def square_off(samples, run_parallel): """Perform joint calling at all variants within a batch. """ to_process = [] extras = [] for data in [x[0] for x in samples]: added = False if tz.get_in(("metadata", "batch"), data): for add in genotype.handle_multiple_callers(data, "jointcaller"): if _is_jointcaller_compatible(add): added = True to_process.append([add]) if not added: extras.append([data]) processed = grouped_parallel_split_combine( to_process, _split_by_callable_region, multi.group_batches_joint, run_parallel, "square_batch_region", "concat_variant_files", "vrn_file", ["region", "sam_ref", "config"]) return _combine_to_jointcaller(processed) + extras
def square_off(samples, run_parallel): """Perform joint calling at all variants within a batch. """ to_process = [] extras = [] for data in [x[0] for x in samples]: added = False if tz.get_in(("metadata", "batch"), data): for add in genotype.handle_multiple_callers(data, "jointcaller"): if _is_jointcaller_compatible(add): added = True to_process.append([add]) if not added: extras.append([data]) processed = grouped_parallel_split_combine(to_process, _split_by_callable_region, multi.group_batches_joint, run_parallel, "square_batch_region", "concat_variant_files", "vrn_file", ["region", "sam_ref", "config"]) return _combine_to_jointcaller(processed) + extras