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master: 72%

Ran 12 Jan 2026 12:39PM UTC

Files 24

Run time 3s

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Committed 12 Jan 2026 12:27PM UTC coverage: 70.787% (+0.2%) from 70.6%

Job # 20919342230.1

Build Type

Pull #160

github

Committed by

dpark01

Commit Message

Fix sambamba index to create .bai instead of .bam.bai

Sambamba index command creates {file}.bam.bai by default, but WDL
workflows expect {file}.bai naming convention. This caused Terra
workflow failures where the task succeeded (exit code 0) but the
required .bai files were not found during output delocalization.

The fix renames the index file after creation to match the expected
naming convention for compatibility with WDL workflows.

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

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4650 of 6569 relevant lines covered (70.79%)

0.71 hits per line

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master: 72%

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