In collapseClones and DistToNearest foreach implementation is suppressing errors

[Robert Amezquita]

Both have error handling == "pass" - why?

"That seems terrible" -Jason

[ssnn]

I will change handling to 'stop'. With pass, the error was returned as an error object, and distToNearest would fail in the next step, when attempting to convert the list into a data.frame. See 895a0e8

[Jason Vander Heiden]

The bigger question is "why is it producing an error in the first place"?

[ssnn]

I needed an error for testing purposes, so I forced an error by commenting the sequence validation part in the code and changing the 'A's in one the junctions to 'J'. Then, nearestDist, which is the function called inside foreach, results in an error, because 'J' is not a valid DNA character.

[Jason Vander Heiden]

Ah, so the errors that it wants to pass are invalid character errors. okay.

[ssnn]

895a0e8