Class VariantBnd

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.Variant
org.snpeff.interval.VariantBnd
All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, TxtSerializable
public class VariantBnd extends Variant
A 'BND' variant (i.e. translocation) consisting of two endpoints
Author:
pcingola
See Also:

  • Constructor Details

    • VariantBnd

      public VariantBnd()

    • VariantBnd

      public VariantBnd(Marker parent, int start, String ref, String alt, Chromosome chrTr, int startTr, boolean left, boolean before)

  • Method Details

    • getEndPoint

      public Marker getEndPoint()

    • isBefore

      public boolean isBefore()

    • isBnd

      public boolean isBnd()
      Overrides:
      isBnd in class Variant

    • isLeft

      public boolean isLeft()

    • isStructural

      public boolean isStructural()
      Overrides:
      isStructural in class Variant

    • query

      public Markers query(IntervalForest intervalForest)
      Return a collection of intervals that intersect both ends of this variant
      Overrides:
      query in class Marker

    • realignLeft

      public Variant realignLeft()
      Description copied from class: Variant
      Create a new variant realigning it towards the leftmost position
      Overrides:
      realignLeft in class Variant

    • toString

      public String toString()
      Overrides:
      toString in class Variant