Package net.sf.picard.illumina

Interface Summary

IlluminaBasecallsConverter.ClusterDataConverter<OUTPUT_RECORD>
IlluminaBasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD>

Class Summary

CheckIlluminaDirectory	Program to check a lane of an Illumina output directory.
ClusterDataToSamConverter	Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.
ExtractIlluminaBarcodes	Determine the barcode for each read in an Illumina lane.
ExtractIlluminaBarcodes.BarcodeMetric	Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
IlluminaBasecallsConverter<CLUSTER_OUTPUT_RECORD>	Manages the conversion of Illumina basecalls into some output format.
IlluminaBasecallsToFastq
IlluminaBasecallsToSam	IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM or BAM file format.