FlatGFA: A prototype odgi extract reimplementation
#165
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This is what odgi seems to do. In general, the big datasets don't have overlaps at all...
Now we can emit either plain GFA or FlatGFA.
No idea why this is showing up now.
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I wanted to try implementing a more complicated odgi operator, so I tried
odgi extract. I learned a lot and added to the library of stuff for interacting with FlatGFA data structures. Unfortunately, I can't really figure out exactly howodgi extractis supposed to work, so this doesn't match its behavior exactly. Something is weird about the way it finds a "neighborhood" of the selected segment that doesn't match my intuition. A closer look could perhaps make the two agree…