Class VcfIndexDataChromo

java.lang.Object
org.snpsift.annotate.VcfIndexDataChromo

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

  • Constructor Details

    • VcfIndexDataChromo

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

      public VcfIndexDataChromo(org.snpeff.interval.Genome genome, String chromosome)
  • Method Details

    • 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 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 String toString()
      Overrides:
      toString in class Object