• Fixed "--adjust gc log10" bug that caused UNADJ and GC values to be garbled, and "--adjust log10" bug that sometimes caused the .adjusted header to be misaligned with the body (no GC heading, but body contained that column).
• Fixed bug which could cause --adjust t-test (--linear, quantitative-trait --assoc) GC values (and downstream values under "--adjust gc") to be computed from another variant's t/df values when missingness rate varied. "--adjust gc" step procedures are now consistently applied in GC p-value order in this case.
• --recode + --set-hh-missing / --set-mixed-mt-missing should now work properly.
• --pca/GRM construction now prints a strongly worded warning if a monomorphic variant is present, and --pca var-wts / PCA projection errors out.
• Fixed bug that caused --clump-best to report the wrong best proxy.
• --grm-bin + --rel-cutoff + --make-grm-{gz,bin} should now work properly instead of producing a "File read failure" error.
• Fixed "--distance triangle bin 1-ibs" bug that caused it to write too many entries.
• "--distance ibs bin[4] square0" now writes 1s instead of 0s on the diagonal.
• Fixed --test-missing bug which affected post-chrY results when nonempty chrY was skipped due to no male cases or no male controls.
• Fixed "--recode lgen tab[x]" segfault.
• Fixed "--recode beagle[-nomap]"'s behavior when the first variant was filtered out of the main dataset.
• "--recode list" now handles chromosome codes longer than 2 characters properly.