Replace HashMaps with a bit-vector for unique depth computation #201
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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/null
on this graph is now 90% printing stuff and 10% actual depth computation, so I think we'll call that good.