Package htsjdk.tribble

Class TabixFeatureReader<T extends Feature,SOURCE>

java.lang.Object
htsjdk.tribble.AbstractFeatureReader<T,SOURCE>
htsjdk.tribble.TabixFeatureReader<T,SOURCE>
All Implemented Interfaces:
FeatureReader<T>, Closeable, AutoCloseable
public class TabixFeatureReader<T extends Feature,SOURCE> extends AbstractFeatureReader<T,SOURCE>
Since:
2/11/12

  • Constructor Details

    • 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 Details

    • 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