TODO
-----------------------

    o remove naming of ORFs with "_"
    o remove unnecesary type checking
    o split files into smaller files, tests too
    o remove whole utils file?
    o create upstreamFrom function
    o understand why coverageByWindow is so slow

    CageSeq:
    o remove cageFromFile etc. so that we don't load the data for the user
    o remove filterCage so that we don't filter, user filters himself

    RiboSeq:
    o parseCigar implement into C++ (this is not the slow part thought)

    Features:
    o better docs with inherit params
