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feat: secondary/supplementary alignments inherit from AuxAlignment #208

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@clintval clintval commented Dec 31, 2024

This is a draft PR to explore a common hierarchy for "alignments from SAM tags".

Motivated by:

The diff is ugly but there are only 3 classes. I suggest reviewing like:

I was able to make almost everything backwards compatible except:

  • SupplementaryAlignment is now a dataclass vs attrs
  • SupplementaryAlignment had a few init fields renamed

@tfenne what do you think?

I'm looking for a quick 👍 👎 so I can abandon the idea, or merge it into my actual feature branch for additional polish and a real round of review.

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codecov bot commented Dec 31, 2024

Codecov Report

Attention: Patch coverage is 87.73006% with 20 lines in your changes missing coverage. Please review.

Project coverage is 90.82%. Comparing base (2b4197c) to head (fb6825e).

Files with missing lines Patch % Lines
fgpyo/sam/__init__.py 87.73% 16 Missing and 4 partials ⚠️
Additional details and impacted files
@@                   Coverage Diff                    @@
##           cv_secondary_from_xb     #208      +/-   ##
========================================================
- Coverage                 91.48%   90.82%   -0.67%     
========================================================
  Files                        18       18              
  Lines                      2385     2431      +46     
  Branches                    350      354       +4     
========================================================
+ Hits                       2182     2208      +26     
- Misses                      133      149      +16     
- Partials                     70       74       +4     

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