def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
coverage = cov.coverage(data, out_dir)
problem_regions = dd.get_problem_region_dir(data)
annotated = None
if problem_regions and priority:
annotated = cov.decorate_problem_regions(priority, problem_regions)
return None
def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
coverage = cov.coverage(data, out_dir)
problem_regions = dd.get_problem_region_dir(data)
annotated = None
if problem_regions and priority:
annotated = cov.decorate_problem_regions(priority, problem_regions)
return None
def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
out = dict()
total_reads = sambamba.number_of_reads(data, bam_file)
out['Total_reads'] = total_reads
mapped = sambamba.number_of_mapped_reads(data, bam_file)
out['Mapped_reads'] = mapped
if total_reads:
out['Mapped_reads_pct'] = 100.0 * mapped / total_reads
if mapped:
mapped_unique = sambamba.number_of_mapped_reads(data, bam_file, keep_dups=False)
out['Mapped_unique_reads'] = mapped
mapped_dups = mapped - mapped_unique
out['Duplicates'] = mapped_dups
out['Duplicates_pct'] = 100.0 * mapped_dups / mapped
if dd.get_coverage(data):
cov_bed_file = clean_file(dd.get_coverage(data), data, prefix="cov-", simple=True)
merged_bed_file = bedutils.merge_overlaps(cov_bed_file, data)
target_name = "coverage"
else:
merged_bed_file = dd.get_variant_regions_merged(data)
target_name = "variant_regions"
ontarget = sambamba.number_mapped_reads_on_target(
data, merged_bed_file, bam_file, keep_dups=False, target_name=target_name)
if mapped_unique:
out["Ontarget_unique_reads"] = ontarget
out["Ontarget_pct"] = 100.0 * ontarget / mapped_unique
out['Offtarget_pct'] = 100.0 * (mapped_unique - ontarget) / mapped_unique
padded_bed_file = bedutils.get_padded_bed_file(merged_bed_file, 200, data)
ontarget_padded = sambamba.number_mapped_reads_on_target(
data, padded_bed_file, bam_file, keep_dups=False, target_name=target_name + "_padded")
out["Ontarget_padded_pct"] = 100.0 * ontarget_padded / mapped_unique
if total_reads:
out['Usable_pct'] = 100.0 * ontarget / total_reads
avg_coverage = get_average_coverage(data, bam_file, merged_bed_file, target_name)
out['Avg_coverage'] = avg_coverage
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
region_coverage_file = cov.coverage_region_detailed_stats(data, out_dir)
# Re-enable with annotations from internally installed
# problem region directory
# if priority:
# annotated = cov.decorate_problem_regions(priority, problem_regions)
return out
def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
out = dict()
if dd.get_coverage(data):
bed_file = bedutils.merge_overlaps(dd.get_coverage(data), data)
target_name = "coverage"
elif dd.get_variant_regions_merged(data):
bed_file = dd.get_variant_regions_merged(data)
target_name = "variant_regions"
else:
bed_file = None
target_name = "wgs"
bed_file = clean_file(bed_file, data, prefix="cov-", simple=True)
offtarget_stats_file = calculate_offtarget_stats(bam_file, data, bed_file,
target_name)
if offtarget_stats_file and utils.file_exists(offtarget_stats_file):
with open(offtarget_stats_file) as in_handle:
stats = yaml.safe_load(in_handle)
offtarget = stats.get('offtarget')
mapped_unique = stats['mapped_unique']
if offtarget and mapped_unique:
out['offtarget_rate'] = 1.0 * offtarget / mapped_unique
mapped = stats['mapped']
if mapped:
out['Duplicates'] = mapped - mapped_unique
out['Duplicates_pct'] = 1.0 * (mapped - mapped_unique) / mapped
total_reads = stats['total_reads']
if total_reads:
out['usable_rate'] = 1.0 * (mapped_unique -
offtarget) / total_reads
avg_coverage = get_average_coverage(data, bam_file, bed_file, target_name)
out['avg_coverage'] = avg_coverage
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
region_coverage_file = cov.coverage_region_detailed_stats(data, out_dir)
# Re-enable with annotations from internally installed
# problem region directory
# if priority:
# annotated = cov.decorate_problem_regions(priority, problem_regions)
return out
def coverage_report(data):
"""
Run heavy coverage and variants process in parallel
"""
data = cov.coverage(data)
data = cov.variants(data)
data = cov.priority_coverage(data)
data = cov.priority_total_coverage(data)
problem_regions = dd.get_problem_region_dir(data)
name = dd.get_sample_name(data)
if "coverage" in data:
coverage = data['coverage']
annotated = None
if problem_regions and coverage:
annotated = cov.decorate_problem_regions(coverage, problem_regions)
data['coverage'] = {'all': coverage, 'problems': annotated}
return [[data]]
def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
out = dict()
total_reads = sambamba.number_of_reads(data, bam_file)
out['Total_reads'] = total_reads
mapped = sambamba.number_of_mapped_reads(data, bam_file)
out['Mapped_reads'] = mapped
if total_reads:
out['Mapped_reads_pct'] = 100.0 * mapped / total_reads
if mapped:
mapped_unique = sambamba.number_of_mapped_reads(data,
bam_file,
keep_dups=False)
out['Mapped_unique_reads'] = mapped
mapped_dups = mapped - mapped_unique
out['Duplicates'] = mapped_dups
out['Duplicates_pct'] = 100.0 * mapped_dups / mapped
if dd.get_coverage(data):
cov_bed_file = clean_file(dd.get_coverage(data),
data,
prefix="cov-",
simple=True)
merged_bed_file = bedutils.merge_overlaps(cov_bed_file, data)
target_name = "coverage"
else:
merged_bed_file = dd.get_variant_regions_merged(data)
target_name = "variant_regions"
ontarget = sambamba.number_mapped_reads_on_target(
data,
merged_bed_file,
bam_file,
keep_dups=False,
target_name=target_name)
if mapped_unique:
out["Ontarget_unique_reads"] = ontarget
out["Ontarget_pct"] = 100.0 * ontarget / mapped_unique
out['Offtarget_pct'] = 100.0 * (mapped_unique -
ontarget) / mapped_unique
padded_bed_file = bedutils.get_padded_bed_file(
merged_bed_file, 200, data)
ontarget_padded = sambamba.number_mapped_reads_on_target(
data,
padded_bed_file,
bam_file,
keep_dups=False,
target_name=target_name + "_padded")
out["Ontarget_padded_pct"] = 100.0 * ontarget_padded / mapped_unique
if total_reads:
out['Usable_pct'] = 100.0 * ontarget / total_reads
avg_coverage = get_average_coverage(data, bam_file, merged_bed_file,
target_name)
out['Avg_coverage'] = avg_coverage
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
region_coverage_file = cov.coverage_region_detailed_stats(data, out_dir)
# Re-enable with annotations from internally installed
# problem region directory
# if priority:
# annotated = cov.decorate_problem_regions(priority, problem_regions)
return out
def _run_coverage_qc(bam_file, data, out_dir):
"""Run coverage QC analysis"""
priority = cov.priority_coverage(data, out_dir)
cov.priority_total_coverage(data, out_dir)
coverage = cov.coverage(data, out_dir)