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

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


CHANGES IN VERSION 1.3.0-1.3.11
-------------------------

    o update GENEVA website address

    o add a new function `snpgdsPairScore()`

    o improve `snpgdsGRM()`

    o support the SeqArray data format (requiring SeqArray >= v1.9.2)

    o modification according to gdsfmt_1.5.7

    o bug fix in `snpgdsLDMat()` when genotype data are from SeqArray

    o bug fix: https://github.com/zhengxwen/SNPRelate/issues/14

    o `snpgdsLDMat()` supports multiple threads and covariance

    o `snpgdsPCA()`: non-computed eigenvalues are NaN to avoid misuse of
      'eigenval' when `eigen.method="DSPEVX"`


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

    o The version number was bumped for the Bioconductor release version


CHANGES IN VERSION 1.1.0-1.1.11
-------------------------

    o fix a bug in `snpgdsVCF2GDS()` when 'method="biallelic.only"'

    o add `snpgdsVCF2GDS_R()` for the R implementation

    o fix a bug in `snpgdsBED2GDS()` if 'family=TRUE'

    o `snpgdsGDS2BED()` allows the file name of GDS

    o improve `snpgdsSlidingWindow()`

    o add an option 'ignore.chr.prefix' to the function `snpgdsVCF2GDS()`

    o a new function `snpgdsHWE()`

    o v1.1.5: add "Fst estimation" to the vignette

    o v1.1.6: bug fix if `requireNamespace("SNPRelate")` is called from
      other packages

    o v1.1.7: `snpgdsPCA()` uses 'DSPEVX' to compute eigenvalues and
      eigenvectors instead of 'DSPEV' if top eigenvalues are required only
      (significant improvement on computing speed)

    o v1.1.8: the original Rnw vignette is replaced by a R Markdown vignette

    o v1.1.9: a new function `snpgdsPED2GDS()`


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

    o The version number was bumped for the Bioconductor release version


CHANGES IN VERSION 0.99.1-0.99.3
-------------------------

    o an option to create an integer snp.id when converting from PLINK

    o a new function `snpgdsFst()` to estimate Fst

    o minor fixes


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

    o be a Bioconductor package

    o fully support long vectors (>= R v3.0)

    o >5x speedup in the function `snpgdsVCF2GDS()`

    o SNP GDS format allows character-type chromosome codes

    o add a new argument 'ref.allele' in `snpgdsVCF2GDS()`

    o add new functions `snpgdsOpen()` and `snpgdsClose()`

    o add a new function `snpgdsTranspose()` to transpose the genotypic matrix

    o add a new function `snpgdsAlleleSwitch()` to switch alleles if needed

    o add a new function `snpgdsApartSelection()`

    o add a new function `snpgdsGEN2GDS()` to import Oxford GEN data

    o use NA instead of 3 as missing value in `snpgdsGetGeno()`

    o add a new argument 'snpfirstdim' in the function `snpgdsGDS2BED()`

    o add a new argument 'with.id' in the functions `snpgdsSNPRateFreq()`
      and `snpgdsSampMissRate()`

    o return a numeric vector instead of data.frame in `snpgdsLDpair()`

    o add estimating nine Jacquard's coefficients in `snpgdsIBDMLE()`

    o fix the memory issues reported by valgrind


CHANGES IN VERSION 0.9.15-0.9.19
-------------------------

    o improve `snpgdsIBDKING()` to avoid misleading arguments and examples

    o improve `snpgdsIBDSelection()`

    o the names of column 'sample1', 'sample2' and 'kinshipcoeff' are changed
      to 'ID1', 'ID2' and 'kinship' in the output of `snpgdsIBDSelection()`

    o avoid compiler issues when the version of R < v3.0

    o minor fixes in `snpgdsIBDSelection()`: allow non-character-type sample
      IDs and missing IBD coefficients


CHANGES IN VERSION 0.9.14:
-------------------------

    o `snpgdsGDS2BED()` gives a warning if the allele information is missing

    o add `snpgdsIBDKING()` (KING robust relationship inference in genome-wide
      association studies)

    o bug fixes in `snpgdsIBS()` and `snpgdsIBSNum()`

    o some warnings in `snpgdsSummary()` are replaced by hints

    o bug fix in `snpgdsVCF2GDS()`: duplicate SNP id when importing multiple
      VCF files

    o improve hint information in `snpgdsGDS2BED()`


CHANGES IN VERSION 0.9.10-0.9.13
-------------------------

    o disable parallel functions in the Windows version of SNPRelate, until
      the internal multi-thread funcitons are replaced by the functions
      in win-pthreads

    o fix compiling issues in the Windows version of SNPRelate

    o add 'GetRNGstate' and 'PutRNGstate' to the C function `gnrDistPerm()`

    o remove the upper limit of 200 chromosomes in `snpgdsVCF2GDS()` according
      to scaffolds/contigs from a de novo assembly not chromosomes

    o improve `snpgdsSummary()`

    o bug fixes in `snpgdsPairIBD()`

    o bug fix in `snpgdsVCF2GDS()`: to use "\t" as the field separator
      character

    o bug fixes according to gdsfmt v0.9.11

    o improve the vignette


CHANGES IN VERSION 0.9.8-0.9.9
-------------------------

    o adds a new argument 'family' to `snpgdsBED2GDS()`

    o improves `snpgdsCutTree()`

    o adds a new function `snpgdsDrawTree()`

    o adds an argument 'option' to the function `snpgdsBED2GDS()`

    o outputs chromosome codes according to `snpgdsOption()` in
      `snpgdsGDS2BED()`

    o add an alternative method extracting variants from a VCF file in
      `snpgdsVCF2GDS()`

    o supports multiple files in `snpgdsVCF2GDS()`

    o add `snpgdsOption()`

    o add `snpgdsHCluster()`

    o add `snpgdsCutTree()`

    o add `snpgdsDiss()`


CHANGES IN VERSION 0.9.1-0.9.7
-------------------------

    o bug fix: an important bug of missing genotypes in `snpgdsVCF2GDS()`

    o bug fix: a bug in `snpgdsGDS2BED()` (output 23, 24, ..., instead of
      X, Y, XY)

    o bug fix: a bug in `snpgdsCombineGeno()` (due to duplicate SNPs)

    o `snpgdsLDpair()` provides haplotype frequency estimates

    o `snpgdsLDMat()` allows specifying sliding window size

    o add RUnit tests

    o add a vignette

    o bug fixes

    o add functions to `snpgdsIBDMLE()` and `snpgdsIBDMoM()`

    o add a new function `snpgdsVCF2GDS()`


CHANGES IN VERSION 0.9.0 (03-Aug-2011)
-------------------------

    o first public release of SNPRelate
