Changes in version 1.1.2 (2016-10-21):

Minor changes

    o   README indicates status on BioC-release, BioC-devel, and Travis CI.

Changes in version 1.1.1 (2016-10-21):

Minor changes

    o   Updates to README: weblinks, installation, unit tests.

    o   Branches tracked by Travis CI.

    o   Coverage: exclude AllClasses.R, tSVE.R.

    o   Four-space indents in DESCRIPTION.

Changes in version 1.0.2 (2016-10-23):

Minor changes

    o   Bug fix. Release only requires R version 3.3.1.

Changes in version 1.0.1 (2016-10-23):

Minor changes

    o   Merged devel branch version 1.1.2.

    o   Travis CI uses release version of _R_ and _Bioconductor_.

Changes in version 0.99.9 (2016-10-14):

Minor changes

    o   Fixed outdated information in _Introduction_ vignette.

Changes in version 0.99.8 (2016-10-12):

Minor changes

    o   Set vignette output format to BiocStyle::html_document2.

Changes in version 0.99.7 (2016-10-12):

Minor changes

    o   Fixed a closign bracket in NEWS file.

Changes in version 0.99.6 (2016-10-12):

Experimental changes

    o   Replaced BiocStyle::pdf_document2() by BiocStyle::pdf_document();
	 the former fails at the pandoc step of vignette production, the
	 latter does not.

Changes in version 0.99.5 (2016-10-12):

Bug fix

    o   Fixed Collate: field of the DESCRIPTION file.

Changes in version 0.99.4 (2016-10-12):

Experimental changes

    o   Reverted changes applied in version 0.99.3. BiocParallel does not
	 seem to be causing the build error on Windows Server.

Changes in version 0.99.3 (2016-10-12):

Experimental changes

    o   Disabled BiocParallel code to see if it resolves build errors on the
	 _Bioconductor_ Windows Server. Note that the documentation was not
	 yet updated to reflect this experimental change; this is intended
	 to facilitate code reversion-or alternatively document the
	 change-in the next commit.

Changes in version 0.99.2 (2016-10-11):

Bug fixes

    o   Use suffix accessor in add*Frequencies methods.

Changes in version 0.99.1 (2016-10-10):

Major changes

    o   New dedicated Genotypes class to store homozygote reference,
	 heterozygote, and homozygote alternate genotype codes, along with
	 the suffixes that define the INFO keys used to store their
	 respective data in the VCF object.

    o   Removed families of methods tabulate* and density* from the
	 NAMESPACE. The features may be revisited in the future.  The
	 associated code and documentation was saved in the inst/sandbox
	 subfolder for future reference.

    o   New slot svp in TVTBparam class to store ScanVcfParam objects. New
	 associated accessor methods.  Moreover, TVTBparam may be coerced to
	 ScanVcfParam.

    o   New signatures for method readVcf that supports param=TVTBparam, and
	 optional phenotypes.  The method stores TVTBparam in the metadata
	 slot of the VCF object, and phenotypes using the colData accessor.

    o   TVTBparam are no longer an argument of downstream methods; instead,
	 they must be stored in metadata(vcf)[["TVTBparam"]]

Minor changes

    o   hRef and hAlt accessors renamed to refand alt, respectively.

    o   suffix accessor to returned named character vector for classes
	 Genotypes and TVTBparam.

    o   Removed functions relevant only to the _Shiny_ application from the
	 NAMESPACE (getEdb, EnsDbFilter, chr2file).

    o   VcfFilterRules can also store instances of the parent FilterRules
	 class.

    o   Defined default return value for accessors vep and type, to avoid
	 unnecessary switch statements.

    o   Simplified code of inherited methods following updates to the
	 relevant packages (_e.g._ S4Vectors).

    o   Better respect of coding standards: removed superfluous usage of
	 explicit argument naming, removed superfluous initialize methods.

    o   Man pages, vignettes, unit tests and _Shiny_ application updated to
	 reflect changes to the package.

Changes in version 0.99.0 (2015-09-15):

New features

    o   First release submitted to the Bioconductor review process See
	 DESCRIPTION file for details.