Package org.snpsift.annotate

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