Package org.snpsift.annotate

Class VcfIndexTree

  • All Implemented Interfaces:
    java.lang.Iterable<org.snpeff.interval.Marker>, org.snpeff.interval.tree.Itree
    public class VcfIndexTree
extends java.lang.Object
implements org.snpeff.interval.tree.Itree
    Interval tree structure for an 'VcfIndexChromo' The whole tree is stored in a single class as a set of arrays. Nodes are referenced by index in the array
    Author:
    pcingola

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void add​(org.snpeff.interval.Marker interval)  
      void add​(org.snpeff.interval.Markers markers)  
      void build()  
      java.lang.String getChromosome()  
      org.snpeff.interval.Markers getIntervals()  
      boolean isEmpty()  
      boolean isInSync()  
      java.util.Iterator<org.snpeff.interval.Marker> iterator()  
      boolean load​(java.io.DataInputStream in)
      Read data from input stream
      void load​(java.lang.String fileName, org.snpeff.interval.Genome genome)  
      org.snpeff.interval.Markers query​(org.snpeff.interval.Interval queryMarker)
      Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'
      protected void query​(org.snpeff.interval.Interval queryMarker, int idx, org.snpeff.interval.Markers results)
      Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'
      protected void queryIntersects​(org.snpeff.interval.Interval queryMarker, int idx, org.snpeff.interval.Markers results)
      Query VCF entries intersecting 'marker' at node 'idx'
      void save​(java.io.DataOutputStream out)
      Save to output stream
      void setDebug​(boolean debug)  
      void setMaxBlockSize​(int maxBlockSize)  
      void setVcf​(org.snpeff.fileIterator.VcfFileIterator vcf)  
      void setVerbose​(boolean verbose)  
      int size()  
      org.snpeff.interval.Markers stab​(int point)  
      java.lang.String toString()  
      java.lang.String toString​(int idx)  
      java.lang.String toStringAll()  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator

    • Constructor Detail

      • VcfIndexTree

        public VcfIndexTree()

      • VcfIndexTree

        public VcfIndexTree​(org.snpeff.fileIterator.VcfFileIterator vcf,
                    VcfIndexDataChromo vcfIndexChromo)

    • Method Detail

      • add

        public void add​(org.snpeff.interval.Marker interval)
        Specified by:
        add in interface org.snpeff.interval.tree.Itree

      • add

        public void add​(org.snpeff.interval.Markers markers)
        Specified by:
        add in interface org.snpeff.interval.tree.Itree

      • build

        public void build()
        Specified by:
        build in interface org.snpeff.interval.tree.Itree

      • getChromosome

        public java.lang.String getChromosome()

      • getIntervals

        public org.snpeff.interval.Markers getIntervals()
        Specified by:
        getIntervals in interface org.snpeff.interval.tree.Itree

      • isEmpty

        public boolean isEmpty()
        Specified by:
        isEmpty in interface org.snpeff.interval.tree.Itree

      • isInSync

        public boolean isInSync()
        Specified by:
        isInSync in interface org.snpeff.interval.tree.Itree

      • iterator

        public java.util.Iterator<org.snpeff.interval.Marker> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<org.snpeff.interval.Marker>

      • load

        public boolean load​(java.io.DataInputStream in)
        Read data from input stream
        Returns:
        true on success

      • load

        public void load​(java.lang.String fileName,
                 org.snpeff.interval.Genome genome)
        Specified by:
        load in interface org.snpeff.interval.tree.Itree

      • query

        public org.snpeff.interval.Markers query​(org.snpeff.interval.Interval queryMarker)
        Query index to find all VCF entries intersecting 'marker' Store VCF entries in 'results'
        Specified by:
        query in interface org.snpeff.interval.tree.Itree

      • query

        protected void query​(org.snpeff.interval.Interval queryMarker,
                     int idx,
                     org.snpeff.interval.Markers results)
        Query index to find all VCF entries intersecting 'marker', starting from node 'idx' Store VCF entries in 'results'

      • queryIntersects

        protected void queryIntersects​(org.snpeff.interval.Interval queryMarker,
                               int idx,
                               org.snpeff.interval.Markers results)
        Query VCF entries intersecting 'marker' at node 'idx'

      • save

        public void save​(java.io.DataOutputStream out)
        Save to output stream

      • setDebug

        public void setDebug​(boolean debug)

      • setMaxBlockSize

        public void setMaxBlockSize​(int maxBlockSize)

      • setVcf

        public void setVcf​(org.snpeff.fileIterator.VcfFileIterator vcf)

      • setVerbose

        public void setVerbose​(boolean verbose)

      • size

        public int size()
        Specified by:
        size in interface org.snpeff.interval.tree.Itree

      • stab

        public org.snpeff.interval.Markers stab​(int point)
        Specified by:
        stab in interface org.snpeff.interval.tree.Itree

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • toString

        public java.lang.String toString​(int idx)

      • toStringAll

        public java.lang.String toStringAll()