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 = []
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"])
