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