NEWS

---

SeqVarTools 1.27.1

• Add 'parallel' argument to methods.

SeqVarTools 1.25.1

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

SeqVarTools 1.23.1

• Add minorAlleleCount method.

SeqVarTools 1.21.5

• getGenotype and getGenotypeAlleles work for haploid genotypes.

SeqVarTools 1.21.4

• Add vignette describing iterators.

SeqVarTools 1.21.1

• Add method to return imputed dosage.

SeqVarTools 1.19.4

• Reduce memory usage when creating a SeqVarData object.

SeqVarTools 1.19.3

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

SeqVarTools 1.19.2

• Add methods currentVariants and currentRanges for SeqVarIterator classes.

SeqVarTools 1.17.8

• Add method alleleCount to return count of alleles.

SeqVarTools 1.17.7

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

SeqVarTools 1.17.6

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

• Improve speed of reading dosages by using seqBlockApply.

SeqVarTools 1.17.2

• 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.

SeqVarTools 1.15.3

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

SeqVarTools 1.15.2

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

• 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.

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

SeqVarTools 1.15.1

• Following SeqArray, remove dependency on VariantAnnotation

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

SeqVarTools 1.11.3

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

• Add countSingletons method

SeqVarTools 1.11.1

• Add variantData slot to SeqVarData class

SeqVarTools 1.9.11

• Add Firth test option to regression

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

SeqVarTools 1.9.10

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

SeqVarTools 1.9.9

• 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

SeqVarTools 1.9.8

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

SeqVarTools 1.9.4

• alleleDosage returns list with dosage of each allele separately

SeqVarTools 1.9.2

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

SeqVarTools 1.7.9

• added more options to return dosage of different alleles

SeqVarTools 1.7.7

• added methods to calculate and plot reference allele fraction

SeqVarTools 1.7.6

• HWE method returns additional columns and allows permutation of genotypes

SeqVarTools 1.7.5

• Added SeqVarData class to combine sample annotation with GDS object

SeqVarTools 1.7.4

• HWE works on biallelic INDELs as well as SNVs

SeqVarTools 1.7.3

• Add methods for duplicateDiscordance with two datasets

• Add alternateAlleleDetection

SeqVarTools 1.5.1

• Use existing isSNV generic from VariantAnnotation instead of redefining

• Use BiocStyle for vignette