- r -

• readline() : InteractiveConsole
• readLine() : MatrixFileAnalyzer
• refShiftUpdateFd() : D2Zim
• remove_arg() : arg_parser
• repopulate() : EST
• report() : ResultLog
• reportLine() : ResultLog
• ResultLog() : ResultLog
• rightShiftUpdateFd() : D2Zim
• runD2() : D2
• runD2Asymmetric() : TwoPassD2
• runD2Bounded() : TwoPassD2
• runFilter() : Filter , LengthFilter , LCFilter
• runHeuristic() : TVHeuristic , NewUVHeuristic , Heuristic , UVSampleHeuristic