def _run_delly(bam_files, chrom, ref_file, work_dir, items):
"""Run delly, calling structural variations for the specified type.
"""
batch = sshared.get_cur_batch(items)
ext = "-%s-svs" % batch if batch else "-svs"
out_file = os.path.join(
work_dir, "%s%s-%s.bcf" %
(os.path.splitext(os.path.basename(bam_files[0]))[0], ext, chrom))
final_file = "%s.vcf.gz" % (utils.splitext_plus(out_file)[0])
cores = min(
utils.get_in(items[0], ("config", "algorithm", "num_cores"), 1),
len(bam_files))
if not utils.file_exists(out_file) and not utils.file_exists(final_file):
with file_transaction(items[0], out_file) as tx_out_file:
if sshared.has_variant_regions(items, out_file, chrom):
exclude = ["-x", _delly_exclude_file(items, out_file, chrom)]
cmd = ["delly", "call", "-g", ref_file, "-o", tx_out_file
] + exclude + bam_files
multi_cmd = "export OMP_NUM_THREADS=%s && export LC_ALL=C && " % cores
try:
do.run(multi_cmd + " ".join(cmd),
"delly structural variant")
except subprocess.CalledProcessError as msg:
# delly returns an error exit code if there are no variants
if "No structural variants found" not in str(msg):
raise
return [_bgzip_and_clean(out_file, items)]
def _run_delly(bam_files, chrom, sv_type, ref_file, work_dir, items):
"""Run delly, calling structural variations for the specified type.
"""
batch = sshared.get_cur_batch(items)
ext = "-%s-svs" % batch if batch else "-svs"
out_file = os.path.join(work_dir, "%s%s-%s-%s.bcf"
% (os.path.splitext(os.path.basename(bam_files[0]))[0], ext, chrom, sv_type))
final_file = "%s.vcf.gz" % (utils.splitext_plus(out_file)[0])
cores = min(utils.get_in(items[0], ("config", "algorithm", "num_cores"), 1),
len(bam_files))
if not utils.file_exists(out_file) and not utils.file_exists(final_file):
with file_transaction(items[0], out_file) as tx_out_file:
if sshared.has_variant_regions(items, out_file, chrom):
exclude = ["-x", _delly_exclude_file(items, out_file, chrom)]
# uses -n to skip small indel detection for speed, not yet optimized:
# https://github.com/dellytools/delly/issues/36
cmd = ["delly", "call", "-n", "-t", sv_type, "-g", ref_file, "-o", tx_out_file] + exclude + bam_files
multi_cmd = "export OMP_NUM_THREADS=%s && export LC_ALL=C && " % cores
try:
do.run(multi_cmd + " ".join(cmd), "delly structural variant")
except subprocess.CalledProcessError as msg:
# delly returns an error exit code if there are no variants
if "No structural variants found" not in str(msg):
raise
return [_bgzip_and_clean(out_file, items)]
def _run_delly(bam_files, chrom, sv_type, ref_file, work_dir, items):
"""Run delly, calling structural variations for the specified type.
"""
batch = sshared.get_cur_batch(items)
ext = "-%s-svs" % batch if batch else "-svs"
out_file = os.path.join(work_dir, "%s%s-%s-%s.vcf"
% (os.path.splitext(os.path.basename(bam_files[0]))[0], ext, chrom, sv_type))
cores = min(utils.get_in(items[0], ("config", "algorithm", "num_cores"), 1),
len(bam_files))
if not utils.file_exists(out_file):
with file_transaction(items[0], out_file) as tx_out_file:
names = [tz.get_in(["rgnames", "sample"], x) for x in items]
if not sshared.has_variant_regions(items, out_file, chrom):
vcfutils.write_empty_vcf(tx_out_file, samples=names)
else:
exclude = ["-x", _delly_exclude_file(items, out_file, chrom)]
map_qual = ["--map-qual", "1"]
cmd = ["delly", "-t", sv_type, "-g", ref_file, "-o", tx_out_file] + exclude + bam_files
multi_cmd = "export OMP_NUM_THREADS=%s && export LC_ALL=C && " % cores
try:
do.run(multi_cmd + " ".join(cmd), "delly structural variant")
# Delly will write nothing if no variants found
if not utils.file_exists(tx_out_file):
vcfutils.write_empty_vcf(tx_out_file, samples=names)
except subprocess.CalledProcessError, msg:
# delly returns an error exit code if there are no variants
if "No structural variants found" in str(msg):
vcfutils.write_empty_vcf(tx_out_file, samples=names)
else:
raise
def _run_delly(bam_files, chrom, ref_file, work_dir, items):
"""Run delly, calling structural variations for the specified type.
"""
batch = sshared.get_cur_batch(items)
ext = "-%s-svs" % batch if batch else "-svs"
out_file = os.path.join(work_dir, "%s%s-%s.bcf"
% (os.path.splitext(os.path.basename(bam_files[0]))[0], ext, chrom))
final_file = "%s.vcf.gz" % (utils.splitext_plus(out_file)[0])
cores = min(utils.get_in(items[0], ("config", "algorithm", "num_cores"), 1),
len(bam_files))
if not utils.file_exists(out_file) and not utils.file_exists(final_file):
with file_transaction(items[0], out_file) as tx_out_file:
if sshared.has_variant_regions(items, out_file, chrom):
exclude = ["-x", _delly_exclude_file(items, out_file, chrom)]
cmd = ["delly", "call", "-g", ref_file, "-o", tx_out_file] + exclude + bam_files
multi_cmd = "export OMP_NUM_THREADS=%s && export LC_ALL=C && " % cores
try:
do.run(multi_cmd + " ".join(cmd), "delly structural variant")
except subprocess.CalledProcessError as msg:
# Small input samples, write an empty vcf
if "Sample has not enough data to estimate library parameters" in str(msg):
pass
# delly returns an error exit code if there are no variants
elif "No structural variants found" not in str(msg):
raise
return [_bgzip_and_clean(out_file, items)]
