Interface FeatureReader<T extends Feature>

    • Method Detail

      • query

        CloseableTribbleIterator<T> query​(String chr,
                                          int start,
                                          int end)
                                   throws IOException
        Query the reader for a particular interval corresponding to a contig and a 1-based closed
        Parameters:
        chr - the contig to be queried
        start - the start of the interval (1-based) to be queried
        end - the last base in the interval to be queried
        Returns:
        an iterator containing the features that at in the interval.
        Throws:
        IOException - If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.
      • query

        default CloseableTribbleIterator<T> query​(Locatable locus)
                                           throws IOException
        Query the reader for a particular interval corresponding to a contig and a 1-based closed
        Parameters:
        locus - The locus to be queried
        Returns:
        an iterator containing the features that at in the interval.
        Throws:
        IOException - If there's a problem reading or if the reader is not queryable, e.g. if it doesn't have an index.
      • getSequenceNames

        List<String> getSequenceNames()
        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.
      • getHeader

        Object getHeader()
        Provide access to the header of the reader
        Returns:
        the header of the reader. May be null.
      • isQueryable

        default boolean isQueryable()
        Returns:
        true if the reader has an index, which means that it can be queried. Must be implemented to return true if the implementation supports query(Locatable)