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