broadinstitute / viral-classify

65%

master: 65%

Pull #53

github

Fix TestFilterLastal.test_filter_lastal_bam_polio for Ubuntu 24.04

Update expected output file for test_filter_lastal_bam_polio to match
results from LAST aligner on Ubuntu 24.04 (GitHub Actions runner).

The newer version of LAST (post-Ubuntu 20.04->24.04 upgrade in PR #51)
produces less spurious alignments, resulting in 3 additional coxsackievirus
read pairs being retained in the polio-filtered output:
- gi|743485545|gb|KM609478.1|_1615_2117_3:0:0_1:0:0_7
- gi|743485545|gb|KM609478.1|_4745_5304_2:0:1_2:0:0_6
- gi|743485545|gb|KM609478.1|_5348_5900_1:0:0_0:0:0_8

New expected file: test-reads.taxfilt.imperfect-2.bam (36 reads vs 30 previously)
Old expected file: test-reads.taxfilt.imperfect.bam (preserved for reference)

This fixes the CI failure on master after PR #51 merge.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

308 of 532 branches covered (57.89%)

Branch coverage included in aggregate %.

1604 of 2421 relevant lines covered (66.25%)

0.66 hits per line