def _goleft_indexcov(bam_file, data, out_dir):
"""Use goleft indexcov to estimate coverage distributions using BAM index.
Only used for whole genome runs as captures typically don't have enough data
to be useful for index-only summaries.
"""
if not dd.get_coverage_interval(data) == "genome":
return []
out_dir = utils.safe_makedir(os.path.join(out_dir, "indexcov"))
out_files = [os.path.join(out_dir, "%s-indexcov.%s" % (dd.get_sample_name(data), ext))
for ext in ["roc", "ped", "bed.gz"]]
if not utils.file_uptodate(out_files[-1], bam_file):
with transaction.tx_tmpdir(data) as tmp_dir:
tmp_dir = utils.safe_makedir(os.path.join(tmp_dir, dd.get_sample_name(data)))
gender_chroms = [x.name for x in ref.file_contigs(dd.get_ref_file(data)) if chromhacks.is_sex(x.name)]
gender_args = "--sex %s" % (",".join(gender_chroms)) if gender_chroms else ""
cmd = "goleft indexcov --directory {tmp_dir} {gender_args} -- {bam_file}"
try:
do.run(cmd.format(**locals()), "QC: goleft indexcov")
except subprocess.CalledProcessError as msg:
if not ("indexcov: no usable" in str(msg) or
("indexcov: expected" in str(msg) and "sex chromosomes, found:" in str(msg))):
raise
for out_file in out_files:
orig_file = os.path.join(tmp_dir, os.path.basename(out_file))
if utils.file_exists(orig_file):
utils.copy_plus(orig_file, out_file)
# MultiQC needs non-gzipped/BED inputs so unpack the file
out_bed = out_files[-1].replace(".bed.gz", ".tsv")
if utils.file_exists(out_files[-1]) and not utils.file_exists(out_bed):
with transaction.file_transaction(data, out_bed) as tx_out_bed:
cmd = "gunzip -c %s > %s" % (out_files[-1], tx_out_bed)
do.run(cmd, "Unpack indexcov BED file")
out_files[-1] = out_bed
return [x for x in out_files if utils.file_exists(x)]
def _goleft_indexcov(bam_file, data, out_dir):
"""Use goleft indexcov to estimate coverage distributions using BAM index.
Only used for whole genome runs as captures typically don't have enough data
to be useful for index-only summaries.
"""
if not dd.get_coverage_interval(data) == "genome":
return []
out_dir = utils.safe_makedir(os.path.join(out_dir, "indexcov"))
out_files = [os.path.join(out_dir, "%s-indexcov.%s" % (dd.get_sample_name(data), ext))
for ext in ["roc", "ped", "bed.gz"]]
if not utils.file_uptodate(out_files[-1], bam_file):
with transaction.tx_tmpdir(data) as tmp_dir:
tmp_dir = utils.safe_makedir(os.path.join(tmp_dir, dd.get_sample_name(data)))
gender_chroms = [x.name for x in ref.file_contigs(dd.get_ref_file(data)) if chromhacks.is_sex(x.name)]
gender_args = "--sex %s" % (",".join(gender_chroms)) if gender_chroms else ""
cmd = "goleft indexcov --directory {tmp_dir} {gender_args} -- {bam_file}"
try:
do.run(cmd.format(**locals()), "QC: goleft indexcov")
except subprocess.CalledProcessError as msg:
if not ("indexcov: no usable" in str(msg) or
("indexcov: expected" in str(msg) and "sex chromosomes, found:" in str(msg))):
raise
for out_file in out_files:
orig_file = os.path.join(tmp_dir, os.path.basename(out_file))
if utils.file_exists(orig_file):
utils.copy_plus(orig_file, out_file)
# MultiQC needs non-gzipped/BED inputs so unpack the file
out_bed = out_files[-1].replace(".bed.gz", ".tsv")
if utils.file_exists(out_files[-1]) and not utils.file_exists(out_bed):
with transaction.file_transaction(data, out_bed) as tx_out_bed:
cmd = "gunzip -c %s > %s" % (out_files[-1], tx_out_bed)
do.run(cmd, "Unpack indexcov BED file")
out_files[-1] = out_bed
return [x for x in out_files if utils.file_exists(x)]