Interface BAMIndex

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void close()
      Close the index and release any associated resources.
      BAMIndexMetaData getMetaData​(int reference)
      Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
      BAMFileSpan getSpanOverlapping​(int referenceIndex, int startPos, int endPos)
      Gets the compressed chunks which should be searched for the contents of records contained by the span referenceIndex:startPos-endPos, inclusive.
      long getStartOfLastLinearBin()
      Gets the start of the last linear bin in the index.
    • Method Detail

      • getSpanOverlapping

        BAMFileSpan getSpanOverlapping​(int referenceIndex,
                                       int startPos,
                                       int endPos)
        Gets the compressed chunks which should be searched for the contents of records contained by the span referenceIndex:startPos-endPos, inclusive. See the BAM spec for more information on how a chunk is represented.
        Parameters:
        referenceIndex - The contig.
        startPos - Genomic start of query.
        endPos - Genomic end of query.
        Returns:
        A file span listing the chunks in the BAM file.
      • getStartOfLastLinearBin

        long getStartOfLastLinearBin()
        Gets the start of the last linear bin in the index.
        Returns:
        The chunk indicating the start of the last bin in the linear index.
      • getMetaData

        BAMIndexMetaData getMetaData​(int reference)
        Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
        Parameters:
        reference - the reference of interest
        Returns:
        meta data for the reference
      • close

        void close()
        Close the index and release any associated resources.
        Specified by:
        close in interface AutoCloseable
        Specified by:
        close in interface Closeable