[FEATURE] Track occupancy in IBF #257
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
seqan-actions
added
lint
|
Documentation preview available at https://docs.seqan.de/preview/seqan/hibf/257 |
eseiler
force-pushed
the
feature/dynamic
branch
from
8a9524c to
758f80e
Compare
seqan-actions
added
lint
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #257 +/- ##
=======================================
Coverage 99.59% 99.59%
=======================================
Files 51 52 +1
Lines 1973 1996 +23
Branches 5 5
=======================================
+ Hits 1965 1988 +23
Misses 8 8 ☔ View full report in Codecov by Sentry. |
eseiler
force-pushed
the
feature/dynamic
branch
from
758f80e to
bb09d78
Compare
seqan-actions
added
lint
eseiler
force-pushed
the
feature/dynamic
branch
from
bb09d78 to
55017fc
Compare
seqan-actions
added
lint
smehringer
reviewed
Dec 12, 2024
| @@ -51,7 +51,9 @@ seqan::hibf::interleaved_bloom_filter construct_ibf(robin_hood::unordered_flat_s | |||
| local_index_allocation_timer.start(); | |||
| seqan::hibf::interleaved_bloom_filter ibf{bin_count, | |||
| bin_size, | |||
| seqan::hibf::hash_function_count{data.config.number_of_hash_functions}}; | |||
| seqan::hibf::hash_function_count{data.config.number_of_hash_functions}, | |||
| data.config.empty_bin_fraction > 0.0}; | |||
There was a problem hiding this comment.
Suggested change
| data.config.empty_bin_fraction > 0.0}; | |
| data.config.empty_bin_fraction > 0.0}; // track occupancy if handling empty bins |
| ibf.emplace(value, bin_idx); | ||
| } | ||
|
|
||
| assert(chunk_view.size() <= number_of_bins); | ||
| // Edge case: If there are not enough k-mers to emplace at least one value into each bin, set the occupancy of |
There was a problem hiding this comment.
Suggested change
| // Edge case: If there are not enough k-mers to emplace at least one value into each bin, set the occupancy of | |
| // Small number edge case: If there are not enough k-mers to emplace at least one value into each bin, set the occupancy of |
eseiler
force-pushed
the
feature/dynamic
branch
from
55017fc to
6f8ad12
Compare
seqan-actions
added
lint
eseiler
force-pushed
the
feature/dynamic
branch
from
6f8ad12 to
e9e25fe
Compare
seqan-actions
added
lint
eseiler
force-pushed
the
feature/dynamic
branch
from
e9e25fe to
5b8980e
Compare
seqan-actions
added
lint
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
Blocked by