CHANGES IN VERSION 1.4.0
------------------------

USER VISIBLE CHANGES

    o The function 'scores()' has been deprecated and replaced by the function 'gscores()'.

    o The argument 'scores.only' in the function 'scores()' has been deprecated and replaced by calling the function 'score()'.

    o The 'MafDb' class has been deprecated and now the 'GScores' class supports former 'MafDb' objects. The 'mafByOverlaps()' and 'mafById()' functions have been deprecated and replaced by the function 'gscores()'. The 'populations()' function from the 'MafDb' API has been integrated into the 'GScores' API.

    o Added metadata on genomic scores groups, available through the function 'gscoresGroups()', on availability of non-single nucleotide regions through the function 'gscoresNonSNRs()', and on the default population used through the function 'defaultPopulation()'.

    o New AnnotationHub resources have been added during this release cycle: phyloP60way.UCSC.mm10, LINSIGHT, phastCons46wayPlacental, phastcons46wayPrimates.

    o Added a BiocSticker at https://github.com/Bioconductor/BiocStickers/tree/master/GenomicScores

    o Added citation information after package publication has been accepted at Bioinformatics.


CHANGES IN VERSION 1.2.0
------------------------

USER VISIBLE CHANGES

    o Added methods 'name()' and 'type()' for GScores objects.

    o Enabled the retrieval of multiple score values per genomic position (e.g., as in CADD or M-CAP scores).

    o Added method 'citation()' to fetch citation information for genomic scores.

    o Added function 'makeGScoresPackage()' to create an annotation package from an AnnotationHub genomic scores resource.

    o Added 'qfun()' and 'dqfun()' methods to fetch the quantization and dequantization functions from used to store and retrieved genomic scores.

    o Added 'quantized' argument to the 'scores()' method to obtain quantized values if the user wants to dequantize the values him or herself.

    o Fallback to local AnnotationHub when there is no internet connection to fetch genomic scores through AnnotationHub resources.

    o Added 'MafDb' class, derived from 'GScores' to store and access minor allele frequency values. This was originally defined in the 'VariantFiltering' package.

    o The vignette has been updated to illustrate the use of some of the previous changes.

CHANGES IN VERSION 0.99.0
-------------------------

USER VISIBLE CHANGES

    o Submission of the first version to the Bioconductor project.

(start date: March 17, 2017)
