implement opt.rcAssignment which integrates the parameters related to assigning read classes to transcripts

[SuiYue-2308]

This issue is to separate the parameters (related to assign read class to transcript) from opt.discovery, and reorganize them into opt.rcAssignment (min.exonDistance, min.primarySecondaryDist, min.primarySecondaryDistStartEnd1, primarySecondaryDistStartEnd2)