def call_gt(bam_path, search_threshold, chr, read_id_list, max_cluster_bias,
gt_round):
import pysam
querydata = set()
bamfile = pysam.AlignmentFile(bam_path)
search_start = max(int(search_threshold) - max_cluster_bias, 0)
search_end = min(
int(search_threshold) + max_cluster_bias,
bamfile.get_reference_length(chr))
up_bound = threshold_ref_count(len(read_id_list))
status = count_coverage(chr, search_start, search_end, bamfile, querydata,
up_bound, gt_round)
bamfile.close()
if status == -1:
DR = '.'
GT = "./."
GL = ".,.,."
GQ = "."
QUAL = "."
# elif status == 1:
# pass
else:
DR = 0
for query in querydata:
if query not in read_id_list:
DR += 1
GT, GL, GQ, QUAL = cal_GL(DR, len(read_id_list))
return len(read_id_list), DR, GT, GL, GQ, QUAL
def call_gt(bam_path, pos_1, pos_2, chr_1, chr_2, read_id_list,
max_cluster_bias, gt_round):
import pysam
bamfile = pysam.AlignmentFile(bam_path)
querydata = set()
search_start = max(int(pos_1) - max_cluster_bias, 0)
search_end = min(
int(pos_1) + max_cluster_bias, bamfile.get_reference_length(chr_1))
up_bound = threshold_ref_count(len(read_id_list))
status = count_coverage(chr_1, search_start, search_end, bamfile,
querydata, up_bound, gt_round)
if status == -1:
DR = '.'
GT = "./."
GL = ".,.,."
GQ = "."
QUAL = "."
elif status == 1:
DR = 0
for query in querydata:
if query not in read_id_list:
DR += 1
GT, GL, GQ, QUAL = cal_GL(DR, len(read_id_list))
else:
search_start = max(int(pos_2) - max_cluster_bias, 0)
search_end = min(
int(pos_2) + max_cluster_bias, bamfile.get_reference_length(chr_2))
status_2 = count_coverage(chr_2, search_start, search_end, bamfile,
querydata, up_bound, gt_round)
# status_2 judgement
DR = 0
for query in querydata:
if query not in read_id_list:
DR += 1
GT, GL, GQ, QUAL = cal_GL(DR, len(read_id_list))
bamfile.close()
return len(read_id_list), DR, GT, GL, GQ, QUAL
