Class VcfIndexTree

java.lang.Object
org.snpsift.annotate.VcfIndexTree
All Implemented Interfaces:
Iterable<org.snpeff.interval.Marker>, org.snpeff.interval.tree.Itree

public class VcfIndexTree extends 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
  • Field Details

  • Constructor Details

    • VcfIndexTree

      public VcfIndexTree()
    • VcfIndexTree

      public VcfIndexTree(org.snpeff.fileIterator.VcfFileIterator vcf, VcfIndexDataChromo vcfIndexChromo)
  • Method Details

    • 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 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 Iterator<org.snpeff.interval.Marker> iterator()
      Specified by:
      iterator in interface Iterable<org.snpeff.interval.Marker>
    • load

      public boolean load(DataInputStream in)
      Read data from input stream
      Returns:
      true on success
    • load

      public void load(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(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 String toString()
      Overrides:
      toString in class Object
    • toString

      public String toString(int idx)
    • toStringAll

      public String toStringAll()