Class CRAIIndex


  • public class CRAIIndex
    extends Object
    CRAI index used for CRAM files.
    • Constructor Detail

      • CRAIIndex

        public CRAIIndex()
    • Method Detail

      • addEntry

        public void addEntry​(CRAIEntry entry)
        Add a single entry to the CRAI index.
        Parameters:
        entry - entry to be added
      • addEntries

        public void addEntries​(Collection<CRAIEntry> toAdd)
        Add multiple entries to the CRAI index.
        Parameters:
        toAdd - entries to be added
      • writeIndex

        public void writeIndex​(OutputStream os)
        Write out the index to an output stream;
        Parameters:
        os - Stream to write index to
      • processContainer

        public void processContainer​(Container container)
        Create index entries for a single container.
        Parameters:
        container - the container to index
      • find

        public static List<CRAIEntry> find​(List<CRAIEntry> list,
                                           int seqId,
                                           int start,
                                           int span)
        Currently unused, but retained for the native rai query implementation
      • getLeftmost

        public static CRAIEntry getLeftmost​(List<CRAIEntry> list)
        Currently unused, but retained for the native rai query implementation
      • findLastAlignedEntry

        public static int findLastAlignedEntry​(List<CRAIEntry> list)
        Currently unused, but retained for the native rai query implementation