Support for array designs without coordinate/position information for features

[Nicklas Nordborg]

The current way of using an ArrayDesign with features is to lookup the reporter positioned at a given coordinate. There is a problem with this for platform which doesn't have a positioning system, for example Illumina. In this case you only know that a given set of reporters is present, but not their exact location. The current solution has been to generate "fake" coordinates by for example using block=1, column=1 and row=row number in file. The problem with this solution is that it only works if all data files are sorted in the same way. This is not always the case.

We propose that BASE can somehow be aware of that the positioning for some array designs are irrelevant. We can call these array design for virtual array design.

For backwards compatibility we must still generate fake coordinates, but this should be done in the background and need not be visible to importer file configurations. This means that the reporter map importer doesn't have to provide mappings for the block, row and column coordinates. This is done automatically by BASE in the background. For the raw data importer this means that array design validation should be done only with the reporter ID:s, not the coordinates. In the background BASE does still use fake coordinates, but this should never be visible externally.

This approach requires that a single reporter is only present once on the array desing, or that some pre-processing step has been performed that averages over identical reporters. This is exactly what is done with Illumina Beadstudio.