Constructor Detail

• TabixFeatureReader

  public TabixFeatureReader​(String featureFile,
                            AsciiFeatureCodec codec)
                     throws IOException

  Parameters:

  featureFile - - path to a feature file. Can be a local file, http url, or ftp url

  codec -

  Throws:

  IOException

• TabixFeatureReader

  public TabixFeatureReader​(String featureFile,
                            String indexFile,
                            AsciiFeatureCodec codec)
                     throws IOException

  Parameters:

  featureFile - - path to a feature file. Can be a local file, http url, or ftp url

  indexFile - - path to the index file.

  codec -

  Throws:

  IOException

• TabixFeatureReader

  public TabixFeatureReader​(String featureFile,
                            String indexFile,
                            AsciiFeatureCodec codec,
                            Function<SeekableByteChannel,​SeekableByteChannel> wrapper,
                            Function<SeekableByteChannel,​SeekableByteChannel> indexWrapper)
                     throws IOException

  Parameters:

  featureFile - path to a feature file. Can be a local file, http url, or ftp url

  indexFile - path to the index file.

  wrapper - a wrapper to apply to the byte stream from the featureResource allowing injecting features like caching and prefetching of the stream, may be null, will only be applied if featureFile is a uri representing a Path

  indexWrapper - a wrapper to apply to the byte stream from the indexResource, may be null, will only be applied if indexFile is a uri representing a Path

  Throws:

  IOException

Method Detail

• hasIndex

  public boolean hasIndex()

  Description copied from class: AbstractFeatureReader
  Whether the reader has an index or not Default implementation returns false

  Overrides:

  hasIndex in class AbstractFeatureReader<T extends Feature,​SOURCE>

  Returns:

  false

• getSequenceNames

  public List<String> getSequenceNames()

  Description copied from interface: FeatureReader
  Provides the list of sequenceNames if known. Otherwise will return an empty list.

  Returns:

  the list of sequenceNames if known. Otherwise will return an empty list.

• query

  public CloseableTribbleIterator<T> query​(String chr,
                                           int start,
                                           int end)
                                    throws IOException

  Return iterator over all features overlapping the given interval

  Parameters:

  chr -

  start -

  end -

  Returns:

  Throws:

  IOException

• iterator

  public CloseableTribbleIterator<T> iterator()
                                       throws IOException

  Description copied from interface: FeatureReader
  Provides access to all the features in the reader

  Returns:

  an iterator to all the features in the reader

  Throws:

  IOException - If there's a problem reading.

• close

  public void close()
             throws IOException

  Description copied from interface: FeatureReader
  Closes the reader

  Throws:

  IOException