Package picard.illumina.parser

Class ClusterData

java.lang.Object
picard.illumina.parser.ClusterData
public class ClusterData extends Object
Store the information from Illumina files for a single cluster with one or more reads.

  • Constructor Details

    • ClusterData

      public ClusterData(ReadData... reads)
      Used for testing, reads is set directly with no copying to the input array

    • ClusterData

      public ClusterData(ReadType[] readTypes)
      Creates a ClusterData with one read for each type provided

  • Method Details

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • getTile

      public int getTile()

    • setTile

      public void setTile(int tile)

    • tileIsSet

      public boolean tileIsSet()

    • getRead

      public ReadData getRead(int index)

    • getNumReads

      public int getNumReads()

    • setOrCheckTile

      public void setOrCheckTile(int tile)
      Either set this value if not already set, or if already set, throw an exception if new value != current value.

    • getLane

      public int getLane()

    • setLane

      public void setLane(int lane)

    • laneIsSet

      public boolean laneIsSet()

    • setOrCheckLane

      public void setOrCheckLane(int lane)
      Either set this value if not already set, or if already set, throw an exception if new value != current value.

    • getX

      public int getX()

    • setX

      public void setX(int x)

    • xIsSet

      public boolean xIsSet()

    • setOrCheckX

      public void setOrCheckX(int x)
      Either set this value if not already set, or if already set, throw an exception if new value != current value.

    • getY

      public int getY()

    • setY

      public void setY(int y)

    • yIsSet

      public boolean yIsSet()

    • setOrCheckY

      public void setOrCheckY(int y)
      Either set this value if not already set, or if already set, throw an exception if new value != current value.

    • isPf

      public Boolean isPf()

    • setPf

      public void setPf(boolean pf)

    • setOrCheckPf

      public void setOrCheckPf(boolean pf)
      Either set this value if not already set, or if already set, throw an exception if new value != current value.

    • getMatchedBarcode

      public String getMatchedBarcode()
      Returns:
      The barcode matched (not the actual sequence from the read, which may not perfectly match the barcode).

    • setMatchedBarcode

      public void setMatchedBarcode(String matchedBarcode)