Class DiskBasedBAMFileIndex

    • Method Detail

      • getSpanOverlapping

        public BAMFileSpan getSpanOverlapping​(int referenceIndex,
                                              int startPos,
                                              int endPos)
        Get list of regions of 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:
        array of pairs of virtual file positions. Each pair is the first and last virtual file position in a range that can be scanned to find SAMRecords that overlap the given positions. The last position in each pair is a virtual file pointer to the first SAMRecord beyond the range that may contain the indicated SAMRecords.