CHANGES IN VERSION 1.42.0 ------------------------- o the input of `hlaUniqueAllele()` can be a hlaAttrBagClass object or a hlaAttrBagObj object o `hlaAlleleToVCF()` outputs 0 instead of NaN if the location of HLA gene is unknown or unspecified o update the C codes according to '_R_USE_STRICT_R_HEADERS_=true' & '_R_CXX_USE_NO_REMAP_=true' CHANGES IN VERSION 1.40.0 ------------------------- o new option 'all' in `hlaUniqueAllele()` CHANGES IN VERSION 1.38.3 ------------------------- o fix compiler warnings: -Wformat & -Wformat-security o new 'use.matching=TRUE' in `hlaPredMerge()`; to set 'use.matching=FALSE' for backward compatibility o 'ret.postprob=FALSE' by default in `hlaPredMerge()` CHANGES IN VERSION 1.38.1 ------------------------- o fix a compiler warning of "unused-but-set-variable" on Apple ARM chips o fix the failure of package loading on Apple ARM chips in the R console CHANGES IN VERSION 1.36.3 ------------------------- o the output of `hlaPredict(, type="response+prob")` includes dosages o new arguments 'ret.dosage', 'ret.postprob', 'max.resolution' and 'rm.suffix' in `hlaPredMerge()` o new arguments 'allele.list' and 'prob.cutoff' in `hlaAlleleToVCF()` for more possible outputs o `hlaAlleleToVCF()` accepts a list of 'hlaAlleleClass' as the first argument: output multiple 'hlaAlleleClass' objects to a single VCF file CHANGES IN VERSION 1.34.1 ------------------------- o fix the compiler warning: sprintf is deprecated o show "64-bit" correctly when run on Windows CHANGES IN VERSION 1.34.0 ------------------------- o fix the compiler issue on Mac M1 chip o 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 CHANGES IN VERSION 1.32.0 ------------------------- o fix the issue on Win32 because of using deprecated tbb::task_scheduler_init CHANGES IN VERSION 1.30.2 ------------------------- o require GCC >= v8.0 for compiling the AVX-512VPOPCNTDQ intrinsics o fix `hlaGDS2Geno()` when loading a SeqArray GDS file CHANGES IN VERSION 1.30.0 ------------------------- o add the support of Intel AVX-512VPOPCNTDQ intrinsics (faster than AVX512BW) CHANGES IN VERSION 1.28.0 ------------------------- o `hlaPredict()` returns the dosage of HLA alleles when type="response+dosage", and `hlaPredict()` returns the best guess and dosages by default o 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 o `hlaGDS2Geno()` supports SeqArray GDS files o a new option 'maf' in `hlaAttrBagging()` and `hlaParallelAttrBagging()` o 'pos.start' and 'pos.end' are replaced by 'pos.mid' in `hlaFlankingSNP()` and `hlaGenoSubsetFlank()` o new function `hlaAlleleToVCF()` for converting the imputed HLA classical alleles to a VCF file CHANGES IN VERSION 1.26.1 ------------------------- o the hlaAttrBagging object can be removed in garbage collection without calling `hlaClose()` o enable internal GPU API o improved multithreaded performance compared with v1.26.0 CHANGES IN VERSION 1.26.0 ------------------------- o users can interrupt the model building in an interactive R session o remove `hlaErrMsg()` since it is never used o a new option 'nthread' in `hlaAttrBagging()` as a complement to `hlaParallelAttrBagging()` o 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 o new function `hlaSetKernelTarget()` to automatically select the CPU target the algorithm is optimized for CHANGES IN VERSION 1.24.0 ------------------------- o fix a Win32 compiler issue CHANGES IN VERSION 1.22.0 ------------------------- o change the file name "vignettes/HIBAG_Tutorial.Rmd" to "vignettes/HIBAG.Rmd", so `vignette("HIBAG")` can work directly CHANGES IN VERSION 1.18.0 ------------------------- o new function `hlaDistance()` o `match.type="Position"` is the default option in `hlaPredict()` CHANGES IN VERSION 1.16.0 ------------------------- o KIR information in `hlaLociInfo()` o new functions `hlaGenoSubsetFlank()` and `hlaLDMatrix()` CHANGES IN VERSION 1.14.0 ------------------------- o modify the kernel to support the GPU extension o add matching proportion to measure the similarity of SNP haplotypes between training and test datasets o new function `hlaReportPlot()` o the argument 'cl' in `predict.hlaAttrBagClass()`, `hlaPredict()` and `hlaParallelAttrBagging()` allows a numeric value for the number of cores CHANGES IN VERSION 1.12.0 ------------------------- 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