Replace HashMaps with a bit-vector for unique depth computation#201
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Replace HashMaps with a bit-vector for unique depth computation#201
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On chr22 (already converted to FlatGFA), this seems like a pretty big performance win: depth goes from 14.7 to 2.2 seconds.
Further speeds up chr22 depth computation, from 2.2 to 2.0 seconds.
Seems to have no impact on performance, but it makes me feel better anyway.
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Just a low-hanging fruit optimization for this op: instead of a
Vec<HashMap<usize>>, we can use a singleBitVec.I did this in three steps and measured their performance on the chr22 GFA:
Anyway, a quick profiling run suggests that running
fgfa depth > /dev/nullon this graph is now 90% printing stuff and 10% actual depth computation, so I think we'll call that good.