def call(call_gt_args, idx, row_count, para, strands, seq, var_type):
rname_list = []
if var_type == 'INS' or var_type == 'DEL':
gt_re, DR, genotype, GL, GQ, QUAL = call_gt_indel(*call_gt_args)
rname_list = call_gt_args[3]
if var_type == 'DUP':
gt_re, DR, genotype, GL, GQ, QUAL = call_gt_dup(*call_gt_args)
rname_list = call_gt_args[4]
if var_type == 'INV':
gt_re, DR, genotype, GL, GQ, QUAL = call_gt_inv(*call_gt_args)
rname_list = call_gt_args[4]
if var_type == 'TRA':
gt_re, DR, genotype, GL, GQ, QUAL = call_gt_tra(*call_gt_args)
rname_list = call_gt_args[5]
rname = ','.join(rname_list)
if rname == '':
rname = 'NULL'
result = [
para.chrom, para.pos, genotype,
var_type, para.svlen, para.end, para.cipos, para.cilen,
[gt_re, DR, GL, GQ,
QUAL], rname, para.id, para.ref, para.alts, para.qual, strands, seq
]
if idx > 0 and idx % 5000 == 0:
logging.info(
str(math.floor(idx / row_count * 100)) +
'% SV calls of the given vcf has been processed.')
return result
def call_gt_wrapper(call_gt_args, gt_list, idx, row_count, record, var_type):
if var_type == 'INS' or var_type == 'DEL':
gt_re, DR, genotype, GL, GQ, QUAL = call_gt_indel(*call_gt_args)
if var_type == 'DUP':
gt_re, DR, genotype, GL, GQ, QUAL = call_gt_dup(*call_gt_args)
if var_type == 'INV':
gt_re, DR, genotype, GL, GQ, QUAL = call_gt_inv(*call_gt_args)
if var_type == 'TRA':
gt_re, DR, genotype, GL, GQ, QUAL = call_gt_tra(*call_gt_args)
gt_list[idx] = [
record.CHROM, record.POS, genotype, record.INFO['SVTYPE'],
record.INFO['SVLEN'], record.INFO['END'], record.INFO['CIPOS'],
record.INFO['CIEND'], gt_re, ','.join(call_gt_args[3]), record.ID,
record.REF, record.ALT[0], record.QUAL, record.INFO['STRANDS'],
record.FILTER
]
if idx > 0 and idx % 5000 == 0:
logging.info(
str(math.floor(idx / row_count * 100)) +
'% SV calls of the given vcf has been processed.')