Improve support for "square" Cooler files

[robomics]

No description provided.

[robomics]

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:

• balance: should be possible (TODO double check)
• convert: does not make sense
• dump: should be possible except when dumping selected regions of the pixel table
• fix-mcool: broken for "square" Cooler files. Throw an error
• load: requires a lot of work in order to support "square" Cooler files (need to rewrite parts of Cooler::Index)
• merge: same as load
• metadata: no changes required
• rename-chromosomes: no changes required
• validate: need to think a bit about what can be done here
• zoomify: same as load

[codecov]

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 ⚠️
src/hictk/validate/validate.cpp	41.66%	7 Missing ⚠️
src/hictk/cli/cli_convert.cpp	25.00%	6 Missing ⚠️
src/hictk/cli/cli_zoomify.cpp	0.00%	3 Missing and 2 partials ⚠️
...ler/include/hictk/cooler/impl/utils_merge_impl.hpp	25.00%	3 Missing ⚠️
...oler/include/hictk/cooler/impl/validation_impl.hpp	40.00%	3 Missing ⚠️
src/hictk/cli/cli_fix_mcool.cpp	50.00%	2 Missing ⚠️

Additional details and impacted files

@@            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]

Superseded by #249.