コード例 #1
0
def test_run_sambamba(tmpdir, bed_path, bam_path):
    out_path = tmpdir.join('ccds.coverage.bed')
    run_sambamba(bam_path,
                 bed_path,
                 outfile=str(out_path),
                 cov_thresholds=THRESHOLDS)
    assert out_path.exists()
コード例 #2
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def test_run_sambamba_missing(tmpdir, reset_path, bed_path, bam_path):
    out_path = tmpdir.join('ccds.coverage.bed')
    with pytest.raises(OSError):
        run_sambamba(bam_path,
                     bed_path,
                     outfile=str(out_path),
                     cov_thresholds=THRESHOLDS)
コード例 #3
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ファイル: sambamba.py プロジェクト: biocyberman/chanjo
def sambamba(context, bam_file, regions, cov_thresholds, outfile):
    """Run Sambamba from chanjo."""
    LOG.info("Running chanjo sambamba")
    try:
        run_sambamba(bam_file, regions, outfile, cov_thresholds)
    except Exception:
        LOG.exception('something went really wrong :_(')
        context.abort()
コード例 #4
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ファイル: test_sambamba.py プロジェクト: biocyberman/chanjo
def test_run_sambamba(tmpdir, bed_path, bam_path):
    out_path = tmpdir.join('ccds.coverage.bed')
    run_sambamba(bam_path, bed_path, outfile=str(out_path),
                 cov_thresholds=THRESHOLDS)
    assert out_path.exists()
コード例 #5
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ファイル: test_sambamba.py プロジェクト: biocyberman/chanjo
def test_run_sambamba_missing(tmpdir, reset_path, bed_path, bam_path):
    out_path = tmpdir.join('ccds.coverage.bed')
    with pytest.raises(OSError):
        run_sambamba(bam_path, bed_path, outfile=str(out_path),
                     cov_thresholds=THRESHOLDS)