Examples with ProcessingContext au.edu.wehi.idsv.ProcessingContext used on opensource projects

Example 46 with ProcessingContext

use of au.edu.wehi.idsv.ProcessingContext in project gridss by PapenfussLab.

the class StaticDeBruijnPathGraphGexfExporterTest method getCommandlineContext.

@Override
public ProcessingContext getCommandlineContext() {
    ProcessingContext pc = super.getCommandlineContext();
    pc.getAssemblyParameters().errorCorrection.maxBaseMismatchForCollapse = 1;
    pc.getAssemblyParameters().errorCorrection.collapseBubblesOnly = true;
    pc.getConfig().getVisualisation().assemblyGraph = true;
    pc.getConfig().getVisualisation().directory.mkdirs();
    return pc;
}