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()