def _prep_grabix_indexes(in_files, dirs, config):
if in_files[0].endswith(".bam") and in_files[1] is None:
out = _bgzip_from_bam(in_files[0], dirs, config)
else:
out = [_bgzip_from_fastq(x, dirs, config) if x else None for x in in_files]
items = [[{"bgzip_file": x, "config": copy.deepcopy(config)}] for x in out if x]
run_multicore(_grabix_index, items, config,
config["algorithm"].get("num_cores", 1))
return out
def _do_merge(orig_files, out_file, config, region):
"""Do the actual work of merging with bcftools merge.
"""
if not utils.file_exists(out_file):
with file_transaction(out_file) as tx_out_file:
with short_filenames(run_multicore(p_bgzip_and_index, [[x, config] for x in orig_files], config)) as fs:
prep_files = " ".join(fs)
bcftools = config_utils.get_program("bcftools", config)
output_type = "z" if out_file.endswith(".gz") else "v"
region_str = "-r {}".format(region) if region else ""
cmd = "{bcftools} merge -o {output_type} {region_str} {prep_files} > {tx_out_file}"
do.run(cmd.format(**locals()), "Merge variants")
if out_file.endswith(".gz"):
bgzip_and_index(out_file, config)
return out_file
def parallel_combine_variants(orig_files, out_file, ref_file, config, run_parallel):
"""Combine variants in parallel by chromosome, concatenating final outputs.
"""
file_key = "vcf_files"
def split_by_region(data):
base, ext = utils.splitext_plus(os.path.basename(out_file))
args = []
for region in [x.name for x in ref.file_contigs(ref_file, config)]:
region_out = os.path.join(os.path.dirname(out_file), "%s-regions" % base,
"%s-%s%s" % (base, region, ext))
utils.safe_makedir(os.path.dirname(region_out))
args.append((region_out, ref_file, config, region))
return out_file, args
config = copy.deepcopy(config)
config["file_key"] = file_key
prep_files = run_multicore(p_bgzip_and_index, [[x, config] for x in orig_files], config)
items = [[{file_key: prep_files}]]
parallel_split_combine(items, split_by_region, run_parallel,
"merge_variant_files", "concat_variant_files",
file_key, ["region", "sam_ref", "config"], split_outfile_i=0)
return out_file
