NEWS

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HIBAG 1.42.0

• the input of 'hlaUniqueAllele()' can be a hlaAttrBagClass object or a hlaAttrBagObj object
• 'hlaAlleleToVCF()' outputs 0 instead of NaN if the location of HLA gene is unknown or unspecified
• update the C codes according to '_R_USE_STRICT_R_HEADERS_=true' & '_R_CXX_USE_NO_REMAP_=true'

HIBAG 1.40.0

• new option 'all' in 'hlaUniqueAllele()'

HIBAG 1.38.3

• fix compiler warnings: -Wformat & -Wformat-security
• new 'use.matching=TRUE' in ‘hlaPredMerge()'; to set ’use.matching=FALSE' for backward compatibility
• 'ret.postprob=FALSE' by default in 'hlaPredMerge()'

HIBAG 1.38.1

• fix a compiler warning of "unused-but-set-variable" on Apple ARM chips
• fix the failure of package loading on Apple ARM chips in the R console

HIBAG 1.36.3

• the output of 'hlaPredict(, type="response+prob")' includes dosages
• new arguments 'ret.dosage', 'ret.postprob', 'max.resolution' and 'rm.suffix' in 'hlaPredMerge()'
• new arguments 'allele.list' and 'prob.cutoff' in 'hlaAlleleToVCF()' for more possible outputs
• ‘hlaAlleleToVCF()' accepts a list of ’hlaAlleleClass' as the first argument: output multiple 'hlaAlleleClass' objects to a single VCF file

HIBAG 1.34.1

• fix the compiler warning: sprintf is deprecated
• show "64-bit" correctly when run on Windows

HIBAG 1.34.0

• fix the compiler issue on Mac M1 chip
• fix the C stack error in RStudio (RStudio tries to capture the internal R object structure, but fails in an infinite loop); there is no such error when running R in the terminal

HIBAG 1.32.0

• fix the issue on Win32 because of using deprecated tbb::task_scheduler_init

HIBAG 1.30.2

• require GCC >= v8.0 for compiling the AVX-512VPOPCNTDQ intrinsics
• fix 'hlaGDS2Geno()' when loading a SeqArray GDS file

HIBAG 1.30.0

• add the support of Intel AVX-512VPOPCNTDQ intrinsics (faster than AVX512BW)

HIBAG 1.28.0

• 'hlaPredict()' returns the dosage of HLA alleles when type="response+dosage", and 'hlaPredict()' returns the best guess and dosages by default
• a new option "Pos+Allele" in 'hlaPredict()', 'hlaGenoCombine()', 'hlaGenoSwitchStrand()', 'hlaSNPID()' and 'hlaCheckSNPs()' for matching genotypes by positions, reference and alternative alleles; it is particularly useful when the training and test set are both matched to the same reference genome, e.g., 1000 Genomes Project
• 'hlaGDS2Geno()' supports SeqArray GDS files
• a new option 'maf' in 'hlaAttrBagging()' and 'hlaParallelAttrBagging()'
• 'pos.start' and 'pos.end' are replaced by 'pos.mid' in 'hlaFlankingSNP()' and 'hlaGenoSubsetFlank()'
• new function 'hlaAlleleToVCF()' for converting the imputed HLA classical alleles to a VCF file

HIBAG 1.26.1

• the hlaAttrBagging object can be removed in garbage collection without calling 'hlaClose()'
• enable internal GPU API
• improved multithreaded performance compared with v1.26.0

HIBAG 1.26.0

• users can interrupt the model building in an interactive R session
• remove 'hlaErrMsg()' since it is never used
• a new option 'nthread' in 'hlaAttrBagging()' as a complement to 'hlaParallelAttrBagging()'
• kernel version 1.5: generates the same training model as v1.4, but 2-6x faster, by taking advantage of Intel AVX, AVX2 and AVX512 intrinsics
• new function 'hlaSetKernelTarget()' to automatically select the CPU target the algorithm is optimized for

HIBAG 1.24.0

• fix a Win32 compiler issue

HIBAG 1.22.0

• change the file name "vignettes/HIBAG_Tutorial.Rmd" to "vignettes/HIBAG.Rmd", so 'vignette("HIBAG")' can work directly

HIBAG 1.18.0

• new function 'hlaDistance()'
• 'match.type="Position"' is the default option in 'hlaPredict()'

HIBAG 1.16.0

• KIR information in 'hlaLociInfo()'
• new functions 'hlaGenoSubsetFlank()' and 'hlaLDMatrix()'

HIBAG 1.14.0

• modify the kernel to support the GPU extension
• add matching proportion to measure the similarity of SNP haplotypes between training and test datasets
• new function 'hlaReportPlot()'
• the argument 'cl' in 'predict.hlaAttrBagClass()', 'hlaPredict()' and 'hlaParallelAttrBagging()' allows a numeric value for the number of cores

HIBAG 1.12.0

• change "hg20" to "hg38" according to the UCSC Genome Browser datasets and documentation
• add "DRB3" and "DRB4" to the HLA gene list

HIBAG 1.10.0

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

HIBAG 1.9.0-1.9.3

• the development version

HIBAG 1.8.0-1.8.3

• the version number was bumped for the Bioconductor release version 3.3
• new arguments 'pos.start' and 'pos.end' in 'hlaFlankingSNP()'

HIBAG 1.7.0-1.7.7

• new functions 'hlaCheckAllele()', 'hlaAssocTest()', 'hlaConvSequence()' and 'summary.hlaAASeqClass()'

HIBAG 1.6.0

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

HIBAG 1.5.0-1.5.1

• increase the test coverage
• fix an issue when 'predict.hlaAttrBagClass(..., allele.check=FALSE)'

HIBAG 1.4.0

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

HIBAG 1.3.0-1.3.2

NEW FEATURES

• support the human genome "hg20"/"hg38"
• add a new function 'hlaGDS2Geno()' to support SNP GDS files (in the R/Bioconductor package SNPRelate)
• 'hlaReport()' outputs text with markdown format

SIGNIFICANT USER-VISIBLE CHANGES

• optimize the calculation of hamming distance using SSE2 and hardware POPCNT instructions if available
• hardware POPCNT: 2.4x speedup for large-scale data, compared to the implementation in v1.2.4
• SSE2 popcount implementation: 1.5x speedup for large-scale data, compared to the implementation in v1.2.4

BUG FIXES

• bug fixes on big-endian machines (like Solaris SPARC, Apple PowerPC)
• minor fix on random sampling from discrete uniform distribution
• bug fix if 'requireNamespace("HIBAG")' instead of 'require(HIBAG)' is called from other packages

HIBAG 1.2.1-1.2.4

NEW FEATURES

• add a new function 'hlaOutOfBag()' offering out-of-bag estimation of overall accuracy, per-allele sensitivity, etc
• improve the display of the function 'hlaReport()'

SIGNIFICANT USER-VISIBLE CHANGES

• improve the display of 'summary.hlaAlleleClass()'
• fix warnings in 'R-3.1.1 CMD check'
• avoid missing values in 'hlaFlankingSNP()'
• add more gene information in 'hlaLociInfo()'

BUG FIXES

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

HIBAG 1.2.0 (2013-07-29)

NEW FEATURES

• add a new function 'hlaPredMerge()' to merge predictions from multiple models via voting
• add assembly information (like hg19) to the objects of 'hlaAttrBagClass' and 'hlaAttrBagObj'
• add a new argument 'stop.cluster' to 'hlaParallelAttrBagging()'
• allow matching SNPs by positions only
• allow imputing HLA alleles in parallel at a single locus

SIGNIFICANT USER-VISIBLE CHANGES

• optimize the C code: replace some intensive 'exp' and 'log' calculations by precalculated values, roughly 2.5x ~ 4x speedup
• optimize the C code of the hamming distance calculation between genotypes and two haplotypes by SSE2 intrinsics, ~50% faster for large datasets
• the code optimization guarantees the same training and predictive accuracies as version 1.1.0
• remove unused row names in the function 'hlaCompareAllele()'
• improve the function 'hlaPublish()'
• improve vignettes and documents

HIBAG 1.1.0 (2013-06-04)

NEW FEATURES

• add genome assembly information (such like hg18, hg19)
• allow class majority voting in 'predict.hlaAttrBagClass()'
• add an autosave function to 'hlaParallelAttrBagging()'
• add a new function 'hlaPublish()'
• allow additional information in the objects of 'hlaAttrBagClass' and 'hlaAttrBagObj'

SIGNIFICANT USER-VISIBLE CHANGES

• update citation information
• change 'hlaModelfromObj()' to 'hlaModelFromObj()' (a typo)
• improvement in mismatching alleles for allelic strands

HIBAG 1.0.0 (2013-03-26)

SIGNIFICANT USER-VISIBLE CHANGES

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

BUG FIXES

• use ‘useDynLib()' in NAMESPACE instead of ’library.dynam()' since R-Ext strongly suggests to use 'useDynLib()'
• update citation information
• add a vignette

HIBAG 0.9.2-0.9.4

NEW FEATURES

• add a load balancing function to 'hlaParallelAttrBagging()'
• add 'hlaUniqueAllele()'
• add an argument 'match.pos' to the functions 'predict.hlaAttrBagClass()', 'hlaGenoCombine()', 'hlaGenoSwitchStrand()'
• add an argument 'with.pos' to the function 'hlaSNPID()'

SIGNIFICANT USER-VISIBLE CHANGES

• give more warnings about missing SNPs in 'predict.hlaAttrBagClass()'
• a warning is given for strand mismatching when calling 'hlaGenoSwitchStrand()'

BUG FIXES

• bug fix: passing only one individual to 'predict.hlaAttrBagClass()'
• avoid the segmentation fault in 'predict.hlaAttrBagClass()' when all SNPs are missing.

HIBAG 0.9.1 (2012-06-21)

• first release of HIBAG in July, 2012