Interface Index

    • Method Detail

      • getBlocks

        List<Block> getBlocks​(String chr,
                              int start,
                              int end)
        Query the index.
        Parameters:
        chr - the chromosome
        start - the start position
        end - the end position
        Returns:
        a list of blocks that contain the specified interval. Can never return null
        Throws:
        IllegalArgumentException - of chr isn't part of this index
      • isCurrentVersion

        boolean isCurrentVersion()
        Returns:
        true if the index is up to date, false otherwise
      • getSequenceNames

        List<String> getSequenceNames()
        Returns:
        a list of the sequence names we've seen during indexing, in order
      • containsChromosome

        boolean containsChromosome​(String chr)
        Parameters:
        chr - the chromosome (or contig) name
        Returns:
        true if we have an entry; false otherwise
      • write

        void write​(LittleEndianOutputStream stream)
            throws IOException
        all indexes are writable to disk
        Parameters:
        stream - the stream to write the index to. Caller must close after invocation.
        Throws:
        IOException - if the index is unable to write to the specified location
      • write

        default void write​(File idxFile)
                    throws IOException
        Writes the index into a file. Default implementation delegates to write(Path)
        Parameters:
        idxFile - Where to write the index.
        Throws:
        IOException - if the index is unable to write to the specified file
      • write

        void write​(Path indexPath)
            throws IOException
        Writes the index into a path.
        Parameters:
        indexPath - Where to write the index.
        Throws:
        IOException - if the index is unable to write to the specified path.
      • writeBasedOnFeatureFile

        default void writeBasedOnFeatureFile​(File featureFile)
                                      throws IOException
        Write an appropriately named and located Index file based on the name and location of the featureFile. Default implementation delegates to writeBasedOnFeaturePath(Path)
        Parameters:
        featureFile -
        Throws:
        IOException - if featureFile is not a normal file.
      • writeBasedOnFeaturePath

        void writeBasedOnFeaturePath​(Path featurePath)
                              throws IOException
        Write an appropriately named and located Index file based on the name and location of the featureFile. If featureFile is not a normal file, the index will silently not be written.
        Parameters:
        featurePath -
        Throws:
        IOException - if featureFile is not a normal file.
      • getProperties

        Map<String,​String> getProperties()
        Returns:
        get the list of properties for this index. Returns null if no properties.
      • equalsIgnoreProperties

        boolean equalsIgnoreProperties​(Object obj)
        Returns true if this and obj are 'effectively' equivalent indices. Ignores the time stamp on the file, as this may not be the same for even identical indices
        Parameters:
        obj -
        Returns: