Interface BrowseableBAMIndex

  • All Superinterfaces:
    AutoCloseable, BAMIndex, Closeable
    All Known Implementing Classes:
    SRAIndex

    public interface BrowseableBAMIndex
    extends BAMIndex
    An index interface with additional functionality for querying and inspecting the structure of a BAM index.
    • Method Detail

      • getLevelSize

        int getLevelSize​(int levelNumber)
        Gets the size (number of bins in) a given level of a BAM index.
        Parameters:
        levelNumber - Level for which to inspect the size.
        Returns:
        Size of the given level.
      • getLevelForBin

        int getLevelForBin​(Bin bin)
        Gets the level associated with the given bin number.
        Parameters:
        bin - The bin for which to determine the level.
        Returns:
        the level associated with the given bin number.
      • getFirstLocusInBin

        int getFirstLocusInBin​(Bin bin)
        Gets the first locus that this bin can index into.
        Parameters:
        bin - The bin to test.
        Returns:
        The last position that the given bin can represent.
      • getLastLocusInBin

        int getLastLocusInBin​(Bin bin)
        Gets the last locus that this bin can index into.
        Parameters:
        bin - The bin to test.
        Returns:
        The last position that the given bin can represent.
      • getBinsOverlapping

        BinList getBinsOverlapping​(int referenceIndex,
                                   int startPos,
                                   int endPos)
        Get a list of bins in the BAM file that may contain SAMRecords for the given range.
        Parameters:
        referenceIndex - sequence of desired SAMRecords
        startPos - 1-based start of the desired interval, inclusive
        endPos - 1-based end of the desired interval, inclusive
        Returns:
        a list of bins that contain relevant data.
      • getSpanOverlapping

        BAMFileSpan getSpanOverlapping​(Bin bin)
        Perform an overlapping query of all bins bounding the given location.
        Parameters:
        bin - The bin over which to perform an overlapping query.
        Returns:
        The file pointers