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()
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)
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()
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()
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)
