ORFik 1.0.0
-----------------------

    o first release of ORFik - find Open Reading Frames, automatic RiboSeq
    footprint shifts, reassignment of Transcription Start Sites with the use of
    CageSeq, plethora of gene identity functions from scientific publications


CHANGES IN VERSION 1.1.12
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Remade many function to handle no names correctly, like tile1 will now
    work even for GRangesList without names. Documentation is more logical, and
    removed coverageByWindow, since GenomicFeatures::coverageByTranscripts now
    works correctly.

CHANGES IN VERSION 1.1.12
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The orf finding function now find the longest orf per stop codon if
      you set longestORF = TRUE in findORFS, findMapORFs and findORFsFasta

CHANGES IN VERSION 1.3.7
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o mapToGRanges is now much faster and uses much less memory. A c++
      reimplementation of pmapFromTranscripts from GenomicFeatures.

CHANGES IN VERSION 1.7.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The ORFik experiment syntax is ready, to simplifiy ORFik usage
    with big data.


CHANGES IN VERSION 1.7.17
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Added pmapToTranscriptsF, a much faster pmapToTranscripts.
    o All of ORFik now supports weights for representing duplicated reads.
    This will speed up all function related to NGS data a lot.

CHANGES IN VERSION 1.13.7
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Massive improvement in speed of coveragePerTiling
    o Improved p-shifting analysis (also added verbose output)
    o Added possible optimization for annotation
    o Rewritten vignettes
