When creating a setup file Piper can add R1 and R2 in an arbitrary order (no matter the sort order of the input). This can screw things up strand-specific applications. This could either be resolved by fixing the setupFileCreator, or by checking the ordering in the SetupXMLReader.
When creating a setup file Piper can add R1 and R2 in an arbitrary order (no matter the sort order of the input). This can screw things up strand-specific applications. This could either be resolved by fixing the setupFileCreator, or by checking the ordering in the SetupXMLReader.