project_issues_log.txt

For data:

rs7359233
Very different p-values between
CLEAN.B58C-WTCCC.HEIGHT.MEN.LE50.UNIFORM.giant-association-results-20090323.txt
and other studies
And also the effect allele is different among studies, some studies use 'G', others use 'T'.


For FlexSC:

The OFFLINE mode in flexsc.Mode is useless. It can be seen from getMode: when the optionValue equals “OFFLINE”, it actually returns OPT mode, but not OFFLINE mode.

Pay attention to the class flex.Flag, where we can find several static configurations. I think “offline” is useless, because whenever it is used, they always first condition on Mode.OFFLINE. And because Mode.OFFLINE is useless, Flag.offline is useless.

Pay attention to Flag.FakeOT. Don’t set it to “true”, otherwise you will run the garbled circuits without actually using oblivious transfer. See gc.GCGenComp constructor for details.