Package org.snpeff.vcf

Class FileIndexChrPos

  • public class FileIndexChrPos
extends java.lang.Object
    Index a file that has "chr \t pos" as the beginning of a line (e.g. VCF) WARNING: It is assumed that the file is ordered by position (chromosome order does not matter)
    Author:
    pcingola

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static int POS_OFFSET  

    • Constructor Summary

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

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void close()
      Close file
      java.lang.String dump​(java.lang.String chr, int posStart, int posEnd, boolean toString)
      Dump all lines in the interval chr:posStart-posEnd
      long find​(java.lang.String chr, int pos, boolean lessEq)
      Find the position in the file for the first character of the first line equal or less than a specific chr:pos
      byte get​(long bytePosition)
      Get a byte from a file
      byte[] get​(long bytePosition, int len)
      Read 'len' bytes after 'bytePosition' or until a '\n' is reached.
      java.util.Set<java.lang.String> getChromos()
      Available chromosomes
      long getEnd​(java.lang.String chr)
      Get position where 'chr' ends
      FileIndexChrPos.LineAndPos getLine​(long pos)
      Get the line where 'pos' hits
      FileIndexChrPos.LineAndPos getLineSlow​(long pos)
      A slow method for getLine
      long getStart​(java.lang.String chr)
      Get position where 'chr' starts
      void index()
      Index chromosomes in the whole file
      void open()
      Open file and initiate mappings
      int pos​(java.lang.String line)
      The position argument of a line (second column in tab-separated format).
      void setDebug​(boolean debug)  
      void setVerbose​(boolean verbose)  
      long size()
      File size
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • FileIndexChrPos

        public FileIndexChrPos​(java.lang.String fileName)

    • Method Detail

      • close

        public void close()
        Close file

      • dump

        public java.lang.String dump​(java.lang.String chr,
                             int posStart,
                             int posEnd,
                             boolean toString)
        Dump all lines in the interval chr:posStart-posEnd
        Parameters:
        chr - : Chromosome
        posStart - : Start coordinate in chromosome (zero-based)
        posEnd - : End coordinate in chromosome (zero-based)
        toString - : Return a sting with file contents?
        Returns:
        If toString is 'true', return a string with file's content between those coordinates (this is used only for test cases and debugging)

      • find

        public long find​(java.lang.String chr,
                 int pos,
                 boolean lessEq)
        Find the position in the file for the first character of the first line equal or less than a specific chr:pos

      • get

        public byte get​(long bytePosition)
        Get a byte from a file

      • get

        public byte[] get​(long bytePosition,
                  int len)
        Read 'len' bytes after 'bytePosition' or until a '\n' is reached. If len is negative, read 'abs(len)' bytes before bytePosition or until '\n' is reached
        Parameters:
        bytePosition -
        len -
        Returns:
        An array of 'len' bytes. null if either end of file (len > 0) or beginning of file (len < 0)

      • getChromos

        public java.util.Set<java.lang.String> getChromos()
        Available chromosomes
        Returns:

      • getEnd

        public long getEnd​(java.lang.String chr)
        Get position where 'chr' ends
        Parameters:
        chr -
        Returns:
        -1 if 'chr' is not in the index

      • getLine

        public FileIndexChrPos.LineAndPos getLine​(long pos)
        Get the line where 'pos' hits
        Returns:
        A string with the line that 'pos' hits, null if it's out of boundaries

      • getStart

        public long getStart​(java.lang.String chr)
        Get position where 'chr' starts
        Parameters:
        chr -
        Returns:
        -1 if 'chr' is not in the index

      • index

        public void index()
        Index chromosomes in the whole file

      • open

        public void open()
        Open file and initiate mappings

      • pos

        public int pos​(java.lang.String line)
        The position argument of a line (second column in tab-separated format). Negative if not found
        Returns:
        The position argument of a line. Negative if not found

      • setDebug

        public void setDebug​(boolean debug)

      • setVerbose

        public void setVerbose​(boolean verbose)

      • size

        public long size()
        File size

      • toString

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