def run(args):
v_info = vaf_info(base_count(args.bam, args.min_MQ, args.min_BQ))
header = ('#chr\tpos\tref\talt\tvaf\t' + 'depth\tref_n\talt_n\tp_binom')
printer(header)
for snv in args.infile:
if snv[0] == '#':
continue
chrom, pos, ref, alt = snv.strip().split()[:4]
printer('{chrom}\t{pos}\t{ref}\t{alt}\t{vaf_info}'.format(
chrom=chrom,
pos=pos,
ref=ref.upper(),
alt=alt.upper(),
vaf_info=v_info.send((chrom, pos, ref, alt))))
def run(args):
alt_BQ_info = alt_BQ_sum(
base_qual_tuple(args.bam, args.min_MQ, args.min_BQ))
header = '#chr\tpos\tref\talt\talt_n\talt_BQ_sum'
printer(header)
for snv in args.infile:
if snv[0] == '#':
continue
chrom, pos, ref, alt = snv.strip().split()[:4]
printer('{chrom}\t{pos}\t{ref}\t{alt}\t{alt_BQ_info}'.format(
chrom=chrom,
pos=pos,
ref=ref.upper(),
alt=alt.upper(),
alt_BQ_info=alt_BQ_info.send((chrom, pos, alt))))
def run(args):
s_info = strand_info(base_count(args.bam, args.min_MQ, args.min_BQ))
header = ('#chr\tpos\tref\talt\t'
+ 'total\ttotal_fwd\ttotal_rev\ttotal_ratio\t'
+ 'p_poisson\t'
+ 'ref_n\tref_fwd\tref_rev\tref_ratio\t'
+ 'alt_n\talt_fwd\talt_rev\talt_ratio\t'
+ 'p_fisher')
printer(header)
for snv in args.infile:
if snv[0] == '#':
continue
chrom, pos, ref, alt = snv.strip().split()[:4]
printer('{chrom}\t{pos}\t{ref}\t{alt}\t{strand_info}'.format(
chrom=chrom, pos=pos, ref=ref.upper(), alt=alt.upper(),
strand_info=s_info.send((chrom, pos, ref, alt))))