def apply_genotypes_to_vcf(src_vcf, out_vcf, genotypes, sample, sum_quals):
# initializations
bnd_cache = {}
src_vcf.write_header(out_vcf)
total_variants = len(list(vcf_variants(src_vcf.filename)))
for i, vline in enumerate(vcf_variants(src_vcf.filename)):
v = vline.rstrip().split('\t')
variant = Variant(v, src_vcf)
if not sum_quals:
variant.qual = 0
if not variant.has_svtype():
msg = ('Warning: SVTYPE missing '
'at variant %s. '
'Skipping.\n') % (variant.var_id)
logit(msg)
variant.write(out_vcf)
continue
if not variant.is_valid_svtype():
msg = ('Warning: Unsupported SVTYPE '
'at variant %s (%s). '
'Skipping.\n') % (variant.var_id, variant.get_svtype())
logit(msg)
variant.write(out_vcf)
continue
# special BND processing
if variant.get_svtype() == 'BND':
if variant.info['MATEID'] in bnd_cache:
variant2 = variant
variant = bnd_cache[variant.info['MATEID']]
del bnd_cache[variant.var_id]
else:
bnd_cache[variant.var_id] = variant
continue
result = genotypes[variant.var_id]
if result is None:
msg = ("Found no genotype results for variant "
"'{}' ({})").format(variant.var_id, variant.get_svtype())
logit(msg)
raise RuntimeError(msg)
variant = assign_genotype_to_variant(variant, sample, result)
variant.write(out_vcf)
# special BND processing
if variant.get_svtype() == 'BND':
variant2.qual = variant.qual
variant2.active_formats = variant.active_formats
variant2.genotype = variant.genotype
variant2.write(out_vcf)
def apply_genotypes_to_vcf(src_vcf, out_vcf, genotypes, sample, sum_quals):
# initializations
bnd_cache = {}
src_vcf.write_header(out_vcf)
total_variants = len(list(vcf_variants(src_vcf.filename)))
for i, vline in enumerate(vcf_variants(src_vcf.filename)):
v = vline.rstrip().split('\t')
variant = Variant(v, src_vcf)
if not sum_quals:
variant.qual = 0
if not variant.has_svtype():
msg = ('Warning: SVTYPE missing '
'at variant %s. '
'Skipping.\n') % (variant.var_id)
logit(msg)
variant.write(out_vcf)
continue
if not variant.is_valid_svtype():
msg = ('Warning: Unsupported SVTYPE '
'at variant %s (%s). '
'Skipping.\n') % (variant.var_id, variant.get_svtype())
logit(msg)
variant.write(out_vcf)
continue
# special BND processing
if variant.get_svtype() == 'BND':
if variant.info['MATEID'] in bnd_cache:
variant2 = variant
variant = bnd_cache[variant.info['MATEID']]
del bnd_cache[variant.var_id]
else:
bnd_cache[variant.var_id] = variant
continue
result = genotypes[variant.var_id]
if result is None:
msg = ("Found no genotype results for variant "
"'{}' ({})").format(variant.var_id, variant.get_svtype())
logit(msg)
raise RuntimeError(msg)
variant = assign_genotype_to_variant(variant, sample, result)
variant.write(out_vcf)
# special BND processing
if variant.get_svtype() == 'BND':
variant2.qual = variant.qual
variant2.active_formats = variant.active_formats
variant2.genotype = variant.genotype
variant2.write(out_vcf)
def collect_breakpoints(vcf, max_ci_dist):
breakpoints = []
for vline in vcf_variants(vcf.filename):
v = vline.rstrip().split('\t')
variant = Variant(v, vcf)
if not variant.has_svtype(): continue
if not variant.is_valid_svtype(): continue
brkpts = vcf.get_variant_breakpoints(variant, max_ci_dist)
if brkpts is None: continue
breakpoints.append(brkpts)
return breakpoints
def collect_breakpoints(vcf, max_ci_dist):
breakpoints = []
for vline in vcf_variants(vcf.filename):
v = vline.rstrip().split('\t')
variant = Variant(v, vcf)
if not variant.has_svtype(): continue
if not variant.is_valid_svtype(): continue
brkpts = vcf.get_variant_breakpoints(variant, max_ci_dist)
if brkpts is None: continue
breakpoints.append(brkpts)
return breakpoints
def genotype_serial(src_vcf, out_vcf, sample, z, split_slop, min_aligned,
sum_quals, split_weight, disc_weight, max_reads,
max_ci_dist, debug):
# initializations
bnd_cache = {}
src_vcf.write_header(out_vcf)
total_variants = len(list(vcf_variants(src_vcf.filename)))
# cleanup unused library attributes
for rg in sample.rg_to_lib:
sample.rg_to_lib[rg].cleanup()
for i, vline in enumerate(vcf_variants(src_vcf.filename)):
v = vline.rstrip().split('\t')
variant = Variant(v, src_vcf)
if i % 1000 == 0:
logit("[ {} | {} ] Processing variant {}".format(
i, total_variants, variant.var_id))
if not sum_quals:
variant.qual = 0
if not variant.has_svtype():
msg = ('Warning: SVTYPE missing '
'at variant %s. '
'Skipping.\n') % (variant.var_id)
logit(msg)
variant.write(out_vcf)
continue
if not variant.is_valid_svtype():
msg = ('Warning: Unsupported SVTYPE '
'at variant %s (%s). '
'Skipping.\n') % (variant.var_id, variant.get_svtype())
logit(msg)
variant.write(out_vcf)
continue
breakpoints = src_vcf.get_variant_breakpoints(variant, max_ci_dist)
# special BND processing
if variant.get_svtype() == 'BND':
if variant.info['MATEID'] in bnd_cache:
variant2 = variant
variant = bnd_cache[variant.info['MATEID']]
del bnd_cache[variant.var_id]
else:
bnd_cache[variant.var_id] = variant
continue
if breakpoints is None:
msg = ("Found no breakpoints for variant "
"'{}' ({})").format(variant.var_id, variant.get_svtype())
logit(msg)
continue
result = serial_calculate_genotype(
sample.bam, get_breakpoint_regions(breakpoints, sample,
z), sample.rg_to_lib,
sample.active_libs, sample.name, split_slop, min_aligned,
split_weight, disc_weight, breakpoints, max_reads, debug)
variant = assign_genotype_to_variant(variant, sample, result)
variant.write(out_vcf)
# special BND processing
if variant.get_svtype() == 'BND':
variant2.qual = variant.qual
variant2.active_formats = variant.active_formats
variant2.genotype = variant.genotype
variant2.write(out_vcf)
def genotype_serial(src_vcf, out_vcf, sample, z, split_slop, min_aligned, sum_quals, split_weight, disc_weight, max_reads, max_ci_dist, debug):
# initializations
bnd_cache = {}
src_vcf.write_header(out_vcf)
total_variants = len(list(vcf_variants(src_vcf.filename)))
# cleanup unused library attributes
for rg in sample.rg_to_lib:
sample.rg_to_lib[rg].cleanup()
for i, vline in enumerate(vcf_variants(src_vcf.filename)):
v = vline.rstrip().split('\t')
variant = Variant(v, src_vcf)
if i % 1000 == 0:
logit("[ {} | {} ] Processing variant {}".format(i, total_variants, variant.var_id))
if not sum_quals:
variant.qual = 0
if not variant.has_svtype():
msg = ('Warning: SVTYPE missing '
'at variant %s. '
'Skipping.\n') % (variant.var_id)
logit(msg)
variant.write(out_vcf)
continue
if not variant.is_valid_svtype():
msg = ('Warning: Unsupported SVTYPE '
'at variant %s (%s). '
'Skipping.\n') % (variant.var_id, variant.get_svtype())
logit(msg)
variant.write(out_vcf)
continue
breakpoints = src_vcf.get_variant_breakpoints(variant, max_ci_dist)
# special BND processing
if variant.get_svtype() == 'BND':
if variant.info['MATEID'] in bnd_cache:
variant2 = variant
variant = bnd_cache[variant.info['MATEID']]
del bnd_cache[variant.var_id]
else:
bnd_cache[variant.var_id] = variant
continue
if breakpoints is None:
msg = ("Found no breakpoints for variant "
"'{}' ({})").format(variant.var_id, variant.get_svtype())
logit(msg)
continue
result = serial_calculate_genotype(
sample.bam,
get_breakpoint_regions(breakpoints, sample, z),
sample.rg_to_lib,
sample.active_libs,
sample.name,
split_slop,
min_aligned,
split_weight,
disc_weight,
breakpoints,
max_reads,
debug
)
variant = assign_genotype_to_variant(variant, sample, result)
variant.write(out_vcf)
# special BND processing
if variant.get_svtype() == 'BND':
variant2.qual = variant.qual
variant2.active_formats = variant.active_formats
variant2.genotype = variant.genotype
variant2.write(out_vcf)
