20899680251
71%
master: 72%

Ran 11 Jan 2026 06:27PM UTC

Jobs 1

Files 25

Run time 1min

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Committed 11 Jan 2026 06:14PM UTC coverage: 70.954% (+0.4%) from 70.6%

Build # 20899680251

Build Type

Pull #160

github

Committed by

dpark01

Commit Message

Disable sambamba merge due to segfault bug in v1.0.1

- Raise NotImplementedError in sambamba.merge() with explanation
- Skip TestSambambaMerge tests with pytest.mark.skip
- Bug occurs on both ARM emulation and native x86 platforms
- Recommend using samtools merge or Picard MergeSamFiles instead

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Pull Request Pull Request #160: Optimize align_and_fix runtime with sambamba and skip_realign option

Run Details

115 of 133 new or added lines in 2 files covered. (86.47%)

4739 of 6679 relevant lines covered (70.95%)

0.71 hits per line

New Missed Lines in Diff

Lines	Coverage	∆	File
2	77.32	0.2%	read_utils.py
16	86.09		tools/sambamba.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	20899680251.1	11 Jan 2026 06:27PM UTC	25	70.95	GitHub Action Run

broadinstitute / viral-core / 20899680251
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master: 72%

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broadinstitute / viral-core / 20899680251 71% master: 72%

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broadinstitute / viral-core / 20899680251
71%
master: 72%

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