.AnalyseMapping.CreateCompareList
    core.AnalyseMapping.GetCompletePath
    core.AnalyseMapping.GetOrderDictionary
    core.AnalyseMapping.ReadArtificialSAMfileHTSeq
    core.AnalyseMapping.ReadFromTab
    core.AnalyseMapping.ReadSAMnoMem
    core.AnalyseMapping.SkipHeader
    core.AnalyseMapping.extendReadDic
    core.AnalyseMapping.getAlignmentLength
    core.AnalyseMapping.getAllID
    core.AnalyseMapping.getCustomRead
    core.AnalyseMapping.getHammingdistance
    core.AnalyseMapping.getMisGap
    core.AnalyseMapping.getNextLine
    core.AnalyseMapping.getNumberOf
    core.AnalyseMapping.getRanks
    core.AnalyseMapping.getTPRead
    core.AnalyseMapping.getmean
    core.AnalyseMapping.getsum
    core.AnalyseMapping.initOutFiles
    core.AnalyseMapping.isSaneAlignment
    core.AnalyseMapping.loadpickle
    core.AnalyseMapping.readInput
    core.AnalyseMapping.readReadQualities
    core.AnalyseMapping.readSAMline
    core.AnalyseMapping.returnIndex
    core.AnalyseMapping.returnSequence
    core.AnalyseMapping.savepickle
    core.AnalyseMapping.writeToTabArt
    core.AnalyseMapping.writeToTabRef
    core.FindOrfs.build_ORF
    core.FindOrfs.find_orfs
    core.FindOrfs.findstop_help
    core.InsertMutations.getMutation
    core.InsertMutations.getdifference
    core.InsertMutations.isvalidposition
    core.InsertMutations.mutate_random
    core.PlotData.CalculateRoc2
    core.PlotData.plotOverviewHist
    core.PlotData.trapezoidal_rule
    core.Prep.createdic
    core.Prep.isvalidtriplet
    core.Prep.loadpickle
    core.Prep.savepickle
    core.Prep.trans_seq
    core.ReadAndWrite.aa_dist_seq
    core.ReadAndWrite.gethammingdistance
    core.ReadAndWrite.nucleotide_dist_file
    core.ReadAndWrite.nucleotide_dist_seq
    core.ReadAndWrite.readdna
    core.ReadAndWrite.writefile
    core.ReadAndWrite.writeoverview
    script-arden_analyze.TestFiles
    script-arden_analyze.main
    script-arden_create.Create
    script-arden_create.printExample
    script-arden_filter.FilterSAM
    script-arden_filter.filter
    script-arden_filter.getMisGapRQ
    script-arden_filter.readHeader
    script-arden_filter.writeFilteredReads
  All Variables
    core.AnalyseMapping.AlignedReadsdic
    core.AnalyseMapping.__package__
    core.AnalyseMapping.algnedToArt
    core.AnalyseMapping.algnedToRef
    core.AnalyseMapping.alngts
    core.FindOrfs.__package__
    core.InsertMutations.__package__
    core.PlotData.__package__
    core.Prep.__package__
    core.Prep.genetic_code
    core.ReadAndWrite.__package__
    core.__package__
    script-arden_analyze.__package__
    script-arden_create.a
    script-arden_create.b
    script-arden_create.bases
    script-arden_filter.__package__
    script-arden_filter.counter1
    script-arden_filter.counter2
[hide private]