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Alpha 5.32: fix chr1_KI270706_random regression, --chr-set no-x/no-y/no-xy

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@chrchang chrchang released this 24 Aug 01:25
  • a5.31 broke handling of contig names like 'chr1_KI270706_random'; this is now fixed.
  • --chr-set's no-x, no-y, and no-xy modifiers would often just filter out variants on a forbidden chromosome; this has been fixed (i.e. PLINK 2 now consistently errors out).
  • Command-line parser now enforces "must be used with --make-[b]pgen/--make-bed and no other non-merge commands" restriction on --set-hh-missing/--set-mixed-mt-missing .