TODO
-----------------------
    General:
    o Add more verbose outputs
    o Add import/export for bigwig
    o Make seqinfo be kept through the chain
    o Make startCodon and stopCodon inherit all exon_ranks

    CAGE:
    o Add more statistics for user if wanted

    RiboSeq:
    o Fix x-axis scales for large samples in RiboQC.plot

    OFST file format:
    o Implement ofst indexing of files

    ORFik experiment:
    o Fix very slow bamVarNames function

    Alignment:
    o Add genomeSAindexNbases 14 check to reduce to 10 if small
    o wrap fastp UMI and barcode demultiplexing
    o Try to include download of tRNA-scan tRNA fasta files

    SRA Download:
    Test if it is possible to speed up EBI download even more

    SRA metadata:
    o Include better Auther and Pubmed detection

    P-shifting
    o Do more tests for RCP-seq 80 libraries (these have different read lengths)
    o Add filter for minimum reads in TIS region.
    o Add count tables for pshifted counts
    o Add used shift to shiftPlots

    QC
    o Add possibility for batch correction of correlation plots
    o Add counts per group in DTEG analysis plots

    Coverage
    o Check if coverage might need a new "append.single"", to make sure each fraction gets a choice.
    o make sure remove.zero.dt, does not make any functions fail!
    o Add new add.flank.zero, to make max and min correct.
    o Updated heatmapRegion to use remove.zero.dt as TRUE
