def parallel_realign_sample(sample_info, parallel_fn): """Realign samples, running in parallel over individual chromosomes. """ to_process = [] finished = [] for x in sample_info: if x[0]["config"]["algorithm"]["snpcall"]: to_process.append(x) else: finished.append(x) if len(to_process) > 0: file_key = "work_bam" split_fn = split_bam_by_chromosome("-realign.bam", file_key, default_targets=["nochr"]) processed = parallel_split_combine( to_process, split_fn, parallel_fn, "realign_sample", "combine_bam", file_key, ["config"] ) finished.extend(processed) return finished
def parallel_variantcall(sample_info, parallel_fn): """Provide sample genotyping, running in parallel over individual chromosomes. """ to_process = [] finished = [] for x in sample_info: if x[0]["config"]["algorithm"]["snpcall"]: to_process.append(x) else: finished.append(x) if len(to_process) > 0: split_fn = split_bam_by_chromosome("-variants.vcf", "work_bam") processed = parallel_split_combine(to_process, split_fn, parallel_fn, "variantcall_sample", "combine_variant_files", "vrn_file", ["sam_ref", "config"]) finished.extend(processed) return finished
def parallel_variantcall(sample_info, parallel_fn): """Provide sample genotyping, running in parallel over individual chromosomes. """ to_process = [] finished = [] for x in sample_info: if x[0]["config"]["algorithm"]["snpcall"]: to_process.append(x) else: finished.append(x) if len(to_process) > 0: split_fn = split_bam_by_chromosome("-variants.vcf", "work_bam") processed = parallel_split_combine(to_process, split_fn, parallel_fn, "variantcall_sample", "combine_variant_files", "vrn_file", ["sam_ref", "config"]) finished.extend(processed) return finished
def parallel_realign_sample(sample_info, parallel_fn): """Realign samples, running in parallel over individual chromosomes. """ to_process = [] finished = [] for x in sample_info: if x[0]["config"]["algorithm"]["snpcall"]: to_process.append(x) else: finished.append(x) if len(to_process) > 0: file_key = "work_bam" split_fn = split_bam_by_chromosome("-realign.bam", file_key, default_targets=["nochr"]) processed = parallel_split_combine(to_process, split_fn, parallel_fn, "realign_sample", "combine_bam", file_key, ["config"]) finished.extend(processed) return finished