def anno(line):
line = line.rstrip().split('\t')
chr, pos, _, ref, alt = line[:5]
line[-3] += ':UDP' # format
line[-2] += ':' # gdna
line[-1] += ':' # cfdna
for i, sam in enumerate((o.cfdna, o.gdna)):
if sam != None:
reads = get_reads(o, sam, chr, pos)
unique_pairs, unique_single, *_ = aggregate_reads(
o, reads, None if o.fast else pad_softclip(sam))
mor, mnr, msr, oor, onr, osr, moa, mna, msa, ooa, ona, osa, _ = count_different_type(
o, unique_pairs, unique_single, alt, ref)
if o.simple:
line[-i - 1] += ','.join(
map(str, (moa, mna + msa, ooa, ona + osa)))
else:
line[-i - 1] += ','.join(
map(str, (mor, mnr, msr, oor, onr, osr, moa, mna,
msa, ooa, ona, osa)))
print(file=fout, sep='\t', *line)
def test_aggregate_reads_2():
"it should aggregate singles"
o = Namespace(verbos=False, qual=20)
reads = (("r1", 'A', 60, 2, 11, 0, 0, False, False),
("r2", 'C', 60, 2, 11, 0, 0, False, False), ("r3", 'C', 60, 2, 11,
0, 0, True, False))
_, unique_single, *_ = aggregate_reads(o, reads)
assert len(unique_single) == 2
def test_aggregate_reads_1():
"it should aggregate pairs"
o = Namespace(verbos=False, qual=20)
reads = (("r1", 'A', 60, 2, 11, 4, 11, False, True), ("r1", 'A', 60, 4, 13,
2, -11, False, True),
("r2", 'C', 60, 2, 11, 4, 11, False, True), ("r2", 'C', 60, 4, 13,
2, -11, False, True))
unique_pairs, *_ = aggregate_reads(o, reads)
assert len(unique_pairs) == 1
def test_aggregate_reads_4():
"it should ignore when base in overlap area inconsistent between two reads"
o = Namespace(verbos=False, qual=20)
reads = (("r1", 'A', 60, 2, 11, 4, 11, False, True), ("r1", 'C', 60, 4, 13,
2, -11, False, True),
("r2", 'C', 60, 3, 12, 5, 11, False, True), ("r2", 'C', 60, 5, 14,
3, -11, False, True))
unique_pairs, unique_single, *_, ninconsis = aggregate_reads(o, reads)
assert len(unique_pairs) == 1
assert ninconsis == 2
def test_aggregate_reads_3():
"it should ignore when 3+ reads share the same name"
o = Namespace(verbos=False, qual=20)
reads = (("r1", 'A', 60, 2, 11, 2, 9, False, True), ("r1", 'C', 60, 2, 11,
2, -9, False, True),
("r1", 'C', 60, 2, 11, 2, 9, True, True), ("r2", 'C', 60, 2, 11,
0, 0, True, False))
unique_pairs, unique_single, _, nerror, *_ = aggregate_reads(o, reads)
assert len(unique_pairs) == 0
assert len(unique_single) == 1
assert nerror == 3
def test_aggregate_reads_5():
"it should drop reads that has too much mismatch"
o = Namespace(verbos=False, qual=20, mismatch_limit=2)
reads = (("r1", 'C', 60, 2, 11, 1, 4, 11, False,
True), ("r1", 'C', 60, 4, 13, 1, 2, -11, True,
True), ("r2", 'C', 60, 3, 12, 3, 5, 11, False, True),
("r2", 'C', 60, 5, 14, 1, 3, -11, True,
True), ("r3", 'C', 60, 6, 14, 3, 0, 0, True,
False), ("r4", 'C', 60, 7, 14, 1, 0, 0, True, False))
unique_pairs, unique_single, *_, nlowq, ninconsis = aggregate_reads(
o, reads)
assert len(unique_pairs) == 1
assert len(unique_single) == 1
assert nlowq == 3