Package org.snpsift.annotate

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()