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