taffy norm -d greedily filters out rows corresponding to duplications that would, if left in, prevent blocks from getting merged. It seemed to work okay on chr22 from a big alignment, but crashed when I tried whole-genome. This PR fixes a few things, which gets it working on the problem region I'd extracted when it first failed
taffy norm -dgreedily filters out rows corresponding to duplications that would, if left in, prevent blocks from getting merged. It seemed to work okay on chr22 from a big alignment, but crashed when I tried whole-genome. This PR fixes a few things, which gets it working on the problem region I'd extracted when it first failed