Interface BrowseableBAMIndex

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

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

    • 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