Field Detail

• mIndex

  protected TabixReader.TIndex[] mIndex

Constructor Detail

• TabixReader

  public TabixReader​(String filePath)
              throws IOException

  Parameters:

  filePath - path to the data file/uri

  Throws:

  IOException

• TabixReader

  public TabixReader​(String filePath,
                     String indexPath)
              throws IOException

  Parameters:

  filePath - path to the of the data file/uri

  indexPath - Full path to the index file. Auto-generated if null

  Throws:

  IOException

• TabixReader

  public TabixReader​(String filePath,
                     String indexPath,
                     Function<SeekableByteChannel,​SeekableByteChannel> wrapper,
                     Function<SeekableByteChannel,​SeekableByteChannel> indexWrapper)
              throws IOException

  Parameters:

  filePath - path to the data file/uri

  indexPath - Full path to the index file. Auto-generated if null

  wrapper - a wrapper to apply to the raw byte stream of the data file if is a uri representing a Path

  indexWrapper - a wrapper to apply to the raw byte stream of the index file if it is a uri representing a Path

  Throws:

  IOException

• TabixReader

  public TabixReader​(String filePath,
                     SeekableStream stream)
              throws IOException

  Parameters:

  filePath - Path to the data file (used for error messages only)

  stream - Seekable stream from which the data is read

  Throws:

  IOException

• TabixReader

  public TabixReader​(String filePath,
                     String indexPath,
                     SeekableStream stream)
              throws IOException

  Parameters:

  filePath - Path to the data file (used for error messages only)

  indexPath - Full path to the index file. Auto-generated if null

  stream - Seekable stream from which the data is read

  Throws:

  IOException

• TabixReader

  public TabixReader​(String filePath,
                     String indexPath,
                     SeekableStream stream,
                     Function<SeekableByteChannel,​SeekableByteChannel> indexWrapper)
              throws IOException

  Parameters:

  filePath - Path to the data file (used for error messages only)

  indexPath - Full path to the index file. Auto-generated if null

  indexWrapper - a wrapper to apply to the raw byte stream of the index file if it is a uri representing a Path

  stream - Seekable stream from which the data is read

  Throws:

  IOException

Method Detail

• getSource

  public String getSource()

  return the source (filename/URL) of that reader

• readInt

  public static int readInt​(InputStream is)
                     throws IOException

  Throws:

  IOException

• readLong

  public static long readLong​(InputStream is)
                       throws IOException

  Throws:

  IOException

• readLine

  public static String readLine​(InputStream is)
                         throws IOException

  Throws:

  IOException

• readLine

  public String readLine()
                  throws IOException

  Read one line from the data file.

  Throws:

  IOException

• chr2tid

  public int chr2tid​(String chr)

  return chromosome ID or -1 if it is unknown

• getChromosomes

  public Set<String> getChromosomes()

  return the chromosomes in that tabix file

• parseReg

  public int[] parseReg​(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 and region_end. On failure, sequence_id==-1.

• query

  public TabixReader.Iterator query​(int tid,
                                    int beg,
                                    int end)

  Return

  Parameters:

  tid - Sequence id

  beg - beginning of interval, genomic coords

  end - end of interval, genomic coords

  Returns:

  an iterator over the lines within the specified interval

• query

  public TabixReader.Iterator query​(String reg)

  Parameters:

  reg - A region string of the form acceptable by parseReg(String)

  Returns:

  See Also:

  parseReg(String)

• query

  public TabixReader.Iterator query​(String reg,
                                    int start,
                                    int end)

  Parameters:

  reg - a chromosome

  start - start interval

  end - end interval

  Returns:

  a tabix iterator

  See Also:

  parseReg(String)

• close

  public void close()

• toString

  public String toString()

  Overrides:

  toString in class Object