Package org.snpsift.annotate

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