# Package picard.illumina

- Interface Summary
  Interface | Description
  --- | ---
  BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD> | Interface that defines a converter that takes ClusterData and returns OUTPUT_RECORD type objects.
  BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD> | Interface that defines a writer that will write out OUTPUT_RECORD type objects.

- Class Summary
  Class | Description
  --- | ---
  BarcodeExtractor | BarcodeExtractor is used to match barcodes and collect barcode match metrics.
  BarcodeExtractor.BarcodeMatch | Utility class to hang onto data about the best match for a given barcode
  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.
  BasecallsConverter<CLUSTER_OUTPUT_RECORD> | BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
  BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD> | BasecallsConverterBuilder creates and configures BasecallsConverter objects.
  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.
  CollectIlluminaBasecallingMetrics | A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
  CollectIlluminaLaneMetrics | Command-line wrapper around `CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector`.
  CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector | Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
  ExtractBarcodesProgram |
  ExtractIlluminaBarcodes | Determine the barcode for each read in an Illumina lane.
  ExtractIlluminaBarcodes.PerTileBarcodeExtractor | Extracts barcodes and accumulates metrics for an entire tile.
  IlluminaBasecallingMetrics | Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
  IlluminaBasecallsToFastq |
  IlluminaBasecallsToSam | IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM, BAM or CRAM file format.
  IlluminaLaneMetrics | Embodies characteristics that describe a lane.
  IlluminaPhasingMetrics | Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
  LanePhasingMetricsCollector | Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
  MarkIlluminaAdapters | Command line program to mark the location of adapter sequences.
  SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> | SortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
  UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> | UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).

- Enum Summary
  Enum | Description
  --- | ---
  DistanceMetric |
  IlluminaBasecallsToFastq.ReadNameFormat | Simple switch to control the read name format to emit.