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
    • Method Detail

      • getMappingQuality

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

        java.lang.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

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

        java.lang.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