def test_merge():
merged_pileup_elements = []
""" :type: list[PileupElement] """
pileups = []
""" :type: list[Pileup] """
reads = [my_read, my_read2, my_read3, my_read4]
for k in range(0, 4):
pile = Pileup.from_reads(reads, k)
pileups.append(pile)
merged_pileup_elements.append(pile.merge(max_qual=45, fraction_agree=0.75))
# test that ties gives N
assert merged_pileup_elements[0].base == 'N' # tie, 2xA 2xG
# test that majority vote works
assert merged_pileup_elements[1].base == 'G' # G wins from 3xG 1xA
# test all 4 bases that were merged
assert "".join([pe.base for pe in merged_pileup_elements]) == 'NGCT'
# test that qualities were properly merged
assert [pe.qual for pe in merged_pileup_elements] == [2, 45, 45, 45]
# test that the size of each pileup works
assert [len(p.bases()) for p in pileups] == [4, 4, 4, 3]
assert ReadMerger.key(a) == ReadMerger.key(b)
assert Pileup.from_reads([a, b], 0).merge(45, .75).base == 'N'
assert Pileup.from_reads([a, b], 0).merge(45, .75).qual == 2
assert Pileup.from_reads([a, b], 1).merge(45, .75).base == 'G'
tmpfilename = tempfile.mkstemp('.bam')[1]
outfile = pysam.AlignmentFile(tmpfilename, "wb", header=header)
readmerger = ReadMerger([a, b], outfile, fraction_agree=0.75, max_qual=45, reads_between_logs=1)
exitcode = readmerger.do_work()
assert exitcode == 0
metrics = readmerger.metrics.dict()
assert 'L1' in metrics
os.remove(tmpfilename)
def test_key():
expected_key = "0_32_250_True_L1"
key = ReadMerger.key(my_read)
assert key == expected_key
