broadinstitute / viral-core / 20390484207

70%

master: 70%

Build Type

Pull #149

github

Committed by dpark01

Commit Message

Add threading to bam2fq_pipe and auto-compression to idxstats output

- Add optional threads parameter to samtools bam2fq_pipe() with -@ flag
- Use 4 threads for BAM decompression in minimap2.idxstats()
- Replace open() with util.file.open_or_gzopen() for idxstats output files
  to support automatic compression based on file extension (.gz, .bz2, .zst, .lz4)

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

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

Pull Request Pull Request #149: Add threading to bam2fq_pipe and auto-compression to idxstats output

Run Details

9 of 10 new or added lines in 2 files covered. (90.0%)

1 existing line in 1 file now uncovered.

4386 of 6283 relevant lines covered (69.81%)

0.7 hits per line