Previously sequenced lines

[Scott Lee]

Hello!

Is there any way to provide lines that have already been sequenced and then build a diversity panel that will maximize diversity while including these lines?

Thanks!

Scott

[Herman De Beukelaer]

Dear Scott,

This feature has been previously requested and is currently under development. We are just about to release Core Hunter 3.1 and have included the requested feature on the roadmap for version 3.2. As soon as we have implemented it I will let you know here. If you want you could then experiment with a development snapshot and perhaps provide some feedback before we release v3.2.

May I ask what is the expected size of the datasets you want to analyze? We have plans to improve the scalability of Core Hunter as well. Feedback on this would also be highly appreciated.

Thanks,

Herman

Op donderdag 26 januari 2017 11:35:40 UTC-8 schreef Scott Lee:

[Herman De Beukelaer]

This feature has now been implemented. In the next release (v3.2) you will be able to specify a set of always and/or never selected accessions when executing Core Hunter. If you would like to experiment with this new feature before the next release, you could install the development snapshot from GitHub (using devtools):

library(devtools)

install_github("corehunter/corehunter3-r", ref = "develop")

Take a look at the new arguments always.selected and never.selected of sampleCore.

Feel free to share your experience with this new feature here.

[jframi]

Dear Herman,

I am interested by this feature. I installed the dev version from github, but I know get an error message when using the sampleCore function: 

> sel<-sampleCore(dist)

Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl,  :

  java.lang.NoSuchMethodException: No suitable method for the given parameters

Rolling back to the 3.1 version fixed the issue.

Do you have any suggestion?

Thanks,

JF

[Herman De Beukelaer]

Hi JF,

Strange, I am unable to reproduce this issue with the current development version. I ran

> dist <- exampleData()$dist

> sel <- sampleCore(dist)

and it works fine.

What is the output of sessionInfo()on your system?

Could you give more details about the code you are trying to run?

How did you read the data?

Herman

[jframi]

Hi Herman

Thanks for your reply,

While getting the information to reply to you, I figured out that my R session was not launched from my home directory, but from some /usr/local/java/ directory..

Quitting R and starting a new session from my home fixed the issue..

Sorry for posting a question too quickly!

JF