def tiered_alignment(in_bam, tier_num, multi_mappers, extra_args, genome_build,
pair_stats, work_dir, dirs, config):
"""Perform the alignment of non-mapped reads from previous tier.
"""
nomap_fq1, nomap_fq2 = select_unaligned_read_pairs(
in_bam, "tier{}".format(tier_num), work_dir, config)
if nomap_fq1 is not None:
base_name = "{}-tier{}out".format(
os.path.splitext(os.path.basename(in_bam))[0], tier_num)
config = copy.deepcopy(config)
dirs = copy.deepcopy(dirs)
config["algorithm"]["bam_sort"] = "queryname"
config["algorithm"]["multiple_mappers"] = multi_mappers
config["algorithm"]["extra_align_args"] = [
"-i", int(pair_stats["mean"]),
int(pair_stats["std"])
] + extra_args
out_bam, ref_file = align_to_sort_bam(
nomap_fq1,
nomap_fq2,
lane.rg_names(base_name, base_name, config),
genome_build,
"novoalign",
dirs,
config,
dir_ext=os.path.join("hydra",
os.path.split(nomap_fq1)[0]))
return out_bam
else:
return None
def tiered_alignment(in_bam, tier_num, multi_mappers, extra_args,
genome_build, pair_stats,
work_dir, dirs, config):
"""Perform the alignment of non-mapped reads from previous tier.
"""
nomap_fq1, nomap_fq2 = select_unaligned_read_pairs(in_bam, "tier{}".format(tier_num),
work_dir, config)
if nomap_fq1 is not None:
base_name = "{}-tier{}out".format(os.path.splitext(os.path.basename(in_bam))[0],
tier_num)
config = copy.deepcopy(config)
dirs = copy.deepcopy(dirs)
config["algorithm"]["bam_sort"] = "queryname"
config["algorithm"]["multiple_mappers"] = multi_mappers
config["algorithm"]["extra_align_args"] = ["-i", int(pair_stats["mean"]),
int(pair_stats["std"])] + extra_args
out_bam, ref_file = align_to_sort_bam(nomap_fq1, nomap_fq2,
lane.rg_names(base_name, base_name, config),
genome_build, "novoalign",
dirs, config,
dir_ext=os.path.join("hydra", os.path.split(nomap_fq1)[0]))
return out_bam
else:
return None