What is bp?

Without exactly knowing what you want I can tell you that your script seems to have 3 loops nested into each other which will make the running time of your script unbearable for non-trivial data. And your problem doesn't seem to need that.

How about this algorithm: Sort the ranges in ascending start position (you need to use a more complex data structure like Array-of-Arrays for this). Store the range of the first cluster into $xstart and $xend. For each new cluster (outer loop) test if the new cluster overlaps and if yes, count the overlap (inner loop) and update $xend with the end of the range

In reply to Re: Help the counting! by jethro
in thread Help the counting! by g-alone

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