Release Bioconductor Release v3.13 · zhengxwen/HIBAG

CHANGES IN VERSION 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

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

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