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fix: sum_of_base_qualities() returns zero when a record has no base qualities #212

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merged 4 commits into from
Jan 23, 2025
Merged

fix: sum_of_base_qualities() returns zero when a record has no base qualities #212

merged 4 commits into from
Jan 23, 2025

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msto
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@msto msto commented Jan 13, 2025

Closes #210

@msto msto requested review from nh13, tfenne and clintval as code owners January 13, 2025 18:24
msto
msto commented Jan 13, 2025
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Walkthrough

The pull request introduces changes to the sum_of_base_qualities function in the fgpyo/sam/__init__.py file, enhancing its handling of records with no base qualities. The function's docstring is updated to clarify its return value of 0 for such cases. A new check is added to handle scenarios where rec.query_qualities is None or indicates unavailable qualities. Additionally, constants related to unavailable string field information and query qualities are modified and introduced. In the test file tests/fgpyo/sam/test_sam.py, a new test function is added to assess the function's behavior with unmapped AlignedSegment records, ensuring that the sum of base qualities is correctly calculated as zero when no qualities are present.

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  • fgpyo/sam/init.py

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Actionable comments posted: 1

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between b0b4227 and 0261da9.

📒 Files selected for processing (3)
  • fgpyo/sam/__init__.py (1 hunks)
  • fgpyo/util/inspect.py (1 hunks)
  • tests/fgpyo/sam/test_sam.py (2 hunks)
🧰 Additional context used
🪛 GitHub Actions: Python package
fgpyo/util/inspect.py

[error] 460-460: "str" not callable [operator]

🔇 Additional comments (4)
fgpyo/sam/__init__.py (2)

852-854: Documentation improvement aligns with samtools fixmate.

Clear explanation of zero return value behavior for records without base qualities.

Also applies to: 860-862

867-869: Explicit None check handles edge case correctly.

Early return of 0 matches samtools fixmate implementation.

tests/fgpyo/sam/test_sam.py (2)

621-643: Test setup is well documented.

Clear explanation of why temporary file is needed. Good reference to issue #211 for future improvement.

643-645: Test verifies core functionality.

Confirms zero return value when query_qualities is None.

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clintval
clintval reviewed Jan 13, 2025
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.09%. Comparing base (b0b4227) to head (4ef48d1).
Report is 3 commits behind head on main.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #212      +/-   ##
==========================================
+ Coverage   91.06%   91.09%   +0.03%     
==========================================
  Files          18       18              
  Lines        2283     2291       +8     
  Branches      337      338       +1     
==========================================
+ Hits         2079     2087       +8     
  Misses        133      133              
  Partials       71       71

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msto
msto commented Jan 21, 2025
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@msto msto requested a review from clintval January 21, 2025 21:30
@clintval clintval removed their assignment Jan 22, 2025
clintval
clintval reviewed Jan 22, 2025
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@msto msto changed the title fix: sum_of_base_qualities should be zero when a read has no base qualities fix: sum_of_base_qualities() returns zero when a record has no base qualities Jan 23, 2025
@msto msto merged commit f1f89e9 into main Jan 23, 2025
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@msto msto deleted the ms_fix-sum-of-query-qualities branch January 23, 2025 19:44
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@clintval clintval clintval approved these changes

@coderabbitai coderabbitai[bot] coderabbitai[bot] approved these changes

@nh13 nh13 Awaiting requested review from nh13 nh13 is a code owner

@tfenne tfenne Awaiting requested review from tfenne tfenne is a code owner

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Successfully merging this pull request may close these issues.

sum_of_base_qualities raises TypeError if the received record has no base qualities
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@msto @nh13 @clintval