chrchang/plink-ng v2.0.0-a.5.45

Alpha 5.45: PCA projection, logistic regression, other misc. fixes

on GitHub

Fixes cover the following:
• --pheno/--covar loading of categorical data when the input file doesn't include all samples in the main fileset
• --glm logistic-regression handling of mixed no-dosages-missing and some-dosages-missing data (results could be nondeterministically slightly off)
• PCA projection workflow:
◦ "--pca allele-wts" scaling of multiallelic variant weights
◦ --score center/variance-standardize missing-dosage imputation
◦ --score variance-standardize tolerance of monomorphic variants
• BGEN 1.2/1.3 export in 32-bit builds
• Several merge CM-column and conflict-handling bugs
• "--make-pgen multiallelics=-" phase handling
• "--bgen ref-first" phase-handling (everything was swapped)
• "--export bcf vcf-dosage=HDS-force" on unphased data
• "--bcf dosage=HDS" on one-value (haploid) HDS fields
• "--export vcf vcf-dosage=DS-force" on multiallelic chrX variants
• "--export vcf vcf-dosage=DS-{force,only}" on multiallelic variants
• Import of old (v1.1) BGEN files containing both dosages and alternate contigs
• Handling of extremely long --q-score-range names
• Swapped HET1_HOM2/HET2_HOM1 in --make-king-table output
• --adjust-file on input without a PROVISIONAL_REF? column
• Detection/handling of corrupted .pgen files
• --ld's handling of phasd ALTx/ALTy genotypes
• Error message on VCF/BCF files with too many (more than (2^31 - 3)) variants for PLINK 2