DistanceEst has two distance estimation algorithms. --mle is the one that you implemented. --mean is a brain-dead difference between the mean observed aligned fragment size between two contigs assuming the gap between the two contigs is 0 (the contigs are adjacent) and the empirical population mean fragment size. The latter is much faster, particularly for mate-pair libraries.
DistanceEst has two distance estimation algorithms.
--mleis the one that you implemented.--meanis a brain-dead difference between the mean observed aligned fragment size between two contigs assuming the gap between the two contigs is 0 (the contigs are adjacent) and the empirical population mean fragment size. The latter is much faster, particularly for mate-pair libraries.