Changes in version 1.25.1                        

    o   Bug fix in minorAlleleCount when all samples have the same sex.

                       Changes in version 1.23.1                        

    o   Add minorAlleleCount method.

                       Changes in version 1.21.5                        

    o   getGenotype and getGenotypeAlleles work for haploid genotypes.

                       Changes in version 1.21.4                        

    o   Add vignette describing iterators.

                       Changes in version 1.21.1                        

    o   Add method to return imputed dosage.

                       Changes in version 1.19.4                        

    o   Reduce memory usage when creating a SeqVarData object.

                       Changes in version 1.19.3                        

    o   Rewrite the duplicateDiscordance method for a single GDS file
	to be much faster and return output consistent with the
	cross-file method.

                       Changes in version 1.19.2                        

    o   Add methods currentVariants and currentRanges for
	SeqVarIterator classes.

                       Changes in version 1.17.8                        

    o   Add method alleleCount to return count of alleles.

                       Changes in version 1.17.7                        

    o   Bug fix in alleleFrequency method for SeqVarData where
	frequency calculation was done twice because the first
	calculation was not returned.

                       Changes in version 1.17.6                        

    o   Add option to return alternate allele dosage in a sparse matrix
	using the Matrix package.

    o   Improve speed of reading dosages by using seqBlockApply.

                       Changes in version 1.17.2                        

    o   Change implementation of iterator classes to identify indices
	of selected variants on object creation and store in
	variantList slot. All iterator classes now extend new class
	SeqVarIterator.

                       Changes in version 1.15.3                        

    o   alleleFrequency method accounts for sex when computing
	frequency for X and Y chromosomes.

                       Changes in version 1.15.2                        

    o   Added iterator classes: SeqVarBlockIterator,
	SeqVarRangeIterator, SeqVarWindowIterator, SeqVarListIterator.

    o   Creating a SeqVarData object with missing sample or variant
	annotation will store 0-column data frames in sampleData or
	variantData, instead of duplicating sample.id and variant.id.

    o   Added methods to return variant data in expanded form, with one
	row per alternate allele.

                       Changes in version 1.15.1                        

    o   Following SeqArray, remove dependency on VariantAnnotation

    o   Add generic isSNV (replacing previous import of this generic
	from VariantAnnotation)

                       Changes in version 1.11.3                        

    o   Add hethom method to calculate heterozygosity / non-reference
	homozygosity in one step

    o   Add countSingletons method

                       Changes in version 1.11.1                        

    o   Add variantData slot to SeqVarData class

                       Changes in version 1.9.11                        

    o   Add Firth test option to regression

    o   Bug fix for refFracPlot: hets significantly different from 0.5
	plotted as triangles, median line shown

                       Changes in version 1.9.10                        

    o   duplicateDiscordance across two GDS files can calculate
	discordance based on heterozygote/homozygote status instead of
	genotype

                        Changes in version 1.9.9                        

    o   duplicateDiscordance across two GDS files can match on either
	position or position and alleles, with the ability to recode
	genotypes if th reference allele in one dataset is the
	alternate allele in the other dataset

                        Changes in version 1.9.8                        

    o   duplicateDiscordance and alternateAlleleDetection require
	SeqVarData objects; both can match on a subject.id instead of
	sample.id

                        Changes in version 1.9.4                        

    o   alleleDosage returns list with dosage of each allele separately

                        Changes in version 1.9.2                        

    o   added by.variant option to duplicateDiscordance for two gds
	files

                        Changes in version 1.7.9                        

    o   added more options to return dosage of different alleles

                        Changes in version 1.7.7                        

    o   added methods to calculate and plot reference allele fraction

                        Changes in version 1.7.6                        

    o   HWE method returns additional columns and allows permutation of
	genotypes

                        Changes in version 1.7.5                        

    o   Added SeqVarData class to combine sample annotation with GDS
	object

                        Changes in version 1.7.4                        

    o   HWE works on biallelic INDELs as well as SNVs

                        Changes in version 1.7.3                        

    o   Add methods for duplicateDiscordance with two datasets

    o   Add alternateAlleleDetection

                        Changes in version 1.5.1                        

    o   Use existing isSNV generic from VariantAnnotation instead of
	redefining

    o   Use BiocStyle for vignette