uci-cbcl/genomix — pull request #145 by jakebiesinger (2014-04-09 23:27:14+00:00)
Title: Scaffolding options are now commandline options.

If you want to override the defaults, you have to set the values explicitly like so:

-scaffold_removeOtherOutgoing true -scaffold_removeOtherIncoming true -scaffold_candidatesScoreWalk true -scaffold_delayPrune true -scaffold_earlyStop false -scaffold_expandCandidateBranchMaxDistance 20