Package net.sf.basedb.plugins

Class IlluminaRawDataImporter

java.lang.Object
net.sf.basedb.core.plugin.AbstractPlugin
net.sf.basedb.plugins.AbstractFlatFileImporter
net.sf.basedb.plugins.IlluminaRawDataImporter
All Implemented Interfaces:
AutoDetectingImporter, InteractivePlugin, Plugin, SignalTarget
public class IlluminaRawDataImporter
extends AbstractFlatFileImporter
implements InteractivePlugin
An importer plug-in for Illumina raw data. The plug-in will create one or more raw bioassays from the data in the file. Optionally, it will add the raw bioassays to an experiment.

Since the data files doesn't have any coordinate information the importer will use one of the following methods.

  • If no array design has been selected or if the array design is using the FeatureIdentificationMethod.COORDINATES method for identifying features: The plug-in create fake coordinates like this: block=1, column=1, row=linenumber in file. The linenmbers start with 1 at the first data line, ie. header lines are not counted.
  • If the array design uses the FeatureIdentificationMethod.POSITION method for identiyfing features: The plug-in sets the position=line number in file. The linenmbers start with 1 at the first data line, ie. header lines are not counted.
  • If the array design uses the FeatureIdentificationMethod.FEATURE_ID method for identifying features. The plug-in assumes that the feature ID is the same as the reporter ID.

NOTE! Since the methods are not conflicting with each other, there will not be an actual check which method to use by this plug-in. We will simple set all values as specified above and let the BASE core handle the identification.

Version:
2.4
Author:
nicklas
Last modified
$Date: 2019-03-21 12:50:52 +0100 (tors, 21 mars 2019) $