Package org.snpeff.interval

Class SpliceSiteRegion

java.lang.Object
org.snpeff.interval.Interval
org.snpeff.interval.Marker
org.snpeff.interval.SpliceSite
org.snpeff.interval.SpliceSiteRegion
All Implemented Interfaces:
Serializable, Cloneable, Comparable<Interval>, TxtSerializable
public class SpliceSiteRegion extends SpliceSite
Interval for a splice site acceptor From Sequence Ontology: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron.
Author:
pcingola
See Also:

  • Constructor Details

    • SpliceSiteRegion

      public SpliceSiteRegion()

    • SpliceSiteRegion

      public SpliceSiteRegion(Exon parent, int start, int end, boolean strandMinus, String id)

    • SpliceSiteRegion

      public SpliceSiteRegion(Intron parent, int start, int end, boolean strandMinus, String id)

  • Method Details

    • intersectsCoreSpliceSite

      public boolean intersectsCoreSpliceSite(Marker marker)
      Description copied from class: SpliceSite
      Core splice sites are defined as CORE_SPLICE_SITE_SIZE bases after exon end or before exon begins. Usually CORE_SPLICE_SITE_SIZE is 2 bases. Other spice sites are considered "non-core".
      Specified by:
      intersectsCoreSpliceSite in class SpliceSite

    • isExonPart

      public boolean isExonPart()

    • isIntronPart

      public boolean isIntronPart()