Class VcfIndex

java.lang.Object
org.snpsift.annotate.VcfIndex

public class VcfIndex extends Object
An index for a VCF file
Author:
pcingola
  • Field Details

    • INDEX_FORMAT_VERSION

      public static int INDEX_FORMAT_VERSION
    • SHOW_EVERY

      public static int SHOW_EVERY
    • INDEX_EXT

      public static final String INDEX_EXT
      See Also:
  • Constructor Details

    • VcfIndex

      public VcfIndex(String fileName)
  • Method Details

    • add

      public void add(org.snpeff.vcf.VcfEntry ve, long filePos)
      Add an interval parse from 'line'
    • close

      public void close()
      Close file and free memory
    • getGenome

      public org.snpeff.interval.Genome getGenome()
    • getOrCreate

      public VcfIndexDataChromo getOrCreate(String chromosome)
      Get IntervalFileChromo by chromosome name. Create a new one if it doesn't exists
    • getTree

      public VcfIndexTree getTree(String chromosome)
    • getVcf

      public org.snpeff.fileIterator.VcfFileIterator getVcf()
    • getVcfIndexChromo

      public VcfIndexDataChromo getVcfIndexChromo(String chromosome)
    • index

      public void index()
      Load or create index
    • loadIndex

      protected void loadIndex(String indexFile)
      Load index form a file
    • open

      public void open()
      Open file
    • query

      public org.snpeff.interval.Markers query(org.snpeff.interval.Marker marker)
      Query interval forest
    • read

      public org.snpeff.vcf.VcfEntry read(long fileIdx)
      Read a VcfEntry at position 'fileIdx'
    • read

      public org.snpeff.vcf.VcfEntry read(MarkerFile markerFile)
      Read a VcfEntry referenced by 'markerFile'
    • save

      public void save(String indexFile)
      Save index file
    • setDebug

      public void setDebug(boolean debug)
    • setMaxBlockSize

      public void setMaxBlockSize(int maxBlockSize)
    • setVerbose

      public void setVerbose(boolean verbose)
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • toStringAll

      public String toStringAll()
      Show all entries