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
