bed_subtract() reports overlapping intervals in larger datasets #316
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In some cases
bed_subtract()
does not drop intervals that overlap. This behavior only occurs with larger datasets. This bug is due to assuming that the output fromfindOverlaps()
is sorted by coordinate, which is not always true when overlapping intervals are in different nodes of the interval tree.Below is an example. Calling
bed_subtract()
on the same bed data with ~20k rows returns a small number of intervals that should have been dropped. If the non-dropped intervals are rerun through bed_subtract() now they are successfully dropped.The proposed fix sorts the output from
findOverlaps()
by start coordinate, and has a negligible impact on performance.Performance with the proposed fix is ~0.5 sec per 1e6 random ivls.
Performance on current master also is ~0.5 sec per 1e6 random ivls.
Created on 2018-01-12 by the reprex package (v0.1.1.9000).