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.
MarkIlluminaAdapters Command line program to mark the location of adapter sequences.
 

Enum Summary
IlluminaBasecallsToFastq.ReadNameFormat Simple switch to control the read name format to emit.