Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Support variable bin sizes #81

Merged
merged 29 commits into from
Dec 15, 2023
Merged

Support variable bin sizes #81

merged 29 commits into from
Dec 15, 2023

Conversation

robomics
Copy link
Contributor

@robomics robomics commented Dec 6, 2023

  • Rename BinTable to BinTableFixed
  • Implement BinTableVariable to support operating on tables with variable bin size
  • BinTable is now a wrapper around BinTableFixed and BinTableVariable
  • Update Reference to store the prefix sum of the chromosome sizes
  • Fix minor bug in Reference ctor when constructing reference from iterators of chromosomes
  • Update hictk load to support loading interactions using tables of variable bin size
  • Update hictk merge to support merging interactions using tables of variable bin size

- Rename BinTable to BinTableFixed
- Implement BinTableVariable to support operating on tables with
  variable bin size
- BinTable is now a wrapper around BinTableFixed and BinTableVariable
- Update Reference to stor the prefix sum of the chromosome sizes
- Fix minor bug in Reference ctor when constructing reference from
  iterators of chromosomes
Copy link

codecov bot commented Dec 6, 2023

Codecov Report

Attention: 75 lines in your changes are missing coverage. Please review.

Comparison is base (d9727c0) 83.65% compared to head (80965a7) 83.92%.
Report is 5 commits behind head on main.

Files Patch % Lines
...ble/include/hictk/impl/bin_table_variable_impl.hpp 87.83% 23 Missing ⚠️
..._table/include/hictk/impl/bin_table_fixed_impl.hpp 92.14% 15 Missing ⚠️
src/hictk/cli/cli_load.cpp 68.42% 6 Missing ⚠️
...include/hictk/cooler/impl/file_validation_impl.hpp 0.00% 4 Missing ⚠️
...ler/include/hictk/cooler/impl/utils_merge_impl.hpp 50.00% 4 Missing ⚠️
...erval/include/hictk/impl/genomic_interval_impl.hpp 88.23% 4 Missing ⚠️
src/hictk/cli/cli_zoomify.cpp 25.00% 3 Missing ⚠️
src/hictk/load/load.cpp 94.33% 3 Missing ⚠️
...oler/include/hictk/cooler/impl/validation_impl.hpp 0.00% 3 Missing ⚠️
src/hictk/convert/cool_to_hic.cpp 33.33% 2 Missing ⚠️
... and 5 more
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #81      +/-   ##
==========================================
+ Coverage   83.65%   83.92%   +0.27%     
==========================================
  Files          91       96       +5     
  Lines        6742     7111     +369     
==========================================
+ Hits         5640     5968     +328     
- Misses       1102     1143      +41     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

@robomics robomics changed the title Refactor BinTable and initial implementation of BinTableVariable Support variable bin sizes Dec 6, 2023
@robomics robomics merged commit a6c1b48 into main Dec 15, 2023
50 checks passed
@robomics robomics deleted the cooler/variable-bins branch December 15, 2023 14:18
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

1 participant