def parallel_variantcall_region(samples, run_parallel): """Perform variant calling and post-analysis on samples by region. """ to_process = [] extras = [] to_group = [] for x in samples: added = False for add in genotype.handle_multiple_variantcallers(x): added = True to_process.append(add) if not added: if "combine" in x[0] and x[0]["combine"].keys()[0] in x[0]: assert len(x) == 1 to_group.append(x[0]) else: extras.append(x) split_fn = _split_by_ready_regions("-variants.vcf.gz", "work_bam", genotype.get_variantcaller) if len(to_group) > 0: extras += group_combine_parts(to_group) return extras + grouped_parallel_split_combine(to_process, split_fn, multi.group_batches, run_parallel, "variantcall_sample", "split_variants_by_sample", "concat_variant_files", "vrn_file", ["region", "sam_ref", "config"])
def parallel_variantcall_region(samples, run_parallel): """Perform variant calling and post-analysis on samples by region. """ to_process = [] extras = [] to_group = [] for x in samples: added = False for add in genotype.handle_multiple_variantcallers(x): added = True to_process.append(add) if not added: if "combine" in x[0] and x[0]["combine"].keys()[0] in x[0]: assert len(x) == 1 to_group.append(x[0]) else: extras.append(x) split_fn = _split_by_ready_regions("-variants.vcf", "work_bam", genotype.get_variantcaller) if len(to_group) > 0: extras += group_combine_parts(to_group) return extras + grouped_parallel_split_combine( to_process, split_fn, multi.group_batches, run_parallel, "variantcall_sample", "split_variants_by_sample", "concat_variant_files", "vrn_file", ["region", "sam_ref", "config"])
def parallel_variantcall_region(samples, run_parallel): """Perform variant calling and post-analysis on samples by region. """ to_process = [] for x in samples: to_process.extend(genotype.handle_multiple_variantcallers(x)) split_fn = _split_by_ready_regions("-variants.vcf", "work_bam", genotype.get_variantcaller) return grouped_parallel_split_combine(to_process, split_fn, multi.group_batches, run_parallel, "variantcall_sample", "split_variants_by_sample", "combine_variant_files", "vrn_file", ["sam_ref", "config"])
def parallel_variantcall_region(samples, run_parallel): """Perform variant calling and post-analysis on samples by region. """ to_process = [] extras = [] for x in samples: added = False for add in genotype.handle_multiple_variantcallers(x): added = True to_process.append(add) if not added: extras.append(x) split_fn = _split_by_ready_regions("-variants.vcf", "work_bam", genotype.get_variantcaller) return extras + grouped_parallel_split_combine( to_process, split_fn, multi.group_batches, run_parallel, "variantcall_sample", "split_variants_by_sample", "concat_variant_files", "vrn_file", ["region", "sam_ref", "config"])
def parallel_variantcall_region(samples, run_parallel): """Perform variant calling and post-analysis on samples by region. """ to_process = [] extras = [] for x in samples: added = False for add in genotype.handle_multiple_variantcallers(x): added = True to_process.append(add) if not added: extras.append(x) split_fn = _split_by_ready_regions("-variants.vcf", "work_bam", genotype.get_variantcaller) return extras + grouped_parallel_split_combine(to_process, split_fn, multi.group_batches, run_parallel, "variantcall_sample", "split_variants_by_sample", "concat_variant_files", "vrn_file", ["region", "sam_ref", "config"])