Package org.snpsift.annotate

Class VcfIndex

  • public class VcfIndex
extends java.lang.Object
    An index for a VCF file
    Author:
    pcingola

    • Constructor Summary

      Constructors 
      Constructor Description
      VcfIndex​(java.lang.String fileName)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void add​(org.snpeff.vcf.VcfEntry ve, long filePos)
      Add an interval parse from 'line'
      void close()
      Close file and free memory
      org.snpeff.interval.Genome getGenome()  
      VcfIndexDataChromo getOrCreate​(java.lang.String chromosome)
      Get IntervalFileChromo by chromosome name.
      VcfIndexTree getTree​(java.lang.String chromosome)  
      org.snpeff.fileIterator.VcfFileIterator getVcf()  
      VcfIndexDataChromo getVcfIndexChromo​(java.lang.String chromosome)  
      void index()
      Load or create index
      protected void loadIndex​(java.lang.String indexFile)
      Load index form a file
      void open()
      Open file
      org.snpeff.interval.Markers query​(org.snpeff.interval.Marker marker)
      Query interval forest
      org.snpeff.vcf.VcfEntry read​(long fileIdx)
      Read a VcfEntry at position 'fileIdx'
      org.snpeff.vcf.VcfEntry read​(MarkerFile markerFile)
      Read a VcfEntry referenced by 'markerFile'
      void save​(java.lang.String indexFile)
      Save index file
      void setDebug​(boolean debug)  
      void setMaxBlockSize​(int maxBlockSize)  
      void setVerbose​(boolean verbose)  
      java.lang.String toString()  
      java.lang.String toStringAll()
      Show all entries

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • INDEX_FORMAT_VERSION

        public static int INDEX_FORMAT_VERSION

      • SHOW_EVERY

        public static int SHOW_EVERY

    • Constructor Detail

      • VcfIndex

        public VcfIndex​(java.lang.String fileName)

    • Method Detail

      • 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​(java.lang.String chromosome)
        Get IntervalFileChromo by chromosome name. Create a new one if it doesn't exists

      • getTree

        public VcfIndexTree getTree​(java.lang.String chromosome)

      • getVcf

        public org.snpeff.fileIterator.VcfFileIterator getVcf()

      • getVcfIndexChromo

        public VcfIndexDataChromo getVcfIndexChromo​(java.lang.String chromosome)

      • index

        public void index()
        Load or create index

      • loadIndex

        protected void loadIndex​(java.lang.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​(java.lang.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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • toStringAll

        public java.lang.String toStringAll()
        Show all entries