Package picard.illumina.parser

Class BaseIlluminaDataProvider

java.lang.Object
picard.illumina.parser.BaseIlluminaDataProvider
All Implemented Interfaces:
AutoCloseable, Iterable<ClusterData>, Iterator<ClusterData>
public abstract class BaseIlluminaDataProvider extends Object implements Iterator<ClusterData>, Iterable<ClusterData>, AutoCloseable
Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.

  • Field Details

    • FILE_NAME_PATTERN

      public static final Pattern FILE_NAME_PATTERN

    • lane

      protected final int lane

  • Constructor Details

    • BaseIlluminaDataProvider

      public BaseIlluminaDataProvider(int lane, OutputMapping outputMapping)

  • Method Details

    • iterator

      public Iterator<ClusterData> iterator()
      Specified by:
      iterator in interface Iterable<ClusterData>

    • close

      public abstract void close()
      Specified by:
      close in interface AutoCloseable

    • addData

      protected void addData(ClusterData clusterData, picard.illumina.parser.PositionalData posData)

    • addData

      protected void addData(ClusterData clusterData, picard.illumina.parser.PfData pfData)

    • addData

      protected void addData(ClusterData clusterData, picard.illumina.parser.BarcodeData barcodeData)

    • addReadData

      protected void addReadData(ClusterData clusterData, int numReads, picard.illumina.parser.BaseData baseData)

    • addReadData

      protected void addReadData(ClusterData clusterData, int numReads, picard.illumina.parser.QualityData qualityData)

    • addReadData

      protected void addReadData(ClusterData clusterData, int numReads, CbclData cbclData)

    • fileToTile

      public static Integer fileToTile(String fileName)