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_variants_qc(bam_file, data, out_dir): """Run variants QC analysis""" cov.variants(data, out_dir) return None