Deprecate set_pair_info and _set_mate_info for set_mate_info

[clintval]

I notice we have two implementations for setting mate info on a pair of alignments.

I've refactored for the following reasons:

• set_pair_info():
  • Unnecessarily disallows unmapped reads
  • Uses assert instead of raise, which can be turned off at runtime
  • Does not set mate quality tag (MQ)
  • Does not set mate score tag (ms)
  • Defaults proper pair status to True (it's easy to forget to change this)
  • Forces you to override the "properly paired" status with True/False
• _set_mate_info():
  • Looks like a direct translation of HTSJDK's implementation (it can be simpler with pysam)
  • Does not always cleanup mate cigar tag (MC)
  • Does not set mate quality tag (MQ)
  • Does not set mate score tag (ms)
  • Forces a reset of properly paired status

Now we have:

• set_pair_info(): annotated as deprecated to avoid an API break
• set_mate_info(): a more useful function for setting mate info on alignments
• set_as_pairs(): this behavior was in set_pair_info() so it is now a sole function

Questions?

• Is it worth keeping set_as_pairs()? What was the motivation for this functionality?
• Since we are still pre-v1, can we remove set_pair_info() without deprecating first?

Along the way I found a bug in SamBuilder.add_pair() and fixed that too.

If initial code review is favorable, I can go and add more unit tests.

[codecov]

Codecov Report

Attention: Patch coverage is 96.96970% with 1 line in your changes missing coverage. Please review.

Project coverage is 90.96%. Comparing base (f9aa849) to head (81cea38).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
fgpyo/sam/__init__.py	96.15%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #202      +/-   ##
==========================================
- Coverage   91.31%   90.96%   -0.36%     
==========================================
  Files          18       18              
  Lines        2281     2257      -24     
  Branches      334      329       -5     
==========================================
- Hits         2083     2053      -30     
- Misses        126      133       +7     
+ Partials       72       71       -1     

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[tfenne]

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[coderabbitai]

Walkthrough

The pull request introduces significant modifications to the SAM/BAM file handling in the fgpyo library. Key changes include adding two new functions in __init__.py: sum_of_base_qualities for calculating base quality scores and set_mate_info for managing mate pair information. The SamBuilder class in builder.py has been simplified by removing the internal mate information setting method and now uses the external set_mate_info function. A minor version update for the typing_extensions dependency was made in pyproject.toml. The test suite has been correspondingly updated to validate these new functions and changes, with enhanced assertions for read record properties and mate information handling.

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📥 Commits

Reviewing files that changed from the base of the PR and between 657d3f4 and 81cea38.

📒 Files selected for processing (1)

• fgpyo/sam/__init__.py (3 hunks)

🧰 Additional context used

🪛 GitHub Check: codecov/patch

fgpyo/sam/__init__.py

[warning] 892-892: fgpyo/sam/init.py#L892
Added line #L892 was not covered by tests

🔇 Additional comments (3)

fgpyo/sam/__init__.py (3)

816-831: LGTM: Efficient implementation of base quality summation.

Implementation matches samtools fixmate behavior.

---

833-867: LGTM: Comprehensive mate info handling.

Correctly sets all mate-related tags and flags, including proper handling of unmapped reads.

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869-892: Add test coverage for the proper_pair lambda.

Line 892 needs test coverage for the lambda function passed to set_mate_info.

Want me to generate test cases for this scenario?

🧰 Tools

🪛 GitHub Check: codecov/patch

[warning] 892-892: fgpyo/sam/init.py#L892
Added line #L892 was not covered by tests

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