Fig. 2

Overview of the chrom-sweep interval intersection algorithm. The chrom-sweep algorithm sweeps from left to right as it progresses along each chromosome. Green intervals from the query VCF in the first row are annotated by annotation files A (blue) and B (orange) in the second and third rows, respectively. The cache row indicates which intervals are currently in the cache at each point in the progression of the sweeping algorithm. Intervals enter the cache in order of their chromosomal start position. First A1 enters the cache followed by Q1. Since Q1 intersects A1, they are associated, as are Q1 and B1 when B1 enters the cache. Each time a new query interval enters the cache, any interval it does not intersect is ejected. Therefore, when Q2 enters the cache, Q1 and A1 are ejected. Since Q1 is a query interval, it is sent to be reported as output. Proceeding to the right, A2 and then Q3 enter the cache; the latter is a query interval and so the intervals that do not overlap it—B1, Q2, and A2—are ejected from the cache with the query interval, Q2, which is sent to the caller. Finally, as we reach the end of the incoming intervals, we clear out the final Q3 interval and finalize the output for this chromosome. EOF: End of File