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