Version 1.1.0 - 1.1.4:

    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'


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


Version 0.99.0:

    o initial submission to Bioconductor
    o moving from CRAN to Bioconductor

    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 0.9.16 - 0.9.19:

    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 0.9.15:

    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'


Changes in 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 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


Changes in 0.9.12:

    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'


Changes in 0.9.10 - 0.9.11:

    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 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'


Changes in 0.9.8:

    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 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


Changes in 0.9.1-0.9.6:

    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