GenoTools 2.2.0

2.2.0

A minor version, not a patch: the change below alters what a default run
leaves on disk. Nothing about your results, final outputs or logs changes, but
a default that deletes files users previously got to keep is more than a patch.

Changed

• Intermediate pfiles are now deleted as the run progresses, at defaults.

  Each QC step reads a genotype file and writes a new one — callrate reads your
  input and writes …_callrate, sex reads that and writes …_sex, and so on —
  so a ten-step run creates ten copies of your data. At GP2 release scale each
  copy is tens of GiB.

  Cleanup used to be skipped whenever warn_only was set, and warn-and-continue
  is the default, so at defaults every copy survived for the whole run. The
  only way to reclaim the disk was --no-warn, which also turns
  warn-and-continue into fail-fast — so you could not have both. That is a bad
  trade on a long run, where warn-and-continue exists precisely so an eight-hour
  job does not die on one recoverable step.

  The two flags no longer interfere:

  	before	now
  (default)	keeps every copy	deletes each copy once the next is written
  --full-output	keeps every copy	keeps every copy
  --no-warn	deletes + fail-fast	fail-fast only
  --no-warn --full-output	keeps + fail-fast	keeps + fail-fast

  --full-output is now the only switch governing retention; --no-warn is
  purely failure policy. Peak disk during a run drops from roughly one working
  copy per step to one overall — on the round-19 full-GP2 run, ~98 GiB written
  against a ~50 GiB peak.

  If you relied on the old default to inspect intermediates, pass
  --full-output — it reproduces the previous behavior exactly. A failed
  step's input is still kept either way, so a broken run can still be examined.