def main(params):
args = parse_args(params)
with open(args.callset1_vcf) as f:
callset1_vcf = vcf.Reader(f)
one_vars = Variants(callset1_vcf, MAX_INDEL_LEN)
with open(args.callset2_vcf) as f:
callset2_vcf = vcf.Reader(f)
two_vars = Variants(callset2_vcf, MAX_INDEL_LEN)
if args.reference:
ref = Genome(args.reference, abbreviate=lambda ctig: ctig.split()[0])
window = args.window
else:
ref = None
window = None
stat_reporter, errors = evaluate_variants(one_vars, two_vars, args.sv_eps,
args.sv_eps, ref, window)
print_results(stat_reporter(VARIANT_TYPE.SNP), "SNP")
print_results(stat_reporter(VARIANT_TYPE.INDEL_DEL), "INDEL DELETIONS")
print_results(stat_reporter(VARIANT_TYPE.INDEL_INS), "INDEL INSERTIONS")
print_results(stat_reporter(VARIANT_TYPE.INDEL_OTH), "INDEL OTHER")
print_results(stat_reporter(VARIANT_TYPE.SV_DEL), "SV DELETIONS")
print_results(stat_reporter(VARIANT_TYPE.SV_INS), "SV INSERTIONS")
print_results(stat_reporter(VARIANT_TYPE.SV_OTH), "SV OTHER")
def main(params):
args = parse_args(params)
with open(args.callset1_vcf) as f:
callset1_vcf = vcf.Reader(f)
one_vars = Variants(callset1_vcf, MAX_INDEL_LEN)
with open(args.callset2_vcf) as f:
callset2_vcf = vcf.Reader(f)
two_vars = Variants(callset2_vcf, MAX_INDEL_LEN)
if args.reference:
ref = Genome(args.reference, abbreviate=lambda ctig: ctig.split()[0])
window = args.window
else:
ref = None
window = None
stat_reporter, errors = evaluate_variants(one_vars, two_vars, args.sv_eps, args.sv_eps, ref, window)
print_results(stat_reporter(VARIANT_TYPE.SNP), "SNP")
print_results(stat_reporter(VARIANT_TYPE.INDEL_DEL), "INDEL DELETIONS")
print_results(stat_reporter(VARIANT_TYPE.INDEL_INS), "INDEL INSERTIONS")
print_results(stat_reporter(VARIANT_TYPE.INDEL_OTH), "INDEL OTHER")
print_results(stat_reporter(VARIANT_TYPE.SV_DEL), "SV DELETIONS")
print_results(stat_reporter(VARIANT_TYPE.SV_INS), "SV INSERTIONS")
print_results(stat_reporter(VARIANT_TYPE.SV_OTH), "SV OTHER")
def main(params):
args = parse_args(params)
if args.normalize and not args.reference:
print("Normalization requires a reference file.",file=sys.stderr)
if args.reference:
ref = Genome(args.reference,abbreviate= lambda ctig: ctig.split()[0])
window = args.window
else:
ref = None
window = None
with open(args.true_vcf) as f:
true_vcf = vcf.Reader(f)
if args.normalize:
true_vcf = normalize(ref,true_vcf)
true_vars = Variants(true_vcf, MAX_INDEL_LEN)
with open(args.predicted_vcf) as f:
pred_vcf = vcf.Reader(f)
if args.normalize:
pred_vcf = normalize(ref,pred_vcf)
pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
if args.knownFP:
with open(args.knownFP) as f:
known_fp_vcf = vcf.Reader(f)
known_fp_vars = Variants(known_fp_vcf,
MAX_INDEL_LEN, knownFP=True)
else:
known_fp_vars = None
sv_eps = args.sv_eps
stat_reporter, annotated_vars = evaluate_variants(
true_vars,
pred_vars,
sv_eps, # tolerance for SV len
sv_eps, # tolerance for SV breakpoints
ref,
window,
known_fp_vars
)
if args.output == "tsv":
print(get_text_header(params),file=sys.stdout)
tsvwriter = csv.writer(sys.stdout, delimiter='\t')
tsvwriter.writerow(get_tsv_header(args.knownFP))
tsvwriter.writerow(tsv_row("SNP",stat_reporter(VARIANT_TYPE.SNP),args.snp_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("Indel Deletions",stat_reporter(VARIANT_TYPE.INDEL_DEL),args.indel_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("Indel Insertions",stat_reporter(VARIANT_TYPE.INDEL_INS),args.indel_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("Indel Inversions",stat_reporter(VARIANT_TYPE.INDEL_INV),args.indel_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("Indel Other",stat_reporter(VARIANT_TYPE.INDEL_OTH),args.indel_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("SV Deletions",stat_reporter(VARIANT_TYPE.SV_DEL),args.sv_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("SV Insertions",stat_reporter(VARIANT_TYPE.SV_INS),args.sv_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("SV Other",stat_reporter(VARIANT_TYPE.SV_OTH),args.sv_err_rate,args.knownFP,args.hideFP))
else:
print(get_text_header(params),file=sys.stdout)
snp_stats = stat_reporter(VARIANT_TYPE.SNP)
print_snp_stats(snp_stats, args.snp_err_rate, known_fp_vars,args.hideFP)
def print_sv(var_type, description,args):
assert 'INDEL' in var_type or 'SV' in var_type
err_rate = args.indel_err_rate if 'INDEL' in var_type else args.sv_err_rate
print_sv_stats(description, stat_reporter(var_type), err_rate,args)
def print_oth(var_type, description):
print_sv_other_results(description, stat_reporter(var_type)['num_true'], stat_reporter(var_type)['num_pred'])
print_sv(VARIANT_TYPE.INDEL_DEL, 'INDEL DELETION',args)
print_sv(VARIANT_TYPE.INDEL_INS, 'INDEL INSERTION',args)
print_sv(VARIANT_TYPE.INDEL_INV, 'INDEL INVERSION',args)
print_oth(VARIANT_TYPE.INDEL_OTH, 'INDEL OTHER')
print_sv(VARIANT_TYPE.SV_DEL, 'SV DELETION',args),
print_sv(VARIANT_TYPE.SV_INS, 'SV INSERTION',args),
print_oth(VARIANT_TYPE.SV_OTH, 'SV OTHER')
if args.output_vcf :
output_annotated_variants(annotated_vars,ref.keys() if ref != None else None, open(args.output_vcf,'w'),get_vcf_header_lines(params))
def main(params):
args = parse_args(params)
with open(args.true_vcf) as f:
true_vcf = vcf.Reader(f)
true_vars = Variants(true_vcf, MAX_INDEL_LEN)
with open(args.predicted_vcf) as f:
pred_vcf = vcf.Reader(f)
pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
if args.reference:
ref = Genome(args.reference, abbreviate=lambda ctig: ctig.split()[0])
window = args.window
else:
ref = None
window = None
if args.knownFP:
with open(args.knownFP) as f:
known_fp_vcf = vcf.Reader(f)
known_fp_vars = Variants(known_fp_vcf, MAX_INDEL_LEN, knownFp=True)
else:
known_fp_vars = None
# Estimated total number of errors in validation data for SNPs, indels and SVs.
snp_err = get_snp_err(true_vars, args.snp_err_rate)
indel_err = get_indel_err(true_vars, args.indel_err_rate)
sv_err = get_sv_err(true_vars, args.sv_err_rate)
sv_eps = args.sv_eps
stat_reporter, errors = evaluate_variants(true_vars, pred_vars, sv_eps,
sv_eps, ref, window,
known_fp_vars)
snp_stats = stat_reporter(VARIANT_TYPE.SNP)
print_snp_stats(snp_stats, snp_err, known_fp_vars)
def print_sv(var_type, description):
assert 'INDEL' in var_type or 'SV' in var_type
err = indel_err if 'INDEL' in var_type else sv_err
print_sv_stats(description, stat_reporter(var_type), err)
def print_oth(var_type, description):
print_sv_other_results(description,
stat_reporter(var_type)['num_true'],
stat_reporter(var_type)['num_pred'])
print_sv(VARIANT_TYPE.INDEL_DEL, 'INDEL DELETION')
print_sv(VARIANT_TYPE.INDEL_INS, 'INDEL INSERTION')
print_oth(VARIANT_TYPE.INDEL_OTH, 'INDEL OTHER')
print_sv(VARIANT_TYPE.SV_DEL, 'SV DELETION'),
print_sv(VARIANT_TYPE.SV_INS, 'SV INSERTION'),
print_oth(VARIANT_TYPE.SV_OTH, 'SV OTHER')
if args.err_vcf:
output_errors(errors,
ref.keys() if ref != None else None,
open(args.err_vcf, 'w'))
def main(params):
args = parse_args(params)
if args.normalize and not args.reference:
print("Normalization requires a reference file.",file=sys.stderr)
if args.reference:
ref = Genome(args.reference,abbreviate= lambda ctig: ctig.split()[0])
window = args.window
else:
ref = None
window = None
contig_lookup = get_contig_lookup(args.refindex)
true_vcf = vcf.Reader(open(args.true_vcf))
if args.normalize:
true_vcf = normalize(ref, true_vcf)
pred_vcf = vcf.Reader(open(args.predicted_vcf))
if args.normalize:
pred_vcf = normalize(ref,pred_vcf)
sv_eps = args.sv_eps
# if args.knownFP:
# known_fp_vcf = vcf.Reader(open(args.knownFP,'r'))
# known_fp_vars = Variants(known_fp_vcf,MAX_INDEL_LEN,knownFP=True)
# else:
# known_fp_vars = None
if args.knownFP:
true_vars = Variants(true_vcf,MAX_INDEL_LEN)
pred_vars = Variants(pred_vcf,MAX_INDEL_LEN)
known_fp_vcf = vcf.Reader(open(args.knownFP,'r'))
known_fp_vars = Variants(known_fp_vcf,MAX_INDEL_LEN,knownFP=True)
stat_reporter, annotated_vars = evaluate_variants(
true_vars,
pred_vars,
sv_eps,
sv_eps,
ref,
window,
known_fp_vars)
if args.output_vcf:
output_annotated_variants(annotated_vars,ref.keys() if ref != None else None, open(args.output_vcf,'w'),get_vcf_header_lines(params))
else:
if args.output_vcf:
outVCF = vcf.Writer(open(args.output_vcf,'w'),true_vcf)
else:
outVCF = None
stat_reporter = evaluate_low_memory(
true_vcf,
pred_vcf,
sv_eps,
sv_eps,
ref,
window,
MAX_INDEL_LEN,
contig_lookup,
outVCF
)
if args.output == "tsv":
print(get_text_header(params),file=sys.stdout)
tsvwriter = csv.writer(sys.stdout, delimiter='\t')
tsvwriter.writerow(get_tsv_header(args.knownFP))
tsvwriter.writerow(tsv_row("SNP",stat_reporter(VARIANT_TYPE.SNP),args.snp_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("Indel Deletions",stat_reporter(VARIANT_TYPE.INDEL_DEL),args.indel_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("Indel Insertions",stat_reporter(VARIANT_TYPE.INDEL_INS),args.indel_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("Indel Inversions",stat_reporter(VARIANT_TYPE.INDEL_INV),args.indel_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("Indel Other",stat_reporter(VARIANT_TYPE.INDEL_OTH),args.indel_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("SV Deletions",stat_reporter(VARIANT_TYPE.SV_DEL),args.sv_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("SV Insertions",stat_reporter(VARIANT_TYPE.SV_INS),args.sv_err_rate,args.knownFP,args.hideFP))
tsvwriter.writerow(tsv_row("SV Other",stat_reporter(VARIANT_TYPE.SV_OTH),args.sv_err_rate,args.knownFP,args.hideFP))
elif args.output == "json":
output_dict = add_json_header(params,{})
output_dict["SNP"] = json_dict(stat_reporter(VARIANT_TYPE.SNP),args.snp_err_rate,args.knownFP,args.hideFP)
output_dict["Indel Deletions"] = json_dict(stat_reporter(VARIANT_TYPE.INDEL_DEL),args.indel_err_rate,args.knownFP,args.hideFP)
output_dict["Indel Insertions"] = json_dict(stat_reporter(VARIANT_TYPE.INDEL_INS),args.indel_err_rate,args.knownFP,args.hideFP)
output_dict["Indel Inversions"] = json_dict(stat_reporter(VARIANT_TYPE.INDEL_INV),args.indel_err_rate,args.knownFP,args.hideFP)
output_dict["Indel Other"] = json_dict(stat_reporter(VARIANT_TYPE.INDEL_OTH),args.indel_err_rate,args.knownFP,args.hideFP)
output_dict["SV Deleitions"] = json_dict(stat_reporter(VARIANT_TYPE.SV_DEL),args.sv_err_rate,args.knownFP,args.hideFP)
output_dict["SV Insertions"] = json_dict(stat_reporter(VARIANT_TYPE.SV_INS),args.sv_err_rate,args.knownFP,args.hideFP)
json.dump(output_dict,sys.stdout)
else:
print(get_text_header(params),file=sys.stdout)
snp_stats = stat_reporter(VARIANT_TYPE.SNP)
print_snp_stats(snp_stats, args.snp_err_rate, args.knownFP,args.hideFP)
def print_sv(var_type, description,args):
assert 'INDEL' in var_type or 'SV' in var_type
err_rate = args.indel_err_rate if 'INDEL' in var_type else args.sv_err_rate
print_sv_stats(description, stat_reporter(var_type), err_rate,args)
def print_oth(var_type, description):
print_sv_other_results(description, stat_reporter(var_type)['num_true'], stat_reporter(var_type)['num_pred'])
print_sv(VARIANT_TYPE.INDEL_DEL, 'INDEL DELETION',args)
print_sv(VARIANT_TYPE.INDEL_INS, 'INDEL INSERTION',args)
print_sv(VARIANT_TYPE.INDEL_INV, 'INDEL INVERSION',args)
print_oth(VARIANT_TYPE.INDEL_OTH, 'INDEL OTHER')
print_sv(VARIANT_TYPE.SV_DEL, 'SV DELETION',args),
print_sv(VARIANT_TYPE.SV_INS, 'SV INSERTION',args),
print_oth(VARIANT_TYPE.SV_OTH, 'SV OTHER')
def main(params):
args = parse_args(params)
if args.normalize and not args.reference:
print("Normalization requires a reference file.", file=sys.stderr)
if args.reference:
ref = Genome(args.reference, abbreviate=lambda ctig: ctig.split()[0])
window = args.window
else:
ref = None
window = None
with open(args.true_vcf) as f:
true_vcf = vcf.Reader(f)
if args.normalize:
true_vcf = normalize(ref, true_vcf)
true_vars = Variants(true_vcf, MAX_INDEL_LEN)
with open(args.predicted_vcf) as f:
pred_vcf = vcf.Reader(f)
if args.normalize:
pred_vcf = normalize(ref, pred_vcf)
pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
if args.knownFP:
with open(args.knownFP) as f:
known_fp_vcf = vcf.Reader(f)
known_fp_vars = Variants(known_fp_vcf, MAX_INDEL_LEN, knownFp=True)
else:
known_fp_vars = None
# Estimated total number of errors in validation data for SNPs, indels and SVs.
snp_err = get_snp_err(true_vars, args.snp_err_rate)
indel_err = get_indel_err(true_vars, args.indel_err_rate)
sv_err = get_sv_err(true_vars, args.sv_err_rate)
sv_eps = args.sv_eps
stat_reporter, annotated_vars = evaluate_variants(true_vars, pred_vars,
sv_eps, sv_eps, ref,
window, known_fp_vars)
if args.output == "tsv":
print(get_text_header(params), file=sys.stdout)
tsvwriter = csv.writer(sys.stdout, delimiter='\t')
tsvwriter.writerow(tsv_header)
tsvwriter.writerow(
tsv_row("SNP", stat_reporter(VARIANT_TYPE.SNP), snp_err))
tsvwriter.writerow(
tsv_row("Indel Deletions", stat_reporter(VARIANT_TYPE.INDEL_DEL),
indel_err))
tsvwriter.writerow(
tsv_row("Indel Insertions", stat_reporter(VARIANT_TYPE.INDEL_INS),
indel_err))
tsvwriter.writerow(
tsv_row("Indel Inversions", stat_reporter(VARIANT_TYPE.INDEL_INV),
indel_err))
tsvwriter.writerow(
tsv_row("Indel Other", stat_reporter(VARIANT_TYPE.INDEL_OTH),
indel_err))
tsvwriter.writerow(
tsv_row("SV Deletions", stat_reporter(VARIANT_TYPE.SV_DEL),
sv_err))
tsvwriter.writerow(
tsv_row("SV Insertions", stat_reporter(VARIANT_TYPE.SV_INS),
sv_err))
tsvwriter.writerow(
tsv_row("SV Other", stat_reporter(VARIANT_TYPE.SV_OTH), sv_err))
else:
print(get_text_header(params), file=sys.stdout)
snp_stats = stat_reporter(VARIANT_TYPE.SNP)
print_snp_stats(snp_stats, snp_err, known_fp_vars)
def print_sv(var_type, description):
assert 'INDEL' in var_type or 'SV' in var_type
err = indel_err if 'INDEL' in var_type else sv_err
print_sv_stats(description, stat_reporter(var_type), err)
def print_oth(var_type, description):
print_sv_other_results(description,
stat_reporter(var_type)['num_true'],
stat_reporter(var_type)['num_pred'])
print_sv(VARIANT_TYPE.INDEL_DEL, 'INDEL DELETION')
print_sv(VARIANT_TYPE.INDEL_INS, 'INDEL INSERTION')
print_sv(VARIANT_TYPE.INDEL_INV, 'INDEL INVERSION')
print_oth(VARIANT_TYPE.INDEL_OTH, 'INDEL OTHER')
print_sv(VARIANT_TYPE.SV_DEL, 'SV DELETION'),
print_sv(VARIANT_TYPE.SV_INS, 'SV INSERTION'),
print_oth(VARIANT_TYPE.SV_OTH, 'SV OTHER')
if args.output_vcf:
output_annotated_variants(annotated_vars,
ref.keys() if ref != None else None,
open(args.output_vcf, 'w'),
get_vcf_header_lines(params))
def main(params):
args = parse_args(params)
if args.normalize and not args.reference:
print("Normalization requires a reference file.", file=sys.stderr)
if args.reference:
ref = Genome(args.reference, abbreviate=lambda ctig: ctig.split()[0])
window = args.window
else:
ref = None
window = None
contig_lookup = get_contig_lookup(args.refindex)
true_vcf = vcf.Reader(open(args.true_vcf))
if args.normalize:
true_vcf = normalize(ref, true_vcf)
pred_vcf = vcf.Reader(open(args.predicted_vcf))
if args.normalize:
pred_vcf = normalize(ref, pred_vcf)
sv_eps = args.sv_eps
# if args.knownFP:
# known_fp_vcf = vcf.Reader(open(args.knownFP,'r'))
# known_fp_vars = Variants(known_fp_vcf,MAX_INDEL_LEN,knownFP=True)
# else:
# known_fp_vars = None
if args.knownFP:
true_vars = Variants(true_vcf, MAX_INDEL_LEN)
pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
known_fp_vcf = vcf.Reader(open(args.knownFP, 'r'))
known_fp_vars = Variants(known_fp_vcf, MAX_INDEL_LEN, knownFP=True)
stat_reporter, annotated_vars = evaluate_variants(
true_vars, pred_vars, sv_eps, sv_eps, ref, window, known_fp_vars)
if args.output_vcf:
output_annotated_variants(annotated_vars,
ref.keys() if ref != None else None,
open(args.output_vcf, 'w'),
get_vcf_header_lines(params))
else:
if args.output_vcf:
outVCF = vcf.Writer(open(args.output_vcf, 'w'), true_vcf)
else:
outVCF = None
stat_reporter = evaluate_low_memory(true_vcf, pred_vcf, sv_eps, sv_eps,
ref, window, MAX_INDEL_LEN,
contig_lookup, outVCF)
if args.output == "tsv":
print(get_text_header(params), file=sys.stdout)
tsvwriter = csv.writer(sys.stdout, delimiter='\t')
tsvwriter.writerow(get_tsv_header(args.knownFP))
tsvwriter.writerow(
tsv_row("SNP", stat_reporter(VARIANT_TYPE.SNP), args.snp_err_rate,
args.knownFP, args.hideFP))
tsvwriter.writerow(
tsv_row("Indel Deletions", stat_reporter(VARIANT_TYPE.INDEL_DEL),
args.indel_err_rate, args.knownFP, args.hideFP))
tsvwriter.writerow(
tsv_row("Indel Insertions", stat_reporter(VARIANT_TYPE.INDEL_INS),
args.indel_err_rate, args.knownFP, args.hideFP))
tsvwriter.writerow(
tsv_row("Indel Inversions", stat_reporter(VARIANT_TYPE.INDEL_INV),
args.indel_err_rate, args.knownFP, args.hideFP))
tsvwriter.writerow(
tsv_row("Indel Other", stat_reporter(VARIANT_TYPE.INDEL_OTH),
args.indel_err_rate, args.knownFP, args.hideFP))
tsvwriter.writerow(
tsv_row("SV Deletions", stat_reporter(VARIANT_TYPE.SV_DEL),
args.sv_err_rate, args.knownFP, args.hideFP))
tsvwriter.writerow(
tsv_row("SV Insertions", stat_reporter(VARIANT_TYPE.SV_INS),
args.sv_err_rate, args.knownFP, args.hideFP))
tsvwriter.writerow(
tsv_row("SV Other", stat_reporter(VARIANT_TYPE.SV_OTH),
args.sv_err_rate, args.knownFP, args.hideFP))
elif args.output == "json":
output_dict = add_json_header(params, {})
output_dict["SNP"] = json_dict(stat_reporter(VARIANT_TYPE.SNP),
args.snp_err_rate, args.knownFP,
args.hideFP)
output_dict["Indel Deletions"] = json_dict(
stat_reporter(VARIANT_TYPE.INDEL_DEL), args.indel_err_rate,
args.knownFP, args.hideFP)
output_dict["Indel Insertions"] = json_dict(
stat_reporter(VARIANT_TYPE.INDEL_INS), args.indel_err_rate,
args.knownFP, args.hideFP)
output_dict["Indel Inversions"] = json_dict(
stat_reporter(VARIANT_TYPE.INDEL_INV), args.indel_err_rate,
args.knownFP, args.hideFP)
output_dict["Indel Other"] = json_dict(
stat_reporter(VARIANT_TYPE.INDEL_OTH), args.indel_err_rate,
args.knownFP, args.hideFP)
output_dict["SV Deleitions"] = json_dict(
stat_reporter(VARIANT_TYPE.SV_DEL), args.sv_err_rate, args.knownFP,
args.hideFP)
output_dict["SV Insertions"] = json_dict(
stat_reporter(VARIANT_TYPE.SV_INS), args.sv_err_rate, args.knownFP,
args.hideFP)
json.dump(output_dict, sys.stdout)
else:
print(get_text_header(params), file=sys.stdout)
snp_stats = stat_reporter(VARIANT_TYPE.SNP)
print_snp_stats(snp_stats, args.snp_err_rate, args.knownFP,
args.hideFP)
def print_sv(var_type, description, args):
assert 'INDEL' in var_type or 'SV' in var_type
err_rate = args.indel_err_rate if 'INDEL' in var_type else args.sv_err_rate
print_sv_stats(description, stat_reporter(var_type), err_rate,
args)
def print_oth(var_type, description):
print_sv_other_results(description,
stat_reporter(var_type)['num_true'],
stat_reporter(var_type)['num_pred'])
print_sv(VARIANT_TYPE.INDEL_DEL, 'INDEL DELETION', args)
print_sv(VARIANT_TYPE.INDEL_INS, 'INDEL INSERTION', args)
print_sv(VARIANT_TYPE.INDEL_INV, 'INDEL INVERSION', args)
print_oth(VARIANT_TYPE.INDEL_OTH, 'INDEL OTHER')
print_sv(VARIANT_TYPE.SV_DEL, 'SV DELETION', args),
print_sv(VARIANT_TYPE.SV_INS, 'SV INSERTION', args),
print_oth(VARIANT_TYPE.SV_OTH, 'SV OTHER')