Class TabixReader

  • All Implemented Interfaces:
    java.lang.Iterable<java.lang.String>

    public class TabixReader
    extends java.lang.Object
    implements java.lang.Iterable<java.lang.String>
    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected boolean showHeader  
    • Constructor Summary

      Constructors 
      Constructor Description
      TabixReader​(java.lang.String fileName)  
      TabixReader​(java.lang.String fileName, boolean debug)  
    • Field Detail

      • showHeader

        protected boolean showHeader
    • Constructor Detail

      • TabixReader

        public TabixReader​(java.lang.String fileName)
                    throws java.io.IOException
        Throws:
        java.io.IOException
      • TabixReader

        public TabixReader​(java.lang.String fileName,
                           boolean debug)
                    throws java.io.IOException
        Throws:
        java.io.IOException
    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
      • readInt

        public static int readInt​(java.io.InputStream is)
                           throws java.io.IOException
        Throws:
        java.io.IOException
      • readLong

        public static long readLong​(java.io.InputStream is)
                             throws java.io.IOException
        Throws:
        java.io.IOException
      • chr2tid

        protected int chr2tid​(java.lang.String chr)
      • close

        public void close()
      • getFilePointer

        public long getFilePointer()
      • getmBc

        public int getmBc()
      • getmEc

        public int getmEc()
      • getmMeta

        public int getmMeta()
      • getmPreset

        public int getmPreset()
      • getmSc

        public int getmSc()
      • iterator

        public TabixIterator iterator()
        Specified by:
        iterator in interface java.lang.Iterable<java.lang.String>
      • parseReg

        public int[] parseReg​(java.lang.String reg)
        Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
        Parameters:
        reg - Region string
        Returns:
        An array where the three elements are [ sequence_id, region_begin, region_end] On failure, sequence_id==-1.
      • query

        public TabixIterator query​(java.lang.String reg)
        Return an iterator for the interval in this query Format: "chr:star-end"
      • readIndex

        public void readIndex()
                       throws java.io.IOException
        Read the Tabix index from the default file.
        Throws:
        java.io.IOException
      • readIndex

        public void readIndex​(java.io.File fp)
                       throws java.io.IOException
        Read the Tabix index from a file
        Parameters:
        fp - File pointer
        Throws:
        java.io.IOException
      • readLine

        public java.lang.String readLine()
                                  throws java.io.IOException
        Read one line from the data file.
        Throws:
        java.io.IOException
      • setDebug

        public void setDebug​(boolean debug)
      • setShowHeader

        public void setShowHeader​(boolean showHeader)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object