def postprocess_alignment(data): """Perform post-processing steps required on full BAM files. Prepares list of callable genome regions allowing subsequent parallelization. """ data = cwlutils.normalize_missing(utils.to_single_data(data)) data = cwlutils.unpack_tarballs(data, data) bam_file = data.get("align_bam") or data.get("work_bam") if vmulti.bam_needs_processing(data) and bam_file and bam_file.endswith(".bam"): ref_file = dd.get_ref_file(data) out_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data))) bam_file_ready = os.path.join(out_dir, os.path.basename(bam_file)) if not utils.file_exists(bam_file_ready): utils.symlink_plus(bam_file, bam_file_ready) bam.index(bam_file_ready, data["config"]) covinfo = callable.sample_callable_bed(bam_file_ready, ref_file, data) callable_region_bed, nblock_bed, callable_bed = \ callable.block_regions(covinfo.raw_callable, bam_file_ready, ref_file, data) data["regions"] = {"nblock": nblock_bed, "callable": callable_bed, "sample_callable": covinfo.callable, "mapped_stats": readstats.get_cache_file(data)} data["depth"] = covinfo.depth_files data = coverage.assign_interval(data) if (os.path.exists(callable_region_bed) and not data["config"]["algorithm"].get("variant_regions")): data["config"]["algorithm"]["variant_regions"] = callable_region_bed data = clean_inputs(data) data = recalibrate.prep_recal(data) data = recalibrate.apply_recal(data) return [[data]]
def postprocess_alignment(data): """Perform post-processing steps required on full BAM files. Prepares list of callable genome regions allowing subsequent parallelization. """ data = cwlutils.normalize_missing(utils.to_single_data(data)) data = cwlutils.unpack_tarballs(data, data) bam_file = data.get("align_bam") or data.get("work_bam") ref_file = dd.get_ref_file(data) artifacts = gatk.collect_artifact_metrics(data) if artifacts: data = dd.update_summary_qc(data, "picard", artifacts.pop(), artifacts) oxog = gatk.collect_oxog_metrics(data) data = dd.update_summary_qc(data, "picard", oxog.pop(), oxog) if vmulti.bam_needs_processing(data) and bam_file and bam_file.endswith( ".bam"): out_dir = utils.safe_makedir( os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data))) bam_file_ready = os.path.join(out_dir, os.path.basename(bam_file)) if not utils.file_exists(bam_file_ready): utils.symlink_plus(bam_file, bam_file_ready) bam.index(bam_file_ready, data["config"]) covinfo = callable.sample_callable_bed(bam_file_ready, ref_file, data) callable_region_bed, nblock_bed = \ callable.block_regions(covinfo.raw_callable, bam_file_ready, ref_file, data) data["regions"] = { "nblock": nblock_bed, "callable": covinfo.raw_callable, "sample_callable": covinfo.callable, "mapped_stats": readstats.get_cache_file(data) } data["depth"] = covinfo.depth_files data = coverage.assign_interval(data) data = samtools.run_and_save(data) data = recalibrate.prep_recal(data) data = recalibrate.apply_recal(data) elif dd.get_variant_regions(data): callable_region_bed, nblock_bed = \ callable.block_regions(dd.get_variant_regions(data), bam_file, ref_file, data) data["regions"] = { "nblock": nblock_bed, "callable": dd.get_variant_regions(data), "sample_callable": dd.get_variant_regions(data) } return [[data]]
def prep_recal(*args): return recalibrate.prep_recal(*args)
def _recal_no_markduplicates(data): orig_config = copy.deepcopy(data["config"]) data["config"]["algorithm"]["mark_duplicates"] = False data = recalibrate.prep_recal(data)[0][0] data["config"] = orig_config return data