Package org.snpsift.annotate

Class VcfIndexDataChromo

  • public class VcfIndexDataChromo
extends java.lang.Object
    Represents a set of VCF entries stored in an (uncompressed) file All entries belong to the same chromosome
    Author:
    pcingola

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static int INITIAL_CAPACITY  

    • Constructor Summary

      Constructors 
      Constructor Description
      VcfIndexDataChromo​(org.snpeff.interval.Genome genome)  
      VcfIndexDataChromo​(org.snpeff.interval.Genome genome, java.lang.String chromosome)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void add​(int start, int end, long fileIdx)
      Add [start, end] => filePos
      long fileSize​(int startIdx, int endIdx)
      File size between startIdx and endIdx inclusive
      java.lang.String getChromosome()  
      int getEnd​(int idx)  
      long getFilePosEnd​(int idx)  
      long getFilePosStart​(int idx)  
      int getStart​(int idx)  
      boolean intersects​(int idx, int pos)
      Does interval at position 'idx' intersect positions 'pos'?
      boolean intersects​(int idx, org.snpeff.interval.Marker marker)
      Does interval at position 'idx' intersect 'marker'?
      org.snpeff.interval.Marker marker​(int idx)
      Create a marker form data at position 'idx'
      void setFilePosEnd​(long filePosEnd)  
      int size()  
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • VcfIndexDataChromo

        public VcfIndexDataChromo​(org.snpeff.interval.Genome genome)

      • VcfIndexDataChromo

        public VcfIndexDataChromo​(org.snpeff.interval.Genome genome,
                          java.lang.String chromosome)

    • Method Detail

      • add

        public void add​(int start,
                int end,
                long fileIdx)
        Add [start, end] => filePos

      • fileSize

        public long fileSize​(int startIdx,
                     int endIdx)
        File size between startIdx and endIdx inclusive

      • getChromosome

        public java.lang.String getChromosome()

      • getEnd

        public int getEnd​(int idx)

      • getFilePosEnd

        public long getFilePosEnd​(int idx)

      • getFilePosStart

        public long getFilePosStart​(int idx)

      • getStart

        public int getStart​(int idx)

      • intersects

        public boolean intersects​(int idx,
                          int pos)
        Does interval at position 'idx' intersect positions 'pos'?

      • intersects

        public boolean intersects​(int idx,
                          org.snpeff.interval.Marker marker)
        Does interval at position 'idx' intersect 'marker'?

      • marker

        public org.snpeff.interval.Marker marker​(int idx)
        Create a marker form data at position 'idx'

      • setFilePosEnd

        public void setFilePosEnd​(long filePosEnd)

      • size

        public int size()

      • toString

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