CHANGES IN VERSION 1.10.0-1.10.6
-------------------------

    o the version number was bumped for the Bioconductor release version 3.2

    o fix a memory issue in `seqAlleleFreq()` when 'ref.allele' is a vector

    o `seqSetFilter()` allows numeric vectors in 'samp.sel' and 'variant.sel'

    o `seqSummary()` returns ploidy and reference

    o `seqStorage.Option()` controls the compression level of FORMAT/DATA

    o `seqVCF2GDS()` allows extract part of VCF files via 'start' and 'count'

    o `seqMerge()` combines multiple GDS files with the same samples

    o export methods for compatibility with VariantAnnotation

    o a new argument '.useraw' in `seqGetFilter()`

    o a new argument 'allow.duplicate' in `seqOpen()`

    o fix a bug in `seqParallel()`
      (https://github.com/zhengxwen/SeqArray/issues/11) and optimize
      its performance

    o 'gdsfile' could be NULL in `seqParallel()`


CHANGES IN VERSION 1.9.0-1.9.19
-------------------------

    o a new function `seqGDS2SNP()`

    o supported by the SNPRelate package

    o support `seqApply(..., margin="by.sample")`

    o new functions `seqOptimize()`, `seqMissing()`, `seqAlleleFreq()`,
      `seqNumAllele()` and `seqSetFilterChrom()`

    o "intersection" and "push+intersection" in `seqSetFilter()`

    o parallel implementation in `seqNumAllele()`, `seqMissing()` and
      `seqAlleleFreq()`

    o a new function `seqExport()`

    o new argument ".useraw" in `seqApply()`

    o fix a bug for duplicated "variant.id",
      https://github.com/zhengxwen/SeqArray/issues/7

    o fix an issue of `seqVCF2GDS()` when there are duplicated format or
      info ID

    o improve access speed (+50%, benchmark on calling
      seqApply(..., FUN=function(x) {}))

    o new functions `seqSNP2GDS()`, `seqBED2GDS()`, `seqAlleleCount()` and
      `seqResetFilter()`

    o `seqCompress.Option` is renamed to `seqStorage.Option`

    o "ZIP_RA" is the default value in `seqStorage.Option()` and other
      functions instead of "ZIP_RA.max"

    o `seqSetFilter()` becomes a S4 method


CHANGES IN VERSION 1.8.0
-------------------------

    o The version number was bumped for the Bioconductor release version 3.1


CHANGES IN VERSION 1.7.1-1.7.5
-------------------------

    o bug fix in getting genotypes if position > 2^31

    o add an option 'ignore.chr.prefix' to the function `seqVCF2GDS()`

    o `seqVCF2GDS()` ignores the INFO or FORMAT variables if they are not
      defined ahead

	o a new action 'push+set' in the function `seqSetFilter()`

    o bug fix if 'requireNamespace("SeqArray")' is called from other packages


CHANGES IN VERSION 1.6.0
-------------------------

    o The version number was bumped for the Bioconductor release version 3.0


CHANGES IN VERSION 1.5.1-1.5.2
-------------------------

    o fix a bug in `seqVCF2GDS()` when the values in the FILTER column are
      all missing

    o enhance `seqVCF.Header()`

    o support the LinkingTo mechanism

    o fix the error in haploid genotypes (Y chromosome)


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

    o The version number was bumped for the Bioconductor release version


CHANGES IN VERSION 1.3.1-1.3.4
-------------------------

    o update according to the new version of VariantAnnotation

    o update test codes to avoid the conflict

    o bumped version as all packages that depend on Rcpp must be rebuilt

    o modify to new biocViews to DESCRIPTION file


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

    o The version number was bumped for the Bioconductor release version


CHANGES IN VERSION 1.1.4-1.1.5
-------------------------

    o add a new argument "action" to the function `seqSetFilter()`

    o add a new function 'seqInfoNewVar' which allows adding new variables
      to the INFO fields

    o minor bug fix in asVCF

    o update man page "SeqVarGDSClass-class.Rd" with new methods

    o in DESCRIPTION, BiocGenerics listed in "Suggests" instead of "Imports"
      as suggested by R CMD check

    o bug fix in seqDelete

    o revise the function 'seqTranspose' according to the update of
      gdsfmt (v1.0.0)


CHANGES IN VERSION 1.1.1-1.1.3
-------------------------

    o revise the argument 'var.index' in the function `seqApply()`

    o basic supports of 'GRanges' and 'DNAStringSetList'

    o added methods 'qual', 'filt', 'asVCF'

    o 'granges' method uses length of reference allele to set width

    o minor bug fix to avoid `seqGetData()` crashing when no value returned
      from a variable-length variable

    o update documents


CHANGES IN VERSION 1.0.0
-------------------------

    o The version number was bumped for the Bioconductor release version


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

    o first submission