def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
coverage = cov.coverage(data, out_dir)
problem_regions = dd.get_problem_region_dir(data)
annotated = None
if problem_regions and priority:
annotated = cov.decorate_problem_regions(priority, problem_regions)
return None
def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
coverage = cov.coverage(data, out_dir)
problem_regions = dd.get_problem_region_dir(data)
annotated = None
if problem_regions and priority:
annotated = cov.decorate_problem_regions(priority, problem_regions)
return None
def coverage_report(data):
"""
Run heavy coverage and variants process in parallel
"""
data = cov.coverage(data)
data = cov.variants(data)
data = cov.priority_coverage(data)
data = cov.priority_total_coverage(data)
problem_regions = dd.get_problem_region_dir(data)
name = dd.get_sample_name(data)
if "coverage" in data:
coverage = data['coverage']
annotated = None
if problem_regions and coverage:
annotated = cov.decorate_problem_regions(coverage, problem_regions)
data['coverage'] = {'all': coverage, 'problems': annotated}
return [[data]]
def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
coverage = cov.coverage(data, out_dir)