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I had the thought that this would work. Further thinking shows I'm wrong. The only way to get this to work is to have a pair-ordered sort/grouping (how I did this in biogo/boom). The general algorithm is here. This would require that we add a pair-based merger.
This will look like the
SortByCoordinate
example forMerger
but have a differentless
and ensure that pairs passed to thefn
matchQNAME
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