CHANGES IN VERSION 1.11.1
-------------------------

    o change "hg20" to "hg38" according to the UCSC Genome Browser datasets
      and documentation

    o add "DRB3" and "DRB4" to the HLA gene list


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

    o the version number was bumped for the Bioconductor release version 3.4


CHANGES IN VERSION 1.9.0-1.9.3
-------------------------

    o the development version


CHANGES IN VERSION 1.8.0-1.8.3
-------------------------

    o the version number was bumped for the Bioconductor release version 3.3

    o new arguments 'pos.start' and 'pos.end' in `hlaFlankingSNP()`


CHANGES IN VERSION 1.7.0-1.7.7
-------------------------

    o new functions `hlaCheckAllele()`, `hlaAssocTest()`,
      `hlaConvSequence()` and `summary.hlaAASeqClass()`


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

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


CHANGES IN VERSION 1.5.0-1.5.1
-------------------------

    o increase the test coverage

    o fix an issue when `predict.hlaAttrBagClass(..., allele.check=FALSE)`


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

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


CHANGES IN VERSION 1.3.0-1.3.2
-------------------------

NEW FEATURES

    o support the human genome "hg20"/"hg38"

    o add a new function `hlaGDS2Geno()` to support SNP GDS files (in the
      R/Bioconductor package SNPRelate)

    o `hlaReport()` outputs text with markdown format

SIGNIFICANT USER-VISIBLE CHANGES

    o optimize the calculation of hamming distance using SSE2 and hardware
      POPCNT instructions if available

    o hardware POPCNT: 2.4x speedup for large-scale data, compared to
      the implementation in v1.2.4

    o SSE2 popcount implementation: 1.5x speedup for large-scale data,
      compared to the implementation in v1.2.4

BUG FIXES

    o bug fixes on big-endian machines (like Solaris SPARC, Apple PowerPC)

    o minor fix on random sampling from discrete uniform distribution

    o bug fix if `requireNamespace("HIBAG")` instead of `require(HIBAG)` is
      called from other packages


CHANGES IN VERSION 1.2.1-1.2.4
-------------------------

NEW FEATURES

    o add a new function `hlaOutOfBag()` offering out-of-bag estimation of
      overall accuracy, per-allele sensitivity, etc

    o improve the display of the function `hlaReport()`

SIGNIFICANT USER-VISIBLE CHANGES

    o improve the display of `summary.hlaAlleleClass()`

    o fix warnings in 'R-3.1.1 CMD check'

    o avoid missing values in `hlaFlankingSNP()`

    o add more gene information in `hlaLociInfo()`

BUG FIXES

    o make the C function 'HIBAG_SortAlleleStr' compatible with the
      clang++ compiler on Mac Mavericks


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

NEW FEATURES

    o add a new function `hlaPredMerge()` to merge predictions from multiple
      models via voting

    o add assembly information (like hg19) to the objects of
      'hlaAttrBagClass' and 'hlaAttrBagObj'

    o add a new argument 'stop.cluster' to `hlaParallelAttrBagging()`

    o allow matching SNPs by positions only

    o allow imputing HLA alleles in parallel at a single locus

SIGNIFICANT USER-VISIBLE CHANGES

    o optimize the C code: replace some intensive 'exp' and 'log'
      calculations by precalculated values, roughly 2.5x ~ 4x speedup

    o optimize the C code of the hamming distance calculation between
      genotypes and two haplotypes by SSE2 intrinsics, ~50% faster
      for large datasets

    o the code optimization guarantees the same training and predictive
      accuracies as version 1.1.0

    o remove unused row names in the function `hlaCompareAllele()`

    o improve the function `hlaPublish()`

    o improve vignettes and documents


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

NEW FEATURES

    o add genome assembly information (such like hg18, hg19)

    o allow class majority voting in `predict.hlaAttrBagClass()`

    o add an autosave function to `hlaParallelAttrBagging()`

    o add a new function `hlaPublish()`

    o allow additional information in the objects of 'hlaAttrBagClass' and
      'hlaAttrBagObj'

SIGNIFICANT USER-VISIBLE CHANGES

    o update citation information

    o change `hlaModelfromObj()` to `hlaModelFromObj()` (a typo)

    o improvement in mismatching alleles for allelic strands


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

SIGNIFICANT USER-VISIBLE CHANGES

    o increase the limit of the possible number of SNPs in a single
      classifier up to 256

BUG FIXES

    o use `useDynLib()` in NAMESPACE instead of 'library.dynam()' since
      R-Ext strongly suggests to use `useDynLib()`

    o update citation information

    o add a vignette


CHANGES IN VERSION 0.9.2-0.9.4
-------------------------

NEW FEATURES

    o add a load balancing function to `hlaParallelAttrBagging()`

    o add `hlaUniqueAllele()`

    o add an argument 'match.pos' to the functions `predict.hlaAttrBagClass()`,
      `hlaGenoCombine()`, `hlaGenoSwitchStrand()`

    o add an argument 'with.pos' to the function `hlaSNPID()`

SIGNIFICANT USER-VISIBLE CHANGES

    o give more warnings about missing SNPs in `predict.hlaAttrBagClass()`

    o a warning is given for strand mismatching when calling
      `hlaGenoSwitchStrand()`

BUG FIXES

    o bug fix: passing only one individual to `predict.hlaAttrBagClass()`

    o avoid the segmentation fault in `predict.hlaAttrBagClass()`
      when all SNPs are missing.


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

    o first release of HIBAG in July, 2012
