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fix: sum_of_base_qualities()
returns zero when a record has no base qualities
#212
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WalkthroughThe pull request introduces changes to the 📜 Recent review detailsConfiguration used: CodeRabbit UI 📒 Files selected for processing (1)
🚧 Files skipped from review as they are similar to previous changes (1)
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Actionable comments posted: 1
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
Plan: Pro
📒 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.
Codecov ReportAll modified and coverable lines are covered by tests ✅
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 ☔ View full report in Codecov by Sentry. |
sum_of_base_qualities()
returns zero when a record has no base qualities
Closes #210