[WIP] Rewrite bubble detection. #181
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Handle nested bubbles, so that only their outer bubbles are collapsed. Fix bubbles with paths of length 1 and 0 (indels).
…n outside of range
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Based on #161, this branch attempts to reimplement bubble detection to guard against overlapping bubbles.
Mirror branch is in this repository at branch
skip-cluster-bubble-rewrite-bubbling.