Module AnalyseMapping
  Classes
    CustomRead
    ReadID
    TPRead
  Functions
    CheckForSameAlignments
    CompareAlignments
    ComputeRQScore
    CreateCompareList
    GetCompletePath
    GetOrderDictionary
    ReadArtificialSAMfileHTSeq
    ReadFromTab
    ReadSAMnoMem
    SkipHeader
    extendReadDic
    getAlignmentLength
    getAllID
    getCustomRead
    getHammingdistance
    getMisGap
    getNextLine
    getNumberOf
    getRanks
    getTPRead
    getmean
    getsum
    initOutFiles
    isSaneAlignment
    loadpickle
    readInput
    readReadQualities
    readSAMline
    returnIndex
    returnSequence
    savepickle
    writeToTabArt
    writeToTabRef
  Variables
    AlignedReadsdic
    __package__
    algnedToArt
    algnedToRef
    alngts
[hide private]