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) problem_regions = dd.get_problem_region_dir(data) name = dd.get_sample_name(data) coverage = data['coverage'] annotated = None if problem_regions and coverage: annotated = decorate_problem_regions(coverage, problem_regions) data['coverage'] = {'all': coverage, 'problems': annotated} return [[data]]