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# Enumerated data type arguments

everywhereMember Posts: 4

I am working on a Queue script that uses the selectVariants walker. Two of the arguments that I am trying to use both use an enumerated type: restrictAllelesTo and selectTypeToInclude. I have tried passing these as strings however I get java type mismatch errors. What is the simplest way to pass these parameters to the selectVariant walker in the qscript?

Tagged:

Hi there,

Have a look at the presentations from our recent Queue workshop, I think we give some examples of how to pass the different types in there:

Geraldine Van der Auwera, PhD

• everywhereMember Posts: 4

Maybe it's my lack of understanding scala but I still can't pass an enumerated data type. The workshop shows this as an example:

@Argument(doc=”gender identity") // some object defined elsewhere
var gender: Gender = Gender.UNKNOWN

my code uses this
@Argument(doc="Select only variants of a particular allelicity.", shortName="restrictAllelesTo", required=false)
var rAT: restrictAllelesTo = restrictAllelesTo.BIALLELIC

I've even tried defining the object itself:

object restrictAllelesTo extends Enumeration {
type restrictAllelesTo = Value
val BIALLELIC, ALLELIC, BOTH = Value
}
import restrictAllelesTo._

##### ERROR ------------------------------------------------------------------------------------------

INFO 09:59:56,745 QCommandLine - Shutting down jobs. Please wait...

Here, I am not sure what to import (So, if there is some specific information/guide that will be great.

Thanks,
Amit