Package ngs

Interface PileupEvent

All Known Subinterfaces:
Pileup, PileupEventIterator, PileupIterator
public interface PileupEvent
Represents a single cell of a sparse 2D matrix with Reference coordinates on one axis and stacked Alignments on the other axis

  • Field Details

  • Method Details

    • getMappingQuality

      int getMappingQuality() throws ErrorMsg
      getMappingQuality
      Returns:
      the mapping quality
      Throws:
      ErrorMsg - upon an error accessing data

    • getAlignmentId

      String getAlignmentId() throws ErrorMsg
      getAlignmentId
      Returns:
      unique AlignmentId within ReadCollection
      Throws:
      ErrorMsg - upon an error accessing data

    • getAlignmentPosition

      long getAlignmentPosition() throws ErrorMsg
      getAlignmentPosition
      Returns:
      Position of the alignment in Reference coordinates
      Throws:
      ErrorMsg - upon an error accessing data

    • getFirstAlignmentPosition

      long getFirstAlignmentPosition() throws ErrorMsg
      getFirstAlignmentPosition
      Returns:
      the position of this Alignment's first event in Reference coordinates
      Throws:
      ErrorMsg - upon an error accessing data

    • getLastAlignmentPosition

      long getLastAlignmentPosition() throws ErrorMsg
      getLastAlignmentPosition
      Returns:
      the position of this Alignment's last event in INCLUSIVE Reference coordinates
      Throws:
      ErrorMsg - upon an error accessing data

    • getEventType

      int getEventType() throws ErrorMsg
      getEventType
      Returns:
      the type of event being represented
      Throws:
      ErrorMsg - upon an error accessing data

    • getAlignmentBase

      char getAlignmentBase() throws ErrorMsg
      getAlignmentBase
      Returns:
      retrieves base aligned at current Reference position
      Throws:
      ErrorMsg - if event is an insertion or deletion

    • getAlignmentQuality

      char getAlignmentQuality() throws ErrorMsg
      getAlignmentQuality
      Returns:
      retrieves base aligned at current Reference position
      Throws:
      ErrorMsg - if event is an insertion or deletion

    • getInsertionBases

      String getInsertionBases() throws ErrorMsg
      getInsertionBases
      Returns:
      bases corresponding to insertion event
      Throws:
      ErrorMsg - upon an error accessing data

    • getInsertionQualities

      String getInsertionQualities() throws ErrorMsg
      getInsertionQualities
      Returns:
      qualities corresponding to insertion event
      Throws:
      ErrorMsg - upon an error accessing data

    • getEventRepeatCount

      int getEventRepeatCount() throws ErrorMsg
      getEventRepeatCount
      Returns:
      the number of times this event repeats, i.e. the distance to the first reference position yielding a different event type for this alignment
      Throws:
      ErrorMsg - upon an error accessing data

    • getEventIndelType

      int getEventIndelType() throws ErrorMsg
      getEventIndelType
      Returns:
      detail about the type of indel when event type is an insertion or deletion
      Throws:
      ErrorMsg - upon an error accessing data