New features:
- EIGENSOFT binary format input/output (--eigfile/--eiggeno/--eigind/--eigsnp, --export eig[t])
- Mendel error reporting/filtering (--mendel, --me, --set-me-missing)
- --extract-if-info/--exclude-if-info and --keep-if/--remove-if now support a wider range of expressions (e.g. &&, ||, !, parentheses, backslash-escaping of special characters)
- --glm permutation tests
- --make-grm-sparse
- --make-king-table concordance-check mode, ibs column-set
- --rename-chrs
- HWE exact test now accurately handles scenarios where two tables have unequal but extremely close likelihoods, instead of treating them as ties.
- --flip[-subset]
- --fill-missing-with-ref
- --zero-cluster
- --allele1234/--alleleACGT
- --import-overlong-var-ids
- --exclude-palindromic-snps
- --make-[b]pgen trim-alts
- --select-sid-representatives
- Improved logging for variant filters applied during import/merge/.pvar-load time.
Other significant behavior changes relative to alpha 6:
- --hwe now errors out, instead of just printing a warning, when filtering parameters are suspiciously strict and no sample-size term was specified.
- --vcf now errors out, instead of just printing a warning, when importing a single-sample VCF that appears to have all hom-REF genotypes filtered out (unless this sanity check was disabled with --vcf-allow-no-nonvar).
- --normalize + variant-split in the same command now errors out, instead of just printing a warning.
- --geno-counts no longer treats mixed chrM genotypes as missing.