paulsengroup / hictk

Blazing fast toolkit to work with .hic and .cool files
MIT License
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Improve support for "square" Cooler files #225

Closed robomics closed 1 day ago

robomics commented 2 weeks ago

On a second thought, there are many operations on "square" Cooler files that work out of the box: basically everything except PixelSelector::fetch(range1, range2, ...) and friends.

So the right thing to do is to support opening "square" Cooler files, and throw an exception when one of the unsupported PixelSelector::fetch() method is called.

This would also be a good time to introduce appropriate checks in the hictk CLI:

codecov[bot] commented 2 weeks ago

Codecov Report

Attention: Patch coverage is 14.81481% with 69 lines in your changes missing coverage. Please review.

Project coverage is 74.37%. Comparing base (2d12134) to head (7265dd8). Report is 10 commits behind head on main.

Files with missing lines Patch % Lines
...hictk/file/include/hictk/impl/utils_merge_impl.hpp 0.00% 43 Missing :warning:
src/hictk/validate/validate.cpp 41.66% 7 Missing :warning:
src/hictk/cli/cli_convert.cpp 25.00% 6 Missing :warning:
src/hictk/cli/cli_zoomify.cpp 0.00% 3 Missing and 2 partials :warning:
...ler/include/hictk/cooler/impl/utils_merge_impl.hpp 25.00% 3 Missing :warning:
...oler/include/hictk/cooler/impl/validation_impl.hpp 40.00% 3 Missing :warning:
src/hictk/cli/cli_fix_mcool.cpp 50.00% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #225 +/- ## ========================================== - Coverage 74.59% 74.37% -0.23% ========================================== Files 144 144 Lines 12058 12090 +32 Branches 1384 1384 ========================================== - Hits 8995 8992 -3 - Misses 1945 1978 +33 - Partials 1118 1120 +2 ```

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robomics commented 1 day ago

Superseded by https://github.com/paulsengroup/hictk/pull/249.