Differing numbers of interactions reported in seqmonk and washU output files

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Issue #10 resolved
Russell Hamilton created an issue

There appear to be different numbers of interactions reported in the seqmonk and washU format files (taking into account the 2 line vs 1 line format). Is this the expected outcome or should the numbers of interactions match?

The table below shows the line counts for a selection of my output files. Seqmonk and ibed are the same, but washU is consistently off by a few thousand

                 washU seqmonk  seqmonk/2   ibed
data1           123142  254394  127197      127198
data2           137212  281394  140697      140698
data3           149581  305370  152685      152686
dataMerged      171783  356412  178206      178207

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