• --split-par no longer mislabels the first variant in the next chromosome when all chrX variants are in PAR1.
• --indep-pairphase no longer makes misaligned memory allocations (which can result in a crash) in non-AVX2 64-bit builds.
• --adjust[-file] + --pfilter no longer crashes when printing the final log line.
• --hwe "observation counts vary by more than 10%" warning now works properly.
• --geno-counts now correctly handles male counts at chrX multiallelic variants.
• Fixed cubic-solver edge case which occasionally resulted in spurious NaNs or crashes in --r2-phased, --clump (without --clump-unphased), and --ld.
• Fixed "--missing scols=" and "--sample-counts cols=" command-line parsing/validation bugs.
• --no-categorical now works as intended on apparently-categorical .psam columns.
• --keep-cats/--keep-cat-names now remove all samples (resulting in a downstream error) instead of no samples when there are no matching categories.
• Allele-uniqueness check (invoked by --score, --pgen-diff, --rm-dup, --update-alleles, --read-freq, --alt-allele, --ref-from-fa, and --clump) now works properly on multiallelic variants.
• --merge-filter-mode now has the documented 'np-union' default, instead of 'nm-first'.