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[bug]: fix handling of Cooler v2 files lacking the "storage-mode" attribute #339

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merged 1 commit into from
Feb 25, 2025

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@robomics robomics commented Feb 25, 2025

According to Cooler docs:

Version 3 introduces the storage-mode metadata attribute to accomodate square matrices that are non-symmetric. Version 2 files which lack the storage-mode attribute should be interpreted as using the “symmetric-upper” storage mode. See Storage mode.

Given this, the check we had in place was too strict.

@robomics robomics added the bug Something isn't working label Feb 25, 2025
@robomics robomics changed the title Fix handling of Cooler v2 files lacking the "storage-mode" attribute [bug]: fix handling of Cooler v2 files lacking the "storage-mode" attribute Feb 25, 2025
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codecov bot commented Feb 25, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 77.35%. Comparing base (2bd1af2) to head (1a444c7).
Report is 2 commits behind head on main.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #339      +/-   ##
==========================================
+ Coverage   77.31%   77.35%   +0.03%     
==========================================
  Files         175      175              
  Lines       21436    21440       +4     
  Branches     2326     2327       +1     
==========================================
+ Hits        16574    16584      +10     
+ Misses       3848     3843       -5     
+ Partials     1014     1013       -1     
Flag Coverage Δ
[tests integration](https://app.codecov.io/gh/paulsengroup/hictk/pull/339/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=paulsengroup) 67.85% <100.00%> (+0.01%)
[tests unittests](https://app.codecov.io/gh/paulsengroup/hictk/pull/339/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=paulsengroup) 75.81% <0.00%> (-0.02%)

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@robomics robomics merged commit 435a213 into main Feb 25, 2025
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@robomics robomics deleted the fix/cooler-v2 branch February 25, 2025 20:34
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